Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 160 of 210
Found at i:48378383 original size:16 final size:17
Alignment explanation
Indices: 48378362--48378425 Score: 78
Period size: 18 Copynumber: 3.7 Consensus size: 17
48378352 AGTTCAGACT
48378362 AAAAAAAACAAAAA-CA
1 AAAAAAAACAAAAATCA
*
48378378 AAAAAAATCAAAAATCA
1 AAAAAAAACAAAAATCA
48378395 AAAAAATCAA-AAAAATCA
1 AAAAAA--AACAAAAATCA
48378413 AAAAAAAATCAAA
1 AAAAAAAA-CAAA
48378426 GTCAAAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
16 15 0.37
17 8 0.20
18 17 0.41
19 1 0.02
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.08
Consensus pattern (17 bp):
AAAAAAAACAAAAATCA
Found at i:48378433 original size:16 final size:17
Alignment explanation
Indices: 48378362--48378425 Score: 80
Period size: 16 Copynumber: 3.8 Consensus size: 17
48378352 AGTTCAGACT
48378362 AAAAAAAA-CAAAAA-C
1 AAAAAAAATCAAAAATC
48378377 AAAAAAAATCAAAAATC
1 AAAAAAAATCAAAAATC
48378394 -AAAAAAATCAAAAAAATC
1 AAAAAAAATC--AAAAATC
48378412 AAAAAAAAATCAAA
1 -AAAAAAAATCAAA
48378426 GTCAAAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.19
16 15 0.35
17 1 0.02
18 10 0.23
20 9 0.21
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.08
Consensus pattern (17 bp):
AAAAAAAATCAAAAATC
Found at i:48378433 original size:25 final size:24
Alignment explanation
Indices: 48378365--48378420 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
48378355 TCAGACTAAA
*
48378365 AAAAACAAAAACA--AAAAAAATC
1 AAAAACAAAAAAATCAAAAAAATC
*
48378387 AAAAATCAAAAAAATCAAAAAAATC
1 -AAAAACAAAAAAATCAAAAAAATC
48378412 AAAAA-AAAA
1 AAAAACAAAA
48378421 TCAAAGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 15 0.54
24 4 0.14
25 9 0.32
ACGTcount: A:0.82, C:0.11, G:0.00, T:0.07
Consensus pattern (24 bp):
AAAAACAAAAAAATCAAAAAAATC
Found at i:48378900 original size:22 final size:22
Alignment explanation
Indices: 48378872--48378914 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
48378862 TTTATTGTTC
48378872 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
48378894 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
48378915 TAGCAAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:48379287 original size:16 final size:15
Alignment explanation
Indices: 48379250--48379288 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
48379240 AAAAATATAT
48379250 ATAAAAAAATGAAAA
1 ATAAAAAAATGAAAA
48379265 ATGAAAAAAATGAAAA
1 AT-AAAAAAATGAAAA
48379281 AGTAAAAA
1 A-TAAAAA
48379289 TGGAGAGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 19 0.86
17 1 0.05
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (15 bp):
ATAAAAAAATGAAAA
Found at i:48380674 original size:88 final size:88
Alignment explanation
Indices: 48380520--48381351 Score: 1349
Period size: 88 Copynumber: 9.4 Consensus size: 88
48380510 ATAAAGTTGT
* * * *
48380520 AGATATTGCCTTCCTGCATTGACAACGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATTG
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
48380585 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * *
48380608 AGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCCAAGACACAAACCTTGCCTCTCTCGATTG
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
48380673 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* *
48380696 AGATCTTGCCTTTTCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTACCTCTCTCGGTT
1 AGATCTTGCC-TTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
48380761 GTGATGGAGCTGGTTGAAGACAAA
65 GTGATGGAGCTGGTTGAAGACAAA
* *
48380785 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGTCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
48380850 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
48380873 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
48380938 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * *
48380961 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCAAAGCCACAAACCTTGCCTCTCTCGGCTG
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
*******
48381026 CCCCCCCCGCTGGTTGAAGACAAA
66 -TGATGGAGCTGGTTGAAGACAAA
* *
48381050 AGATCTTGCCTTTCTGTATTGACAGCGAATCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
48381115 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * *
48381138 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCCCTCGGTTG
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* * *
48381203 TGGTGGAGTTGGTTGAAGACAAT
66 TGATGGAGCTGGTTGAAGACAAA
*
48381226 AGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
48381291 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * *
48381314 AGATCTTGCCTTCCTGTAATGACAGCGAAACAGATCGA
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGA
48381352 GGAAACCATA
Statistics
Matches: 687, Mismatches: 55, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
88 526 0.77
89 161 0.23
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.25
Consensus pattern (88 bp):
AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
TGATGGAGCTGGTTGAAGACAAA
Found at i:48381040 original size:265 final size:264
Alignment explanation
Indices: 48380520--48381351 Score: 1358
Period size: 265 Copynumber: 3.1 Consensus size: 264
48380510 ATAAAGTTGT
* * *
48380520 AGATATTGCCTTCCTGCATTGACAACGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* *
48380585 TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCCAAGAC
66 TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGAC
*
48380650 ACAAACCTTGCCTCTCTCGATTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTTCTGTA
131 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCC-TTTCTGTA
*
48380715 TTGACAGCGAAGCAGGTCGAAGACACAAACCTTACCTCTCTCGGTTGTGATGGAGCTGGTTGAAG
195 TTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAG
48380780 ACAAA
260 ACAAA
*
48380785 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGTCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
48380850 TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGAC
66 TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGAC
*
48380915 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTAT
131 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTAT
* * * *******
48380980 TGACAGCGAAGCAGGTCAAAGCCACAAACCTTGCCTCTCTCGGCTGCCCCCCCCGCTGGTTGAAG
196 TGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG-TGATGGAGCTGGTTGAAG
48381045 ACAAA
260 ACAAA
* * *
48381050 AGATCTTGCCTTTCTGTATTGACAGCGAATCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* *
48381115 TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGAC
66 TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGAC
* * * *
48381180 ACAAACCTTGCCTCCCTCGGTTGTGGTGGAGTTGGTTGAAGACAATAGATCTTGCCTTTCTGTAT
131 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTAT
48381245 TGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGA
196 TGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGA
48381310 CAAA
261 CAAA
* * * *
48381314 AGATCTTGCCTTCCTGTAATGACAGCGAAACAGATCGA
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGA
48381352 GGAAACCATA
Statistics
Matches: 522, Mismatches: 44, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
264 100 0.19
265 422 0.81
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.25
Consensus pattern (264 bp):
AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGAC
ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTAT
TGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGA
CAAA
Found at i:48381178 original size:353 final size:353
Alignment explanation
Indices: 48380520--48381342 Score: 1396
Period size: 353 Copynumber: 2.3 Consensus size: 353
48380510 ATAAAGTTGT
* * * *
48380520 AGATATTGCCTTCCTGCATTGACAACGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATTG
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* *
48380585 TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCCAAGAC
66 TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCAAAGAC
* ** ***
48380650 ACAAACCTTGCCTCTCTCGATTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTTCTGTA
131 ACAAACCTTGCCTCTCTCGACTGCCACCCAGCTGGTTGAAGACAAAAGATCTTGCCTTTTCTGTA
48380715 TTGACAGCGAAGCAGGTCGAAGACACAAACCTTACCTCTCTCGGTTGTGATGGAGCTGGTTGAAG
196 TTGACAGCGAAGCAGGTCGAAGACACAAACCTTACCTCTCTCGGTTGTGATGGAGCTGGTTGAAG
* * *
48380780 ACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGTCTCTCTC
261 ACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCCCTC
48380845 GGTTGTGATGGAGCTGGTTGAAGACAAA
326 GGTTGTGATGGAGCTGGTTGAAGACAAA
48380873 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
*
48380938 TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCAAAGCC
66 TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCAAAGAC
* * *
48381003 ACAAACCTTGCCTCTCTCGGCTGCCCCCCCCGCTGGTTGAAGACAAAAGATCTTGCC-TTTCTGT
131 ACAAACCTTGCCTCTCTCGACTG-CCACCCAGCTGGTTGAAGACAAAAGATCTTGCCTTTTCTGT
* *
48381067 ATTGACAGCGAATCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAA
195 ATTGACAGCGAAGCAGGTCGAAGACACAAACCTTACCTCTCTCGGTTGTGATGGAGCTGGTTGAA
48381132 GACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCCCT
260 GACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCCCT
* * *
48381197 CGGTTGTGGTGGAGTTGGTTGAAGACAAT
325 CGGTTGTGATGGAGCTGGTTGAAGACAAA
*
48381226 AGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
*
48381291 TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTAATGACAGCGAA
66 TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAA
48381343 ACAGATCGAG
Statistics
Matches: 443, Mismatches: 26, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
353 417 0.94
354 26 0.06
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (353 bp):
AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCAAAGAC
ACAAACCTTGCCTCTCTCGACTGCCACCCAGCTGGTTGAAGACAAAAGATCTTGCCTTTTCTGTA
TTGACAGCGAAGCAGGTCGAAGACACAAACCTTACCTCTCTCGGTTGTGATGGAGCTGGTTGAAG
ACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCCCTC
GGTTGTGATGGAGCTGGTTGAAGACAAA
Found at i:48381451 original size:50 final size:50
Alignment explanation
Indices: 48381364--48381735 Score: 301
Period size: 50 Copynumber: 7.7 Consensus size: 50
48381354 AAACCATAGA
* * * ** *
48381364 TTGCAATTTAAAAGATTGAAGCCACAATGGCGAATCTTACTTTTCTAGCG
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTTCTAGCG
** * * **
48381414 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTGC--TTC-CCCG
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTTCTAGCG
* * *
48381461 --GCAGTTAAAAAGATTGAAGCTACAACAGCGAATCTTGC--TTC---CC
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTTCTAGCG
* * *
48381504 TGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTA-TATTCCTAGTG
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACT-TTTCTAGCG
** * * **
48381554 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTGC--TTC-CCCG
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTTCTAGCG
*
48381601 --GCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCG
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTTCTAGCG
* ** * ** *
48381649 TTGTAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCT-GACA
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTTCTAG-CG
* *
48381699 TTGCAATTAAAAAGATTGAAGCTACAACAGCAGATCT
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCT
48381736 CAACTCCTAA
Statistics
Matches: 258, Mismatches: 49, Indels: 30
0.77 0.15 0.09
Matches are distributed among these distances:
43 1 0.00
45 106 0.41
47 7 0.03
48 7 0.03
49 1 0.00
50 136 0.53
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (50 bp):
TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTTCTAGCG
Found at i:48381480 original size:45 final size:45
Alignment explanation
Indices: 48381426--48381735 Score: 314
Period size: 45 Copynumber: 6.6 Consensus size: 45
48381416 GCAGTGGAAC
48381426 AGATTGAAGCTACAACAGCGGATCTTGCTTCCCCGGCAGTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTGCTTCCCCGGCAGTTAAAA
* *
48381471 AGATTGAAGCTACAACAGCGAATCTTGCTTCCCTGGCAGTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTGCTTCCCCGGCAGTTAAAA
** ** ** *
48381516 AGATTGAAGCTACAACAGCGGATCTTATATTCCTAGTGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTT-GCTTCC--CCG--GCAGTTAAAA
48381566 AGATTGAAGCTACAACAGCGGATCTTGCTTCCCCGGCAGTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTGCTTCCCCGGCAGTTAAAA
* * * ** *
48381611 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGTAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTGC-TTCC--CCG--GCAGTTAAAA
* * *
48381661 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTGCTTCCC---C--GGCAGTTAAAA
*
48381711 AGATTGAAGCTACAACAGCAGATCT
1 AGATTGAAGCTACAACAGCGGATCT
48381736 CAACTCCTAA
Statistics
Matches: 220, Mismatches: 30, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
45 102 0.46
46 8 0.04
47 1 0.00
48 4 0.02
49 8 0.04
50 97 0.44
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (45 bp):
AGATTGAAGCTACAACAGCGGATCTTGCTTCCCCGGCAGTTAAAA
Found at i:48381570 original size:95 final size:95
Alignment explanation
Indices: 48381426--48381735 Score: 416
Period size: 95 Copynumber: 3.3 Consensus size: 95
48381416 GCAGTGGAAC
* * ** *
48381426 AGATTGAAGCTACAACAGCGGATCTTGC-TTCC--CCG--GCAGTTAAAAAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAA
*
48381486 CAGCGAATCTTGCTTCCCTGGCAGTTAAAA
66 CAGCGGATCTTGCTTCCCTGGCAGTTAAAA
*
48381516 AGATTGAAGCTACAACAGCGGATCTTA-TATTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACA
1 AGATTGAAGCTACAACAGCGGATCTTACT-TTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACA
*
48381580 ACAGCGGATCTTGCTTCCCCGGCAGTTAAAA
65 ACAGCGGATCTTGCTTCCCTGGCAGTTAAAA
*
48381611 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGTAGTGGAACAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAA
* *
48381676 CAGCGGATCTTACTTCCCTGACATTGCAATTAAAA
66 CAGCGGATCTTGCTTCCCTG-----GCAGTTAAAA
*
48381711 AGATTGAAGCTACAACAGCAGATCT
1 AGATTGAAGCTACAACAGCGGATCT
48381736 CAACTCCTAA
Statistics
Matches: 194, Mismatches: 14, Indels: 14
0.87 0.06 0.06
Matches are distributed among these distances:
90 26 0.13
91 4 0.02
93 1 0.01
95 129 0.66
96 1 0.01
100 33 0.17
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (95 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAA
CAGCGGATCTTGCTTCCCTGGCAGTTAAAA
Found at i:48381625 original size:140 final size:142
Alignment explanation
Indices: 48381373--48381735 Score: 475
Period size: 140 Copynumber: 2.5 Consensus size: 142
48381363 ATTGCAATTT
* ** * *
48381373 AAAAGATTGAAGCCACAATGGCGAATCTTACTTTTCTAGCGTTGCAGTGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTA
*
48381438 CAACAGCGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGCTACAACAGCGAATCTTGCTTCC
66 CAACAGCGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTCC
*
48381503 CTGGCAG-T-TA-
131 CTAGC-GTTGTAG
*
48381513 AAAAGATTGAAGCTACAACAGCGGATCTTA-TATTCCTAGTGTTGCAGTGGAACAGATTGAAGCT
1 AAAAGATTGAAGCTACAACAGCGGATCTTACT-TTCCTAGCGTTGCAGTGGAACAGATTGAAGCT
* *
48381577 ACAACAGCGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTT
65 ACAACAGCGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTC
48381642 CCTAGCGTTGTAGTGG
130 CCTAGCGTTGTA---G
* * * * ** *
48381658 AACAGATTGAAGCTACAACAGCGGATCTTACTTCCCT-GACATTGCAATTAAAAAGATTGAAGCT
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CGTTGCAGTGGAACAGATTGAAGCT
*
48381722 ACAACAGCAGATCT
65 ACAACAGCGGATCT
48381736 CAACTCCTAA
Statistics
Matches: 195, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
139 2 0.01
140 124 0.64
141 2 0.01
144 1 0.01
145 65 0.33
146 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (142 bp):
AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTA
CAACAGCGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTCC
CTAGCGTTGTAG
Found at i:48383465 original size:16 final size:16
Alignment explanation
Indices: 48383429--48383467 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
48383419 CTTTAATTTA
48383429 TATATATACATACTTT
1 TATATATACATACTTT
* **
48383445 CATATATACATGTTTT
1 TATATATACATACTTT
48383461 TATATAT
1 TATATAT
48383468 TTCCATTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (16 bp):
TATATATACATACTTT
Found at i:48386061 original size:17 final size:17
Alignment explanation
Indices: 48386035--48386103 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 17
48386025 ATTAATTTTT
*
48386035 AAATTTTAAAAAATAAA
1 AAATTATAAAAAATAAA
*
48386052 AAATTATAAATAATGAAA
1 AAATTATAAAAAAT-AAA
* *
48386070 ATGATT-TAAAAAGTATAA
1 A-AATTATAAAAAATA-AA
48386088 AAATTATAAAACAATA
1 AAATTATAAAA-AATA
48386104 TTTTTAATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
17 16 0.40
18 18 0.45
19 6 0.15
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (17 bp):
AAATTATAAAAAATAAA
Found at i:48390352 original size:7 final size:7
Alignment explanation
Indices: 48390340--48390364 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
48390330 ATATATACAC
48390340 ATATATT
1 ATATATT
48390347 ATATATT
1 ATATATT
48390354 ATATATT
1 ATATATT
48390361 ATAT
1 ATAT
48390365 CCCATCAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATATATT
Found at i:48400417 original size:24 final size:24
Alignment explanation
Indices: 48400360--48400417 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
48400350 TCTAATTAAA
*
48400360 ATTTATAAATAATTAATATTTATT
1 ATTTATAAATAATTAAAATTTATT
* * *
48400384 ACTTAAAAATATTTAAAATTTA-T
1 ATTTATAAATAATTAAAATTTATT
48400407 ATTTCATAAAT
1 ATTT-ATAAAT
48400418 TAAAATATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTTATAAATAATTAAAATTTATT
Found at i:48407200 original size:16 final size:16
Alignment explanation
Indices: 48407179--48407210 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
48407169 AGTAAGTTAC
48407179 ATGTAAACAATAATTA
1 ATGTAAACAATAATTA
48407195 ATGTAAACAATAATTA
1 ATGTAAACAATAATTA
48407211 CTCATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (16 bp):
ATGTAAACAATAATTA
Found at i:48407441 original size:23 final size:23
Alignment explanation
Indices: 48407415--48407490 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
48407405 ATAAGTGCCA
48407415 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
48407438 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
48407461 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
48407484 CACTGAT
1 CACTGAT
48407491 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:48407590 original size:8 final size:8
Alignment explanation
Indices: 48407577--48407605 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
48407567 ACCCGGGACT
48407577 CACTGTAA
1 CACTGTAA
48407585 CACTGTAA
1 CACTGTAA
48407593 CACTGTAA
1 CACTGTAA
48407601 CACTG
1 CACTG
48407606 GTCTCTAGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:48407736 original size:18 final size:17
Alignment explanation
Indices: 48407710--48407748 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
48407700 ATTTTCCTTC
48407710 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
48407727 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
48407745 CACA
1 CACA
48407749 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:48409407 original size:22 final size:22
Alignment explanation
Indices: 48409379--48409420 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
48409369 TTTCCCTTTT
48409379 AAAATAAA-ATAAAATAACATAA
1 AAAATAAATATAAAA-AACATAA
48409401 AAAATAAATATAAAAAACAT
1 AAAATAAATATAAAAAACAT
48409421 TCATAAGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (22 bp):
AAAATAAATATAAAAAACATAA
Found at i:48409940 original size:41 final size:40
Alignment explanation
Indices: 48409895--48410095 Score: 224
Period size: 41 Copynumber: 4.9 Consensus size: 40
48409885 ACACTAGTAT
* * *
48409895 GAAGCCTGCTAGGCTCAAAGCCTGATGTAACACATCGACAC
1 GAAGCCTGCTAGGCACAAAGCCTGATATAATACA-CGACAC
* * * *
48409936 GAAGCTTGTTAGGCACAAAGCTTGATATAATACATCGACAT
1 GAAGCCTGCTAGGCACAAAGCCTGATATAATACA-CGACAC
* * * *
48409977 GCAGCCCGCTAGGCACAAAGTCTGATATAATACACTAGCAC
1 GAAGCCTGCTAGGCACAAAGCCTGATATAATACACGA-CAC
*
48410018 GAAGCCTGCTAGGCACAACA-CCTGATATAATACACAGGCAC
1 GAAGCCTGCTAGGCACAA-AGCCTGATATAATACAC-GACAC
* *
48410059 GAAGCCTACTAGGCACAATGCCTGATATAATACACGA
1 GAAGCCTGCTAGGCACAAAGCCTGATATAATACACGA
48410096 AATCTAGAAT
Statistics
Matches: 133, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
40 3 0.02
41 129 0.97
42 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (40 bp):
GAAGCCTGCTAGGCACAAAGCCTGATATAATACACGACAC
Found at i:48412911 original size:13 final size:13
Alignment explanation
Indices: 48412895--48412966 Score: 56
Period size: 13 Copynumber: 5.5 Consensus size: 13
48412885 ATCACGATAC
*
48412895 CACTTAGTAGTAT
1 CACTTAGTGGTAT
* *
48412908 CACTTTA-TTGTAG
1 CAC-TTAGTGGTAT
*
48412921 CACTTAGCGGTAT
1 CACTTAGTGGTAT
* * *
48412934 AACTTAGTGTTGT
1 CACTTAGTGGTAT
48412947 CACTTAGTGGTAT
1 CACTTAGTGGTAT
*
48412960 CATTTAG
1 CACTTAG
48412967 CTCCATGTTT
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
12 3 0.07
13 38 0.86
14 3 0.07
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.40
Consensus pattern (13 bp):
CACTTAGTGGTAT
Found at i:48412933 original size:26 final size:27
Alignment explanation
Indices: 48412895--48412966 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 27
48412885 ATCACGATAC
* *
48412895 CACTTAGTAGTATCACTTTATTGTAG-
1 CACTTAGTGGTATCACTTTAGTGTAGT
* * *
48412921 CACTTAGCGGTATAAC-TTAGTGTTGT
1 CACTTAGTGGTATCACTTTAGTGTAGT
48412947 CACTTAGTGGTATCA-TTTAG
1 CACTTAGTGGTATCACTTTAG
48412967 CTCCATGTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
25 7 0.19
26 30 0.81
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.40
Consensus pattern (27 bp):
CACTTAGTGGTATCACTTTAGTGTAGT
Found at i:48417612 original size:9 final size:9
Alignment explanation
Indices: 48417598--48417628 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
48417588 GTTAAACGAA
48417598 TCGAGTTAT
1 TCGAGTTAT
*
48417607 TCGAGTTAA
1 TCGAGTTAT
48417616 TCGAGTTAT
1 TCGAGTTAT
48417625 TCGA
1 TCGA
48417629 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:48417700 original size:9 final size:9
Alignment explanation
Indices: 48417683--48417719 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
48417673 TGAGTTTTCG
48417683 AATTCGAAT
1 AATTCGAAT
*
48417692 AACTCGAAT
1 AATTCGAAT
48417701 AATTCGAAT
1 AATTCGAAT
48417710 AATTCGAAT
1 AATTCGAAT
48417719 A
1 A
48417720 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:48420496 original size:16 final size:16
Alignment explanation
Indices: 48420475--48420520 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
48420465 AATTGGGATG
48420475 AGAAAATTATTTAATT
1 AGAAAATTATTTAATT
*
48420491 AGAAAATTAATTAATT
1 AGAAAATTATTTAATT
48420507 --AAAATTAATTTAAT
1 AGAAAATT-ATTTAAT
48420521 AAATAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 6 0.22
15 6 0.22
16 15 0.56
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (16 bp):
AGAAAATTATTTAATT
Found at i:48423277 original size:21 final size:21
Alignment explanation
Indices: 48423235--48423278 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
48423225 AGGATTAGAG
* *
48423235 TTGGGAACATTATGTCCGACA
1 TTGGGAACATCATGTCCAACA
*
48423256 TTGGGAACATCATGTCTAACA
1 TTGGGAACATCATGTCCAACA
48423277 TT
1 TT
48423279 TTCCAATAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (21 bp):
TTGGGAACATCATGTCCAACA
Found at i:48425690 original size:13 final size:13
Alignment explanation
Indices: 48425672--48425696 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48425662 AAATAGATAT
48425672 TTATTATATTATA
1 TTATTATATTATA
48425685 TTATTATATTAT
1 TTATTATATTAT
48425697 TATTGTTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTATATTATA
Found at i:48427012 original size:23 final size:23
Alignment explanation
Indices: 48426986--48427040 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
48426976 GGTTTTGCCG
*
48426986 ATCAGGCACTTTATGTTTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
48427009 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
*
48427032 TTCAGGCAC
1 ATCAGGCAC
48427041 CTCGTATGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAT
Found at i:48427071 original size:21 final size:22
Alignment explanation
Indices: 48427022--48427071 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
48427012 AGGCACTTTA
*
48427022 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAAGCACCTCG
* *
48427045 TATGTCGTA-TCAAGCACCTGG
1 TGTGTCGTATTCAAGCACCTCG
48427066 TGTGTC
1 TGTGTC
48427072 ATTTCAGGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.65
23 8 0.35
ACGTcount: A:0.16, C:0.24, G:0.26, T:0.34
Consensus pattern (22 bp):
TGTGTCGTATTCAAGCACCTCG
Found at i:48427082 original size:21 final size:21
Alignment explanation
Indices: 48427030--48427082 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
48427020 TATGTGTCGT
48427030 ATTTCAGGCACCTCGTATGTC
1 ATTTCAGGCACCTCGTATGTC
* * * * *
48427051 GTATCAAGCACCTGGTGTGTC
1 ATTTCAGGCACCTCGTATGTC
48427072 ATTTCAGGCAC
1 ATTTCAGGCAC
48427083 TTATGTGTCG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (21 bp):
ATTTCAGGCACCTCGTATGTC
Found at i:48427363 original size:24 final size:24
Alignment explanation
Indices: 48427334--48427381 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
48427324 GAGATTTGAA
* *
48427334 AATGAAATATATGAAATGGTTATT
1 AATGAAATACATGAAATGGATATT
*
48427358 AATGAAATGCATGAAATGGATATT
1 AATGAAATACATGAAATGGATATT
48427382 GATATAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.19, T:0.33
Consensus pattern (24 bp):
AATGAAATACATGAAATGGATATT
Found at i:48428067 original size:16 final size:17
Alignment explanation
Indices: 48428042--48428081 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
48428032 AATTTTTTTT
*
48428042 AAATTTTAAATTA-TAA
1 AAATTATAAATTATTAA
*
48428058 AAATTATAAATTATTAT
1 AAATTATAAATTATTAA
48428075 AAATTAT
1 AAATTAT
48428082 TATTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTATAAATTATTAA
Found at i:48428075 original size:10 final size:10
Alignment explanation
Indices: 48428051--48428084 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
48428041 TAAATTTTAA
*
48428051 ATTATAAA-A
1 ATTATAAATT
48428060 ATTATAAATT
1 ATTATAAATT
48428070 ATTATAAATT
1 ATTATAAATT
48428080 ATTAT
1 ATTAT
48428085 TTTTTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATTATAAATT
Found at i:48441560 original size:44 final size:44
Alignment explanation
Indices: 48441486--48441576 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
48441476 GTAGGTCAAA
48441486 TAATATTAAAGTAACCTACACTAATAAGAGTTTAAG-TGGAAAAC
1 TAATATTAAAGTAACCTACACTAATAAGAGTTTAAGCTGG-AAAC
* * * *
48441530 TAATATTAATGTAACCTATATTAATCAGAGTTTAAGCTGGAAAC
1 TAATATTAAAGTAACCTACACTAATAAGAGTTTAAGCTGGAAAC
48441574 TAA
1 TAA
48441577 AAGTAGAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 39 0.93
45 3 0.07
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (44 bp):
TAATATTAAAGTAACCTACACTAATAAGAGTTTAAGCTGGAAAC
Found at i:48443520 original size:44 final size:44
Alignment explanation
Indices: 48443470--48443555 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
48443460 TTTGTAGGTC
*
48443470 AAATAATATTAAAATAACCTACACTAATTAGAGTTTAAGTGGAA
1 AAATAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGAA
* *
48443514 AAATAATATTAAAGTAATCTACACTAATCAGAGTTTAAGTGG
1 AAATAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGG
48443556 GGAACTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (44 bp):
AAATAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGAA
Found at i:48457344 original size:30 final size:29
Alignment explanation
Indices: 48457309--48457369 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
48457299 ATGTTAATGG
*
48457309 TAATTAGAATAA-ATTAATTAAATATTTAAT
1 TAATTA-AATAAGATTAATT-AAGATTTAAT
* *
48457339 TAATTAACTAAGGTTAATTAAGATTTAAT
1 TAATTAAATAAGATTAATTAAGATTTAAT
48457368 TA
1 TA
48457370 CTGTATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.43
Consensus pattern (29 bp):
TAATTAAATAAGATTAATTAAGATTTAAT
Found at i:48467206 original size:36 final size:36
Alignment explanation
Indices: 48467166--48467237 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
48467156 TATAATGACT
* * *
48467166 GATGTGAAAGTGAATATGA-GGGTGTGTTGTTCATGC
1 GATGTGAAAGTAAATAT-ATGGGTATGTTATTCATGC
*
48467202 GATGTGACAGTAAATATATGGGTATGTTATTCATGC
1 GATGTGAAAGTAAATATATGGGTATGTTATTCATGC
48467238 CATATGACTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 1 0.03
36 30 0.97
ACGTcount: A:0.28, C:0.07, G:0.31, T:0.35
Consensus pattern (36 bp):
GATGTGAAAGTAAATATATGGGTATGTTATTCATGC
Found at i:48469115 original size:29 final size:29
Alignment explanation
Indices: 48469074--48469131 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
48469064 TCCTACATAA
48469074 TTTTCTATTGTTGTTCCGATAATCAATGT
1 TTTTCTATTGTTGTTCCGATAATCAATGT
48469103 TTTTCTATTGTTGTTCCGATAATCAATGT
1 TTTTCTATTGTTGTTCCGATAATCAATGT
48469132 AGCATTCCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.52
Consensus pattern (29 bp):
TTTTCTATTGTTGTTCCGATAATCAATGT
Found at i:48471689 original size:27 final size:27
Alignment explanation
Indices: 48471669--48471813 Score: 191
Period size: 27 Copynumber: 5.4 Consensus size: 27
48471659 GGGTATAACA
*
48471669 GTCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
48471696 GTCATTCTATCTTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
48471723 GTCATTCTACCCTATGGGGATATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
** * *
48471750 ACCATTTTACCCTATGGTGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
48471777 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
48471804 GTCATTTTAC
1 GTCATTTTAC
48471814 TTTATAGGGT
Statistics
Matches: 99, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 99 1.00
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:48477751 original size:17 final size:17
Alignment explanation
Indices: 48477729--48477765 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
48477719 TAATCTCACA
*
48477729 TTAATAAAATTTTTACT
1 TTAATAAAAATTTTACT
*
48477746 TTAATAAAAATTTTATT
1 TTAATAAAAATTTTACT
48477763 TTA
1 TTA
48477766 TCAGAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAATAAAAATTTTACT
Found at i:48481744 original size:28 final size:28
Alignment explanation
Indices: 48481704--48481764 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
48481694 ACATGCAATG
*
48481704 ACAGTTTGGGCCTGAGCCCTAAGCAGTA
1 ACAGTCTGGGCCTGAGCCCTAAGCAGTA
*
48481732 ACAGTCTGGGCCTTAGCCCTAAGCAGTA
1 ACAGTCTGGGCCTGAGCCCTAAGCAGTA
48481760 ACAGT
1 ACAGT
48481765 GTAATGTGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (28 bp):
ACAGTCTGGGCCTGAGCCCTAAGCAGTA
Found at i:48481780 original size:33 final size:31
Alignment explanation
Indices: 48481710--48481799 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 31
48481700 AATGACAGTT
*
48481710 TGGGCCTGAGCCCTAAGCAGTAACA--G-TC
1 TGGGCCTTAGCCCTAAGCAGTAACAGTGTTC
*
48481738 TGGGCCTTAGCCCTAAGCAGTAACAGTGTAATG
1 TGGGCCTTAGCCCTAAGCAGTAACAGTGT--TC
**
48481771 TGGGCCTTAG-CCTATTTCAGTAACAGTGT
1 TGGGCCTTAGCCCTA-AGCAGTAACAGTGT
48481800 GAGCCTTAGC
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
28 24 0.46
30 1 0.02
32 4 0.08
33 23 0.44
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (31 bp):
TGGGCCTTAGCCCTAAGCAGTAACAGTGTTC
Found at i:48482174 original size:27 final size:26
Alignment explanation
Indices: 48482144--48482323 Score: 200
Period size: 27 Copynumber: 6.7 Consensus size: 26
48482134 TCAACTCCCA
** *
48482144 GGGGTATAACAGTCATTTTATCCTATG
1 GGGGTATTTCAGTCATTTTACCCT-TG
48482171 GGGGTATTTCAGTCATTTTACCCTTCG
1 GGGGTATTTCAGTCATTTTACCCTT-G
*
48482198 GGGGTATTTCAGTTATTTTACCCTTTG
1 GGGGTATTTCAGTCATTTTACCC-TTG
** *
48482225 GGGGTATTTTGGTTATTTTACCCTTTG
1 GGGGTATTTCAGTCATTTTACCC-TTG
48482252 GGGGTATTTC-GTTCATTTTACCCTTTG
1 GGGGTATTTCAG-TCATTTTACCC-TTG
* *
48482279 GGGGTATTTCGGTTATTTTACCCTTCG
1 GGGGTATTTCAGTCATTTTACCCTT-G
*
48482306 AGGGTATTTCAGTCATTT
1 GGGGTATTTCAGTCATTT
48482324 GCCCATGAAT
Statistics
Matches: 136, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
26 4 0.03
27 129 0.95
28 3 0.02
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (26 bp):
GGGGTATTTCAGTCATTTTACCCTTG
Found at i:48482216 original size:54 final size:54
Alignment explanation
Indices: 48482144--48482323 Score: 254
Period size: 54 Copynumber: 3.3 Consensus size: 54
48482134 TCAACTCCCA
** * * * *
48482144 GGGGTATAACAGTCATTTTATCCTATGGGGGTATTTCAGTCATTTTACCCTTCG
1 GGGGTATTTCAGTCATTTTACCCTTTGGGGGTATTTCGGTTATTTTACCCTTCG
* * *
48482198 GGGGTATTTCAGTTATTTTACCCTTTGGGGGTATTTTGGTTATTTTACCCTTTG
1 GGGGTATTTCAGTCATTTTACCCTTTGGGGGTATTTCGGTTATTTTACCCTTCG
48482252 GGGGTATTTC-GTTCATTTTACCCTTTGGGGGTATTTCGGTTATTTTACCCTTCG
1 GGGGTATTTCAG-TCATTTTACCCTTTGGGGGTATTTCGGTTATTTTACCCTTCG
*
48482306 AGGGTATTTCAGTCATTT
1 GGGGTATTTCAGTCATTT
48482324 GCCCATGAAT
Statistics
Matches: 111, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
53 1 0.01
54 109 0.98
55 1 0.01
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (54 bp):
GGGGTATTTCAGTCATTTTACCCTTTGGGGGTATTTCGGTTATTTTACCCTTCG
Found at i:48482282 original size:81 final size:81
Alignment explanation
Indices: 48482158--48482314 Score: 244
Period size: 81 Copynumber: 1.9 Consensus size: 81
48482148 TATAACAGTC
*
48482158 ATTTTATCCTATGGGGGTATTTCAGTCATTTTACCCTTCGGGGGTATTTCAGTTATTTTACCCTT
1 ATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTTCGGGGGTATTTCAGTTATTTTACCCTT
* *
48482223 TGGGGGTATTTTGGTT
66 CGAGGGTATTTTGGTT
* * *
48482239 ATTTTACCCTTTGGGGGTATTTC-GTTCATTTTACCCTTTGGGGGTATTTCGGTTATTTTACCCT
1 ATTTTACCCTATGGGGGTATTTCAG-TCATTTTACCCTTCGGGGGTATTTCAGTTATTTTACCCT
48482303 TCGAGGGTATTT
65 TCGAGGGTATTT
48482315 CAGTCATTTG
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
80 1 0.01
81 68 0.99
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.47
Consensus pattern (81 bp):
ATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTTCGGGGGTATTTCAGTTATTTTACCCTT
CGAGGGTATTTTGGTT
Found at i:48483018 original size:5 final size:5
Alignment explanation
Indices: 48482998--48483040 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
48482988 GCACTAGAAT
*
48482998 GAAGA GGAAAA GAAGA GAAGA GAAGA GAAGA GATA-A GAAGA GA
1 GAAGA -GAAGA GAAGA GAAGA GAAGA GAAGA GA-AGA GAAGA GA
48483041 GGATTTGGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
4 1 0.03
5 27 0.82
6 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.02
Consensus pattern (5 bp):
GAAGA
Found at i:48486095 original size:40 final size:38
Alignment explanation
Indices: 48486046--48486140 Score: 93
Period size: 40 Copynumber: 2.5 Consensus size: 38
48486036 AACACAACAG
* *
48486046 TTTGGCACCCAATGCCTCATCAGATAATTCAAAGTAATAA
1 TTTGACACCCAATGCCTCATCAGATAAATCAAAGT-A-AA
** * * *
48486086 TTTGACACCCAATATCTCATCGGCTAAATCGAAGTAAA
1 TTTGACACCCAATGCCTCATCAGATAAATCAAAGTAAA
*
48486124 -TTGACACCCAGTGCCTC
1 TTTGACACCCAATGCCTC
48486141 GTCGAATTAA
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
37 14 0.31
38 2 0.04
39 1 0.02
40 28 0.62
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (38 bp):
TTTGACACCCAATGCCTCATCAGATAAATCAAAGTAAA
Found at i:48487062 original size:13 final size:13
Alignment explanation
Indices: 48487044--48487079 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
48487034 TACGTCTTTC
48487044 TTTCTCTTTTTTG
1 TTTCTCTTTTTTG
48487057 TTTCTCTTTCTTTG
1 TTTCTCTTT-TTTG
48487071 TTT-TCTTTT
1 TTTCTCTTTT
48487080 GGTTTTGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 14 0.64
14 7 0.32
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.78
Consensus pattern (13 bp):
TTTCTCTTTTTTG
Found at i:48490243 original size:2 final size:2
Alignment explanation
Indices: 48490231--48490270 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
48490221 ACGACTTCAG
*
48490231 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48490271 CTTACATCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48497221 original size:6 final size:6
Alignment explanation
Indices: 48497210--48497266 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
48497200 AACGATCTAG
48497210 TTGATA TTGATA TTGATA TTGATA TTGATA TTGATA TTGATA TTGATA
1 TTGATA TTGATA TTGATA TTGATA TTGATA TTGATA TTGATA TTGATA
48497258 TTGATA TTG
1 TTGATA TTG
48497267 TGAGGATGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.51
Consensus pattern (6 bp):
TTGATA
Found at i:48499774 original size:20 final size:20
Alignment explanation
Indices: 48499745--48499789 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
48499735 AGCACATGAA
48499745 TGGA-ACCCCAAATGCCCAC
1 TGGATACCCCAAATGCCCAC
48499764 TGGATACCCCAAATGCCCAC
1 TGGATACCCCAAATGCCCAC
48499784 TGGATA
1 TGGATA
48499790 ATCATTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.31, C:0.36, G:0.18, T:0.16
Consensus pattern (20 bp):
TGGATACCCCAAATGCCCAC
Found at i:48503545 original size:24 final size:25
Alignment explanation
Indices: 48503507--48503566 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 25
48503497 TAAATTTGAA
48503507 CATTTTAAAT-T-ATAAAT-ATTTT
1 CATTTTAAATATAATAAATCATTTT
*
48503529 CATTTTAAATATAATAAGTCATTTT
1 CATTTTAAATATAATAAATCATTTT
*
48503554 -ATTTT-TATATAAT
1 CATTTTAAATATAAT
48503567 GACAACACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 10 0.30
23 8 0.24
24 10 0.30
25 5 0.15
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (25 bp):
CATTTTAAATATAATAAATCATTTT
Found at i:48503711 original size:18 final size:20
Alignment explanation
Indices: 48503667--48503713 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
48503657 TTATTCTATG
*
48503667 ATATTATATGATTTAATGAT
1 ATATTATATGATTTAATAAT
* *
48503687 TTTTTAT-TG-TTTAATAAT
1 ATATTATATGATTTAATAAT
48503705 ATATTATAT
1 ATATTATAT
48503714 TGAAAATTGA
Statistics
Matches: 21, Mismatches: 5, Indels: 3
0.72 0.17 0.10
Matches are distributed among these distances:
18 13 0.62
19 3 0.14
20 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
ATATTATATGATTTAATAAT
Found at i:48506254 original size:105 final size:105
Alignment explanation
Indices: 48506064--48506255 Score: 244
Period size: 105 Copynumber: 1.8 Consensus size: 105
48506054 AATATTTTTT
* * **
48506064 ATTATTAATTAAAAATAAAAAAAGCTTGAAACAACATGAAATAAAAAATACAAATGTCTTTAGAA
1 ATTAGTAATTAAAAATAAAAAAAGCTTGAAACAACATGAAATAAAAAATACAAATATCAGTAGAA
* ** ** *
48506129 GAGGAATTGAACTTGGGACTCAAGAAACTTATGTATTGAA
66 CAGGAATCAAACCCGAGACTCAAGAAACTTATGTATTGAA
*
48506169 ATTAGTAATTAAAAATAAAAGTAAAGCTTGAAACAACATG-AA-AAAAAATACAAATATGAGTAG
1 ATTAGTAATTAAAAATAAAA--AAAGCTTGAAACAACATGAAATAAAAAATACAAATATCAGTAG
*
48506232 GACAGGAATCAAACCCGAGACTCA
64 AACAGGAATCAAACCCGAGACTCA
48506256 GATAAAATCA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
105 53 0.73
106 2 0.03
107 18 0.25
ACGTcount: A:0.52, C:0.10, G:0.15, T:0.23
Consensus pattern (105 bp):
ATTAGTAATTAAAAATAAAAAAAGCTTGAAACAACATGAAATAAAAAATACAAATATCAGTAGAA
CAGGAATCAAACCCGAGACTCAAGAAACTTATGTATTGAA
Found at i:48507277 original size:79 final size:79
Alignment explanation
Indices: 48507181--48507337 Score: 251
Period size: 79 Copynumber: 2.0 Consensus size: 79
48507171 ACTAGTACGT
* * *
48507181 CTCTACGTTACTCTGTTGATGAAGAATGTGCAATATCTGAATATATTGGATTGATGGTTACTGAT
1 CTCTACGTTACTCTGTTGATGAAGAATATACAATATCTGAATATATTAGATTGATGGTTACTGAT
48507246 TCTAATTTATAACA
66 TCTAATTTATAACA
* * *
48507260 CTCTACGTTACTCTGTTGATGAAGAATATACGATATCTGAATATGTTAGATTGATTGTTACTGAT
1 CTCTACGTTACTCTGTTGATGAAGAATATACAATATCTGAATATATTAGATTGATGGTTACTGAT
*
48507325 TCTGATTTATAAC
66 TCTAATTTATAAC
48507338 CGTGCATGTG
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 71 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (79 bp):
CTCTACGTTACTCTGTTGATGAAGAATATACAATATCTGAATATATTAGATTGATGGTTACTGAT
TCTAATTTATAACA
Found at i:48507872 original size:25 final size:25
Alignment explanation
Indices: 48507808--48507894 Score: 104
Period size: 25 Copynumber: 3.5 Consensus size: 25
48507798 AACGTACATG
* *
48507808 CTCTGCTCTGTTATGTTCAATTCTA
1 CTCTGCTCTGTTATGTTTAGTTCTA
48507833 CTCTGCTCTGTTATGTTTAGTTCTA
1 CTCTGCTCTGTTATGTTTAGTTCTA
** *
48507858 CTCTGCTCTACTATG-TTATGTTCTG
1 CTCTGCTCTGTTATGTTTA-GTTCTA
*
48507883 CTCTGCTATGTT
1 CTCTGCTCTGTT
48507895 CTATTCTCTT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
24 3 0.06
25 50 0.94
ACGTcount: A:0.13, C:0.23, G:0.15, T:0.49
Consensus pattern (25 bp):
CTCTGCTCTGTTATGTTTAGTTCTA
Found at i:48507894 original size:15 final size:15
Alignment explanation
Indices: 48507873--48507916 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
48507863 CTCTACTATG
48507873 TTATGTTCTGCTCTGC
1 TTATGTTCTGCTCT-C
**
48507889 -TATGTTCTATTCTC
1 TTATGTTCTGCTCTC
48507903 TTATGTTCTGCTCT
1 TTATGTTCTGCTCT
48507917 ATCCTGTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 1 0.04
15 22 0.96
ACGTcount: A:0.09, C:0.23, G:0.14, T:0.55
Consensus pattern (15 bp):
TTATGTTCTGCTCTC
Found at i:48507901 original size:20 final size:20
Alignment explanation
Indices: 48507852--48507901 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
48507842 GTTATGTTTA
*
48507852 GTTCTACTCTGCTCTACTAT
1 GTTCTATTCTGCTCTACTAT
* * *
48507872 GTTATGTTCTGCTCTGCTAT
1 GTTCTATTCTGCTCTACTAT
48507892 GTTCTATTCT
1 GTTCTATTCT
48507902 CTTATGTTCT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.14, T:0.50
Consensus pattern (20 bp):
GTTCTATTCTGCTCTACTAT
Found at i:48509350 original size:17 final size:16
Alignment explanation
Indices: 48509326--48509364 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
48509316 TTATGCACAC
48509326 TTTATTAATAATATAT
1 TTTATTAATAATATAT
*
48509342 TTGTATTAATAATGTAT
1 TT-TATTAATAATATAT
48509359 TTTATT
1 TTTATT
48509365 GAGTTGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTATTAATAATATAT
Found at i:48510359 original size:59 final size:58
Alignment explanation
Indices: 48510294--48510417 Score: 131
Period size: 59 Copynumber: 2.1 Consensus size: 58
48510284 ATTTTTTAGT
*** **
48510294 TTTTAAGGGGCTTTAAAAAAATTTTAACTTTTAAAGGTCAAAAAAAAGTTTTTACCAAC
1 TTTTAAGGGGCCCAAAAAAAACATTAACTTTTAAAGG-CAAAAAAAAGTTTTTACCAAC
* * ** ***
48510353 TTTTAAGTGGCCCAAAAAAAACATTAGCTTTTAAAGGCCCAAAATTTTTTTTACCAAC
1 TTTTAAGGGGCCCAAAAAAAACATTAACTTTTAAAGGCAAAAAAAAGTTTTTACCAAC
48510411 TTTTAAG
1 TTTTAAG
48510418 AGACCTAAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
58 23 0.43
59 30 0.57
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (58 bp):
TTTTAAGGGGCCCAAAAAAAACATTAACTTTTAAAGGCAAAAAAAAGTTTTTACCAAC
Found at i:48510454 original size:30 final size:31
Alignment explanation
Indices: 48510380--48510457 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 31
48510370 AAAACATTAG
* * *
48510380 CTTTTAA-AGGCCCAAAATTTTTTTTACCAA
1 CTTTTAAGAGACCTAAAATTTTTTCTACCAA
48510410 CTTTTAAGAGACCTAAAATTTTTTCT-CCAA
1 CTTTTAAGAGACCTAAAATTTTTTCTACCAA
48510440 CTTTTAAG-GAACCTAAAA
1 CTTTTAAGAG-ACCTAAAA
48510458 CCTCATATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 1 0.02
30 27 0.63
31 15 0.35
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (31 bp):
CTTTTAAGAGACCTAAAATTTTTTCTACCAA
Found at i:48517216 original size:13 final size:13
Alignment explanation
Indices: 48517191--48517224 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
48517181 TTTTCTTTCA
48517191 TTTCTTT-TTGTT
1 TTTCTTTCTTGTT
48517203 TTTCTTTCTTGTT
1 TTTCTTTCTTGTT
*
48517216 TATCTTTCT
1 TTTCTTTCT
48517225 CTTATTTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (13 bp):
TTTCTTTCTTGTT
Found at i:48517223 original size:17 final size:16
Alignment explanation
Indices: 48517177--48517224 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
48517167 TTTTTGGCTG
48517177 CTTGTTTTCTTTCATTT
1 CTTGTTTTCTTTC-TTT
*
48517194 CTT-TTTGTTTTTCTTT
1 CTTGTTT-TCTTTCTTT
48517210 CTTGTTTATCTTTCT
1 CTTGTTT-TCTTTCT
48517225 CTTATTTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.04, C:0.17, G:0.06, T:0.73
Consensus pattern (16 bp):
CTTGTTTTCTTTCTTT
Found at i:48518314 original size:27 final size:27
Alignment explanation
Indices: 48518268--48518427 Score: 194
Period size: 27 Copynumber: 5.9 Consensus size: 27
48518258 TCTGCTGACT
**
48518268 GAAATACCTTCGAAGGGTAAAATGATC
1 GAAATACCCCCGAAGGGTAAAATGATC
* * ** *
48518295 GAAATACCCTCAAATTGTAAAATGACC
1 GAAATACCCCCGAAGGGTAAAATGATC
* *
48518322 AAAATACCCTCGAAGGGTAAAATGATC
1 GAAATACCCCCGAAGGGTAAAATGATC
* *
48518349 GAAATACCCCCGAAGGGTAAAATAACC
1 GAAATACCCCCGAAGGGTAAAATGATC
48518376 GAAATACCCCCGAAGGGTAAAATGATC
1 GAAATACCCCCGAAGGGTAAAATGATC
***
48518403 GAAATACCTTTGAAGGGTAAAATGA
1 GAAATACCCCCGAAGGGTAAAATGA
48518428 CTGTTATACC
Statistics
Matches: 114, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 114 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (27 bp):
GAAATACCCCCGAAGGGTAAAATGATC
Found at i:48518418 original size:54 final size:54
Alignment explanation
Indices: 48518268--48518425 Score: 226
Period size: 54 Copynumber: 2.9 Consensus size: 54
48518258 TCTGCTGACT
* * ** *
48518268 GAAATACCTTCGAAGGGTAAAATGATCGAAATACCCTCAAATTGTAAAATGACC
1 GAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATAACC
* *
48518322 AAAATACCCTCGAAGGGTAAAATGATCGAAATACCCCCGAAGGGTAAAATAACC
1 GAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATAACC
* * *
48518376 GAAATACCCCCGAAGGGTAAAATGATCGAAATACCTTTGAAGGGTAAAAT
1 GAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCGAAGGGTAAAAT
48518426 GACTGTTATA
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 92 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (54 bp):
GAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATAACC
Found at i:48518636 original size:26 final size:26
Alignment explanation
Indices: 48518607--48518709 Score: 125
Period size: 26 Copynumber: 4.0 Consensus size: 26
48518597 TTGCCACAAA
*
48518607 TACTGTTATTGGCAGCTTTGCTGCGT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* * * *
48518633 TACTGATACTGGCAGCTCTACTGGGT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* *
48518659 TACTGTTAGTGGCAGCTTTGCTGCAT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* *
48518685 TACTATTACTGGCAGTTTTGCTGCG
1 TACTGTTACTGGCAGCTTTGCTGCG
48518710 ATATTAGTGT
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 62 1.00
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.38
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGCTGCGT
Found at i:48518883 original size:30 final size:30
Alignment explanation
Indices: 48518843--48518932 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
48518833 GCTTAAGGCT
48518843 CACACTGTTACTGTATTGGGCTAAGGCCCA
1 CACACTGTTACTGTATTGGGCTAAGGCCCA
* *
48518873 CACTCTGTTACTGTATTGGGCTATGGCCCA
1 CACACTGTTACTGTATTGGGCTAAGGCCCA
* * ** *
48518903 CACACTGCTATTGTATAAGGCTCAGGCCCA
1 CACACTGTTACTGTATTGGGCTAAGGCCCA
48518933 GACTGATTCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (30 bp):
CACACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:48521444 original size:43 final size:42
Alignment explanation
Indices: 48521317--48521432 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 42
48521307 AGCTCGTACA
* * *
48521317 ATGCCATCGTCCCAAACGTGGTCTTATATGTAATCACATATCG
1 ATGCCA-CGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* *
48521360 ATGCCACTATCCCAGACAG-GGTCTTACACGTAATCAGATATCG
1 ATGCCAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATATCG
48521403 ATGCCGACGTCCCAGACGTGGTCTTACACG
1 ATGCC-ACGTCCCAGACGTGGTCTTACACG
48521433 AAAATACATA
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
42 2 0.03
43 58 0.92
44 3 0.05
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (42 bp):
ATGCCACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:48522364 original size:28 final size:28
Alignment explanation
Indices: 48522310--48522366 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
48522300 TATGTTTGTT
*
48522310 TTTATTATAATAACTTTATAATATATTA
1 TTTATTATAAGAACTTTATAATATATTA
*
48522338 TTTATTATTAGAACCTTTATAAT-TATTA
1 TTTATTATAAGAA-CTTTATAATATATTA
48522366 T
1 T
48522367 AAAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (28 bp):
TTTATTATAAGAACTTTATAATATATTA
Found at i:48523578 original size:18 final size:18
Alignment explanation
Indices: 48523551--48523590 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
48523541 TCCGAGGACA
48523551 GAGCCAATTG-CTAGAGTT
1 GAGCCAATTGTC-AGAGTT
*
48523569 GAGCCTATTGTCAGAGTT
1 GAGCCAATTGTCAGAGTT
48523587 GAGC
1 GAGC
48523591 AGACACCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (18 bp):
GAGCCAATTGTCAGAGTT
Found at i:48525239 original size:21 final size:21
Alignment explanation
Indices: 48525213--48525356 Score: 152
Period size: 21 Copynumber: 7.0 Consensus size: 21
48525203 TTTGGGTGAA
*
48525213 TCAGCTCTTACGGGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
* *
48525234 TCAGCTCTTATGAGTTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
* * * *
48525255 TTAGCTCTTAAGAGCTTTTTT
1 TCAGCTCTTACGAGCTTCTGT
* *
48525276 TCAGCT-TT-CAAGCTTTTGT
1 TCAGCTCTTACGAGCTTCTGT
*
48525295 TCAGCT-TT-CAAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
*
48525314 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
*
48525335 TCAGCTCTCACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
48525356 T
1 T
48525357 GGTGTATGCA
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
19 32 0.31
20 4 0.04
21 68 0.65
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTCTGT
Found at i:48525291 original size:19 final size:19
Alignment explanation
Indices: 48525267--48525319 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
48525257 AGCTCTTAAG
*
48525267 AGCTTTTTTTCAGCTTTCA
1 AGCTTTTGTTCAGCTTTCA
48525286 AGCTTTTGTTCAGCTTTCA
1 AGCTTTTGTTCAGCTTTCA
*
48525305 AGCTTCTGTTCAGCT
1 AGCTTTTGTTCAGCT
48525320 CTTATGAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.47
Consensus pattern (19 bp):
AGCTTTTGTTCAGCTTTCA
Found at i:48531208 original size:17 final size:19
Alignment explanation
Indices: 48531188--48531228 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
48531178 ATATAATTTT
*
48531188 AAAATATA-T-AATACATC
1 AAAATATACTAAAAACATC
48531205 AAAA-ATACTAAAAACATC
1 AAAATATACTAAAAACATC
48531223 AAAATA
1 AAAATA
48531229 AATATTTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.15
17 5 0.25
18 11 0.55
19 1 0.05
ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAATATACTAAAAACATC
Found at i:48531353 original size:30 final size:30
Alignment explanation
Indices: 48531309--48531368 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
48531299 ACTTAACAAG
*
48531309 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAAAAACAAAATTAA
* *
48531339 CAAATGTCTTTAAAATAAAAACAAAATTAA
1 CAAATGCCTCTAAAATAAAAACAAAATTAA
48531369 TAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAAAAACAAAATTAA
Found at i:48533400 original size:27 final size:27
Alignment explanation
Indices: 48533370--48533695 Score: 272
Period size: 27 Copynumber: 12.1 Consensus size: 27
48533360 TAAAAGTTAA
* *
48533370 TTTAACCTTTGAGGGTATTTCGATCAT
1 TTTAACCTTCGAGGGTATTTTGATCAT
* * *
48533397 TTTACCCTTCAAGGGTATTTTGGTCAT
1 TTTAACCTTCGAGGGTATTTTGATCAT
*
48533424 TTT-ACCATTTC-AGGGTA-TTTCAGTCAT
1 TTTAACC--TTCGAGGGTATTTTGA-TCAT
*
48533451 TTT-ACCTTCCGAGGGTA-TTTCAGTCAT
1 TTTAACCTT-CGAGGGTATTTTGA-TCAT
* * *
48533478 TTTATCTTTCGAGGGTA-TTTCAGTCAT
1 TTTAACCTTCGAGGGTATTTTGA-TCAT
* * *
48533505 TTTATCTTTCGAGGGTATTTTGGTCAT
1 TTTAACCTTCGAGGGTATTTTGATCAT
* * *
48533532 TTTACCCTTCGGGGGTATTTTGGTCAT
1 TTTAACCTTCGAGGGTATTTTGATCAT
* * * *
48533559 TTTACCCTTCGGGGGTATTTTGGTTAT
1 TTTAACCTTCGAGGGTATTTTGATCAT
* * *
48533586 TTTACCCTTTGAGGGTATTTTGGTCAT
1 TTTAACCTTCGAGGGTATTTTGATCAT
* *
48533613 TTTACCCTTCGGGGGTATTTTGATCAT
1 TTTAACCTTCGAGGGTATTTTGATCAT
* *
48533640 TTTACCCTTC-AGGGGTA-TTTCAGTCAT
1 TTTAACCTTCGA-GGGTATTTTGA-TCAT
*
48533667 TTTAACCTTCGAGGGTATTTTGGTCAT
1 TTTAACCTTCGAGGGTATTTTGATCAT
48533694 TT
1 TT
48533696 GCCCATGAAT
Statistics
Matches: 261, Mismatches: 27, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
25 2 0.01
26 10 0.04
27 236 0.90
28 13 0.05
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.46
Consensus pattern (27 bp):
TTTAACCTTCGAGGGTATTTTGATCAT
Found at i:48533439 original size:54 final size:53
Alignment explanation
Indices: 48533369--48533695 Score: 388
Period size: 54 Copynumber: 6.1 Consensus size: 53
48533359 ATAAAAGTTA
* * *
48533369 ATTTAACCTTTGAGGGTATTTC-GATCATTTTACCCTTCAAGGGTATTTTGGTC
1 ATTTTACCTTTCAGGGTATTTCAG-TCATTTTACCCTTCGAGGGTATTTTGGTC
**
48533422 ATTTTACCATTTCAGGGTATTTCAGTCATTTTA-CCTTCCGAGGGTATTTCAGTC
1 ATTTTACC-TTTCAGGGTATTTCAGTCATTTTACCCTT-CGAGGGTATTTTGGTC
* * *
48533476 ATTTTATCTTTCGAGGGTATTTCAGTCATTTTATCTTTCGAGGGTATTTTGGTC
1 ATTTTACCTTTC-AGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTTGGTC
* * ** * *
48533530 ATTTTACCCTTCGGGGGTATTTTGGTCATTTTACCCTTCGGGGGTATTTTGGTT
1 ATTTTACCTTTC-AGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTTGGTC
* ** * *
48533584 ATTTTACCCTTTGAGGGTATTTTGGTCATTTTACCCTTCGGGGGTATTTTGATC
1 ATTTTA-CCTTTCAGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTTGGTC
* *
48533638 ATTTTACCCTTCAGGGGTATTTCAGTCATTTTAACCTTCGAGGGTATTTTGGTC
1 ATTTTACCTTTCA-GGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTTGGTC
48533692 ATTT
1 ATTT
48533696 GCCCATGAAT
Statistics
Matches: 237, Mismatches: 30, Indels: 13
0.85 0.11 0.05
Matches are distributed among these distances:
53 20 0.08
54 209 0.88
55 8 0.03
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (53 bp):
ATTTTACCTTTCAGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTTGGTC
Found at i:48533478 original size:81 final size:81
Alignment explanation
Indices: 48533370--48533695 Score: 383
Period size: 81 Copynumber: 4.0 Consensus size: 81
48533360 TAAAAGTTAA
* * **
48533370 TTTAACCTTTGAGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTTGGTCATTTTACCATTTC
1 TTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCAGTCATTTTACC-TTTC
**
48533435 -AGGGTATTTCAGTCAT
65 GAGGGTATTTTGGTCAT
* * * *
48533451 TTTA-CCTTCCGAGGGTATTTC-AGTCATTTTATCTTTCGAGGGTATTTCAGTCATTTTATCTTT
1 TTTACCCTT-CGAGGGTATTTCGA-TCATTTTACCCTTCAAGGGTATTTCAGTCATTTTACCTTT
48533514 CGAGGGTATTTTGGTCAT
64 CGAGGGTATTTTGGTCAT
* * * ** ** *
48533532 TTTACCCTTCGGGGGTATTTTGGTCATTTTACCCTTCGGGGGTATTTTGGTTATTTTACCCTTT-
1 TTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCAGTCATTTTA-CCTTTC
48533596 GAGGGTATTTTGGTCAT
65 GAGGGTATTTTGGTCAT
* * *
48533613 TTTACCCTTCGGGGGTATTTTGATCATTTTACCCTTCAGGGGTATTTCAGTCATTTTAACC-TTC
1 TTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCAGTCATTTT-ACCTTTC
48533677 GAGGGTATTTTGGTCAT
65 GAGGGTATTTTGGTCAT
48533694 TT
1 TT
48533696 GCCCATGAAT
Statistics
Matches: 213, Mismatches: 24, Indels: 16
0.84 0.09 0.06
Matches are distributed among these distances:
80 11 0.05
81 193 0.91
82 9 0.04
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.46
Consensus pattern (81 bp):
TTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCAGTCATTTTACCTTTCG
AGGGTATTTTGGTCAT
Found at i:48539893 original size:17 final size:17
Alignment explanation
Indices: 48539871--48539906 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
48539861 CCAGAGTCTA
* *
48539871 CCTACAGTTTCTGTTTT
1 CCTACAGTCTCAGTTTT
48539888 CCTACAGTCTCAGTTTT
1 CCTACAGTCTCAGTTTT
48539905 CC
1 CC
48539907 CTAATTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.31, G:0.11, T:0.44
Consensus pattern (17 bp):
CCTACAGTCTCAGTTTT
Found at i:48540776 original size:28 final size:28
Alignment explanation
Indices: 48540722--48540778 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
48540712 AACAGTGTAA
* *
48540722 TGTGGGCCTTAGCCCATTTCAATAACAG
1 TGTGGGCCTTAGCCCAATACAATAACAG
48540750 TGTGGGCCTTAGCCCAATACAGA-AACAG
1 TGTGGGCCTTAGCCCAATACA-ATAACAG
48540778 T
1 T
48540779 ACAGTGCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAATAACAG
Found at i:48541140 original size:27 final size:27
Alignment explanation
Indices: 48541109--48541566 Score: 511
Period size: 27 Copynumber: 17.3 Consensus size: 27
48541099 GGTTATAACA
**
48541109 GTCATTTTACCCTAGGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * **
48541136 ATCATTTTACCCTTCAAGGGTATTTTA
1 GTCATTTTACCCTTCGAGGGTATTTCG
** * *
48541163 GTCATTTTACATTTTGGGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
48541190 ATCATTTTACCTTTCGAAGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
48541217 GTTATTTTACCGTTCGGGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
48541244 ATCATTTTACCCTTCGAGAGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
48541271 GTCATTTTATCCTTCGAGGGTATTTCT
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
48541298 GTCATTTTATCCTTCTAGGGTATTTCT
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
48541325 GTCATTTTACCCTTCGAGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
48541352 GTTATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
48541379 ATCATTTTACCCTTCG-GGG------G
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
48541399 GTCATTTTATCCTTTGAGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
48541426 GTCATTTTACCTTTCGAGGGCATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* **
48541453 GTCATTTTACCCTTCAAGGGTATTTTA
1 GTCATTTTACCCTTCGAGGGTATTTCG
48541480 GTCATTTTACCCTTCG-GGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
48541506 GTCATTTTACCCTTTG-GGCGTATTTCG
1 GTCATTTTACCCTTCGAGG-GTATTTCG
48541533 GTCATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
48541560 GTTATTT
1 GTCATTT
48541567 GCCCATCAAT
Statistics
Matches: 363, Mismatches: 59, Indels: 18
0.82 0.13 0.04
Matches are distributed among these distances:
20 14 0.04
21 3 0.01
26 28 0.08
27 316 0.87
28 2 0.01
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.45
Consensus pattern (27 bp):
GTCATTTTACCCTTCGAGGGTATTTCG
Found at i:48541458 original size:74 final size:74
Alignment explanation
Indices: 48541325--48541548 Score: 245
Period size: 74 Copynumber: 2.9 Consensus size: 74
48541315 GGGTATTTCT
* *
48541325 GTCATTTTACCCTTCGAGGGTATTTTGGTTATTTTACCCTTCGAGGGTATTTCGATCATTTTACC
1 GTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCTTCGAGGGCATTTCGATCATTTTACC
48541390 CTTCGGGGG
66 CTTCGGGGG
* * * * *
48541399 GTCATTTTATCCTTTGAGGGTATTTTGGTCATTTTACCTTTCGAGGGCATTTTGGTCATTTTACC
1 GTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCTTCGAGGGCATTTCGATCATTTTACC
**
48541464 CTTCAAGGGTATTTTA
66 CTTC--GGG-----GG
* * * *
48541480 GTCATTTTACCCTTCG-GGGTATTTCGGTCATTTTACCCTTTG-GGCGTATTTCGGTCATTTTAC
1 GTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCTTCGAGG-GCATTTCGATCATTTTAC
48541543 CCTTCG
65 CCTTCG
48541549 AGGGTATTTC
Statistics
Matches: 126, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
74 62 0.49
76 3 0.02
78 1 0.01
79 2 0.02
80 44 0.35
81 14 0.11
ACGTcount: A:0.15, C:0.20, G:0.21, T:0.44
Consensus pattern (74 bp):
GTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCTTCGAGGGCATTTCGATCATTTTACC
CTTCGGGGG
Found at i:48541536 original size:80 final size:81
Alignment explanation
Indices: 48541399--48541557 Score: 225
Period size: 80 Copynumber: 2.0 Consensus size: 81
48541389 CCTTCGGGGG
* * * *
48541399 GTCATTTTATCCTTTGAGGGTATTTTGGTCATTTTACCTTTCGAGGGCATTTTGGTCATTTTACC
1 GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCTTTCGAGGGCATTTCGGTCATTTTACC
48541464 CTTCAAGGGTATTTTA
66 CTTCAAGGGTATTTTA
*
48541480 GTCATTTTACCCTTCG-GGGTATTTCGGTCATTTTACCCTTT-G-GGCGTATTTCGGTCATTTTA
1 GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTA-CCTTTCGAGG-GCATTTCGGTCATTTTA
*
48541542 CCCTTCGAGGGTATTT
64 CCCTTCAAGGGTATTT
48541558 CGGTTATTTG
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
79 2 0.03
80 49 0.70
81 19 0.27
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.45
Consensus pattern (81 bp):
GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCTTTCGAGGGCATTTCGGTCATTTTACC
CTTCAAGGGTATTTTA
Found at i:48549255 original size:2 final size:2
Alignment explanation
Indices: 48549248--48549276 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
48549238 AACCAAATTA
48549248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48549277 AATGCTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48550277 original size:2 final size:2
Alignment explanation
Indices: 48550270--48550295 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48550260 ATACTAACTC
48550270 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
48550296 TATTTTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48551932 original size:22 final size:22
Alignment explanation
Indices: 48551907--48551998 Score: 112
Period size: 22 Copynumber: 4.2 Consensus size: 22
48551897 AAATTCAATA
* *
48551907 TCAATTTCTTTCAAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
48551929 TCAATTCCTTTCAAAATTTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
48551951 TCAATTCCCTTCAAAATTTCTA
1 TCAATTCCCTTCAAAAATTCTC
* *
48551973 TCAATTTCCTTCCAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
48551995 TCAA
1 TCAA
48551999 ACTCTCAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 62 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (22 bp):
TCAATTCCCTTCAAAAATTCTC
Found at i:48552014 original size:52 final size:51
Alignment explanation
Indices: 48551948--48552050 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
48551938 TTCAAAATTT
* * *
48551948 CTCTCAATTCCCTT-CAAAATTTCTATCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCCTTCCAAAA-TCCTATCAATTTCCTTCAAAAAATCTC-CAAA
*
48552000 CTCTCAAATT-CCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
48552051 TCCATANNNN
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.33, C:0.32, G:0.00, T:0.35
Consensus pattern (51 bp):
CTCTCAATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
Found at i:48552039 original size:21 final size:22
Alignment explanation
Indices: 48552000--48552041 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
48551990 TTCTCTCAAA
48552000 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
48552022 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
48552042 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:48557737 original size:125 final size:125
Alignment explanation
Indices: 48557515--48557796 Score: 372
Period size: 125 Copynumber: 2.3 Consensus size: 125
48557505 CCACGAGGGC
*
48557515 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGC
1 GCGATTTGACACTATTTCCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGC
* * * * * **
48557580 GAAATCGCATCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 GAAATCACATCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
* *
48557640 GCGATTTTATACTATTTCCTCAGAAAACGTCAAAAAAAAATTATTT-CTCACATGACC-ACTGTA
1 GCGATTTGACACTATTTCCTCAG-AAACGTCAAAAAAAAATTATTTCCT-ACATGACCAACTGTA
* * *
48557703 GCGAAATCACGTCCACGAGGCCACTATTTCACAATTTCTTCTTAAATAGCATCCTAGTAGAA
64 GCGAAATCACATCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
** *
48557765 GCGATTTCCCACTATTTAAC-CAGAAACGTCAA
1 GCGATTTGACACTATTT-CCTCAGAAACGTCAA
48557797 CTGGAAAAAA
Statistics
Matches: 137, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
124 9 0.07
125 97 0.71
126 31 0.23
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (125 bp):
GCGATTTGACACTATTTCCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGC
GAAATCACATCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
Found at i:48559415 original size:24 final size:24
Alignment explanation
Indices: 48559333--48559416 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
48559323 AGAAGGAAAC
48559333 CCTTGGAGGTGGTTTAGGTGGAGG
1 CCTTGGAGGTGGTTTAGGTGGAGG
* * * * *
48559357 CGTCGGAGGAGGGGTT-GGTGGTGG
1 CCTTGGAGG-TGGTTTAGGTGGAGG
*
48559381 CCAT-GATGGTGGTTTAGGTGGAGG
1 CCTTGGA-GGTGGTTTAGGTGGAGG
*
48559405 CTTTGGAGGTGG
1 CCTTGGAGGTGG
48559417 AAAAGGTGGT
Statistics
Matches: 43, Mismatches: 13, Indels: 8
0.67 0.20 0.12
Matches are distributed among these distances:
23 6 0.14
24 31 0.72
25 6 0.14
ACGTcount: A:0.12, C:0.08, G:0.52, T:0.27
Consensus pattern (24 bp):
CCTTGGAGGTGGTTTAGGTGGAGG
Found at i:48559518 original size:36 final size:36
Alignment explanation
Indices: 48559478--48559760 Score: 173
Period size: 36 Copynumber: 7.7 Consensus size: 36
48559468 CGGCCTTGGA
48559478 GGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGGT
1 GGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGGT
**** *
48559514 GGTGGTGCTGGTGGAGGTATAGGAGGTGGAGCTGGT
1 GGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGGT
* * * * *** *
48559550 GGTGG---TGCTGGAGGCGGT-GCTAATGGTGGTTTTGGA
1 GGTGGAAAAGGTGGAGGC-ATAG--GA-GGTGGAGCTGGT
*
48559586 GGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
1 GGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGGT
* *
48559622 GGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGGTGTCGGT
1 GGTGGAAAAGGTGGAGGCATA-G-G-AGGTGG-AG-CT-GGT
* ** * * * *** *
48559664 GGTGGCACTGGAGGCGGTGC-T-GGTGGTGGTTTTGGA
1 GGTGGAAAAGGTGG-AG-GCATAGGAGGTGGAGCTGGT
*
48559700 GGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
1 GGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGGT
48559736 GGTGGAAAAGGTGGAGGCATAGGAG
1 GGTGGAAAAGGTGGAGGCATAGGAG
48559761 TAGGTGGTGG
Statistics
Matches: 182, Mismatches: 47, Indels: 36
0.69 0.18 0.14
Matches are distributed among these distances:
33 9 0.05
34 2 0.01
35 3 0.02
36 123 0.68
37 3 0.02
38 2 0.01
39 19 0.10
40 2 0.01
41 2 0.01
42 13 0.07
43 2 0.01
44 2 0.01
ACGTcount: A:0.20, C:0.06, G:0.53, T:0.21
Consensus pattern (36 bp):
GGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGGT
Found at i:48559518 original size:102 final size:102
Alignment explanation
Indices: 48559412--48559830 Score: 453
Period size: 114 Copynumber: 3.9 Consensus size: 102
48559402 AGGCTTTGGA
* ** * * * * **
48559412 GGTGGAAAAGGTGGTGGGGTAGGAGTTGGAGGTGGAGCCGG-TGCAGGTGGTGGTGGCGGCCTTG
1 GGTGGAAAAGGTGGAGGCATAGGAGTTGGAGGTGGTGCCGGAGGC-GGTGCTGGTGGTGGTTTTG
*
48559476 GAGGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGGT
65 GAGGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
**** * * * **
48559514 GGTGGTGCTGGTGGAGGTATAGGAGGTGGAGCTGGTGGTGGTGCTGGAGGCGGTGCTAATGGTGG
1 GGTGGAAAAGGTGGAGGCATAGGA-GT-----TGGAGGTGGTGCCGGAGGCGGTGCTGGTGGTGG
48559579 TTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
60 TTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
*
48559622 GGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGGTGTCGGTGGTGGCACTGGAGGCGGTGCTGG
1 GGTGGAAAAGGTGGAGGCATA-G-G-A-GT--T-G-G-AGGTGGT-GC-C-GGAGGCGGTGCTGG
48559687 TGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
54 TGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
* * *
48559736 GGTGGAAAAGGTGGAGGCATAGGAGTAGGTGGTGGTGCTGGAGGCGGTGCTGGTGGTGGTTTTGG
1 GGTGGAAAAGGTGGAGGCATAGGAGTTGGAGGTGGTGCCGGAGGCGGTGCTGGTGGTGGTTTTGG
48559801 AGGTGGAAAAGGTGGAGGGATAGGAGGTGG
66 AGGTGGAAAAGGTGGAGGGATAGGAGGTGG
48559831 TGNNNNNNNN
Statistics
Matches: 270, Mismatches: 31, Indels: 32
0.81 0.09 0.10
Matches are distributed among these distances:
102 73 0.27
103 2 0.01
104 2 0.01
105 6 0.02
106 1 0.00
107 1 0.00
108 80 0.30
109 4 0.01
110 4 0.01
111 11 0.04
112 3 0.01
113 1 0.00
114 82 0.30
ACGTcount: A:0.18, C:0.06, G:0.54, T:0.21
Consensus pattern (102 bp):
GGTGGAAAAGGTGGAGGCATAGGAGTTGGAGGTGGTGCCGGAGGCGGTGCTGGTGGTGGTTTTGG
AGGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
Found at i:48559523 original size:12 final size:12
Alignment explanation
Indices: 48559502--48559570 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
48559492 AGGCATAGGA
*
48559502 GGTGGAGCTGGT
1 GGTGGTGCTGGT
48559514 GGTGGTGCTGGT
1 GGTGGTGCTGGT
* * *
48559526 GGAGGT-ATAGGA
1 GGTGGTGCT-GGT
*
48559538 GGTGGAGCTGGT
1 GGTGGTGCTGGT
*
48559550 GGTGGTGCTGGA
1 GGTGGTGCTGGT
*
48559562 GGCGGTGCT
1 GGTGGTGCT
48559571 AATGGTGGTT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
11 1 0.02
12 42 0.95
13 1 0.02
ACGTcount: A:0.10, C:0.09, G:0.57, T:0.25
Consensus pattern (12 bp):
GGTGGTGCTGGT
Found at i:48559542 original size:114 final size:112
Alignment explanation
Indices: 48559436--48559830 Score: 401
Period size: 108 Copynumber: 3.6 Consensus size: 112
48559426 TGGGGTAGGA
* * *
48559436 GTTGGAGGTGGAGCCGGTGCAGGTGGTGGTGGCGGCCTTGGAGGTGGAAAAGGTGGAGGCATAGG
1 GTTGGTGGTGGAGCCGGTGCAGGTGGTGGTGG-GG-TTTGGAGGTGGAAAAGGTGGAGGGATAGG
**** * *
48559501 AGGTGGAGCTGGTGGTGGTGCTGGTGGAGGTATAGGAGGTGGAGCTGGT
64 AGGTGGAGCTGGTGGTGGAAAAGGTGGAGGCATAGGAGGTGGAGGTGGT
* * * *
48559550 GGTGGTGCTGGAGGCGGTGCTA-ATGGTGGT----TTTGGAGGTGGAAAAGGTGGAGGGATAGGA
1 GTTGGTGGTGGAGCCGGTGC-AGGTGGTGGTGGGGTTTGGAGGTGGAAAAGGTGGAGGGATAGGA
** *
48559610 GGTGGAGCTGGTGGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGGT
65 GGTGGAGCTGGTGGTGGAAAAGGTGGAGGCATAGGAGGTGGAGGTGGT
* * * *
48559658 GTCGGTGGTGGCA-CTGGAGGC-GGTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATA
1 GTTGGTGGTGG-AGCCGG-TGCAGGTGGTGGTGG-GG-TTTGGAGGTGGAAAAGGTGGAGGGATA
48559721 GGAGGTGGAGCTGGTGGTGGAAAAGGTGGAGGCATAGGA-GT--AGGT-G-
62 GGAGGTGGAGCTGGTGGTGGAAAAGGTGGAGGCATAGGAGGTGGAGGTGGT
* * *
48559767 G-TGGTGCTGGAGGCGGTGC---TGGTGGT-GGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAG
1 GTTGGTGGTGGAGCCGGTGCAGGTGGTGGTGGGGTTTGGAGGTGGAAAAGGTGGAGGGATAGGAG
48559827 GTGG
66 GTGG
48559831 TGNNNNNNNN
Statistics
Matches: 236, Mismatches: 34, Indels: 34
0.78 0.11 0.11
Matches are distributed among these distances:
102 35 0.15
103 1 0.00
104 1 0.00
105 6 0.03
107 3 0.01
108 92 0.39
109 4 0.02
110 1 0.00
111 3 0.01
114 89 0.38
115 1 0.00
ACGTcount: A:0.18, C:0.07, G:0.54, T:0.22
Consensus pattern (112 bp):
GTTGGTGGTGGAGCCGGTGCAGGTGGTGGTGGGGTTTGGAGGTGGAAAAGGTGGAGGGATAGGAG
GTGGAGCTGGTGGTGGAAAAGGTGGAGGCATAGGAGGTGGAGGTGGT
Found at i:48559547 original size:24 final size:24
Alignment explanation
Indices: 48559514--48559623 Score: 78
Period size: 24 Copynumber: 4.6 Consensus size: 24
48559504 TGGAGCTGGT
*
48559514 GGTGGTGCTGGTGGAGGTATAGGA
1 GGTGGAGCTGGTGGAGGTATAGGA
* *
48559538 GGTGGAGCTGGTGGTGGTGCT-GGA
1 GGTGGAGCTGGTGGAGGT-ATAGGA
* * ** * * *
48559562 GGCGGTGCTAATGGTGGTTTTGGA
1 GGTGGAGCTGGTGGAGGTATAGGA
*** *
48559586 GGTGGAAAAGGTGGAGGGATAGGA
1 GGTGGAGCTGGTGGAGGTATAGGA
48559610 GGTGGAGCTGGTGG
1 GGTGGAGCTGGTGG
48559624 TGGAAAAGGT
Statistics
Matches: 62, Mismatches: 22, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
23 1 0.02
24 60 0.97
25 1 0.02
ACGTcount: A:0.16, C:0.05, G:0.55, T:0.24
Consensus pattern (24 bp):
GGTGGAGCTGGTGGAGGTATAGGA
Found at i:48559830 original size:36 final size:36
Alignment explanation
Indices: 48559574--48559831 Score: 154
Period size: 36 Copynumber: 7.2 Consensus size: 36
48559564 CGGTGCTAAT
*
48559574 GGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGA
1 GGTGGTTTTGGTGGTGGAAAAGGTGGAGGGATAGGA
*** *
48559610 GGTGGAGCTGGTGGTGGAAAAGGTGGAGGCATAGGAGCA
1 GGTGGTTTTGGTGGTGGAAAAGGTGGAGGGATA-G-G-A
* * ** * * * *
48559649 GGTGGTGGTGTCGGTGGTGGCACTGGAGGCGGTGCT-GGT
1 GGTGGT--T-TTGGTGGTGGAAAAGGTGGAGG-GATAGGA
*
48559688 GGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGA
1 GGTGGTTTTGGTGGTGGAAAAGGTGGAGGGATAGGA
*** *
48559724 GGTGGAGCTGGTGGTGGAAAAGGTGGAGGCATAGGA
1 GGTGGTTTTGGTGGTGGAAAAGGTGGAGGGATAGGA
** * * * * *
48559760 -GTAGGTGGTGGTGCTGG---AGG-CG-GTGCT-GGT
1 GGT-GGTTTTGGTGGTGGAAAAGGTGGAGGGATAGGA
*
48559790 GGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGA
1 GGTGGTTTTGGTGGTGGAAAAGGTGGAGGGATAGGA
48559826 GGTGGT
1 GGTGGT
48559832 GNNNNNNNNN
Statistics
Matches: 159, Mismatches: 47, Indels: 32
0.67 0.20 0.13
Matches are distributed among these distances:
30 12 0.08
31 4 0.03
32 1 0.01
33 6 0.04
34 1 0.01
35 7 0.04
36 95 0.60
37 2 0.01
38 1 0.01
39 12 0.08
40 1 0.01
41 1 0.01
42 15 0.09
43 1 0.01
ACGTcount: A:0.19, C:0.05, G:0.54, T:0.22
Consensus pattern (36 bp):
GGTGGTTTTGGTGGTGGAAAAGGTGGAGGGATAGGA
Found at i:48559958 original size:12 final size:12
Alignment explanation
Indices: 48559941--48559988 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
48559931 NNGCATAGGA
48559941 GCAGGTGGTGGT
1 GCAGGTGGTGGT
*
48559953 GCAGGTGGTGGC
1 GCAGGTGGTGGT
* * *
48559965 GCTGGAGGCGGT
1 GCAGGTGGTGGT
*
48559977 GCTGGTGGTGGT
1 GCAGGTGGTGGT
48559989 TTTGGAGGTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.06, C:0.12, G:0.58, T:0.23
Consensus pattern (12 bp):
GCAGGTGGTGGT
Found at i:48560023 original size:36 final size:36
Alignment explanation
Indices: 48559983--48560245 Score: 129
Period size: 36 Copynumber: 7.5 Consensus size: 36
48559973 CGGTGCTGGT
*
48559983 GGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGA
1 GGTGGTGTTGGAGGTGGAAAAGGTGGAGGGATAGGA
* * * *
48560019 GGTGGAGCTGGTGGTGGAAAAGGTGGAGGCATAGGAGCA
1 GGTGGTGTTGGAGGTGGAAAAGGTGGAGGGATA-G-G-A
* ** **** * * * *
48560058 GGTGGTGGTGCCGGTGGTGGCGTTGGAGGCGGTGCTGGT
1 GGTGGTGTTGGAGGTGGAAAAGGTGGAGG-GAT--AGGA
*
48560097 GGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGA
1 GGTGGTGTTGGAGGTGGAAAAGGTGGAGGGATAGGA
* *
48560133 GGTGGTGTTGGAGGTGG---AGGT-G-GGG-TTGGT
1 GGTGGTGTTGGAGGTGGAAAAGGTGGAGGGATAGGA
* * * * * *
48560163 GGTGGTGGTGGCGCTGG---AGG-GG-GTGCT-GGT
1 GGTGGTGTTGGAGGTGGAAAAGGTGGAGGGATAGGA
48560193 GGTGGCT-TTGGAGGTGGAAAAGGTGGAGGGATAGGA
1 GGTGG-TGTTGGAGGTGGAAAAGGTGGAGGGATAGGA
* *
48560229 GGTGGTGCTGGCGGTGG
1 GGTGGTGTTGGAGGTGG
48560246 TTTTGGAGGT
Statistics
Matches: 166, Mismatches: 45, Indels: 32
0.68 0.19 0.13
Matches are distributed among these distances:
30 38 0.23
31 5 0.03
32 1 0.01
33 7 0.04
34 2 0.01
35 4 0.02
36 61 0.37
37 1 0.01
38 3 0.02
39 41 0.25
40 2 0.01
41 1 0.01
ACGTcount: A:0.16, C:0.05, G:0.57, T:0.22
Consensus pattern (36 bp):
GGTGGTGTTGGAGGTGGAAAAGGTGGAGGGATAGGA
Found at i:48560097 original size:24 final size:24
Alignment explanation
Indices: 48560061--48560209 Score: 104
Period size: 24 Copynumber: 6.2 Consensus size: 24
48560051 AGGAGCAGGT
*
48560061 GGTGGTGCCGGTGGTGGCGTTGGA
1 GGTGGTGCTGGTGGTGGCGTTGGA
* **
48560085 GGCGGTGCTGGTGGTGGTTTTGGA
1 GGTGGTGCTGGTGGTGGCGTTGGA
**** * *
48560109 GGTGGAAAAGGTGGAGG-GATAGGA
1 GGTGGTGCTGGTGGTGGCG-TTGGA
* * * *
48560133 GGTGGTGTTGGAGGTGGAGGTGG-
1 GGTGGTGCTGGTGGTGGCGTTGGA
* *
48560156 GGTTGGTGGTGGTGGTGGCGCTGGA
1 GG-TGGTGCTGGTGGTGGCGTTGGA
* *
48560181 GGGGGTGCTGGTGGTGGCTTTGGA
1 GGTGGTGCTGGTGGTGGCGTTGGA
48560205 GGTGG
1 GGTGG
48560210 AAAAGGTGGA
Statistics
Matches: 92, Mismatches: 29, Indels: 8
0.71 0.22 0.06
Matches are distributed among these distances:
23 2 0.02
24 87 0.95
25 3 0.03
ACGTcount: A:0.09, C:0.06, G:0.59, T:0.26
Consensus pattern (24 bp):
GGTGGTGCTGGTGGTGGCGTTGGA
Found at i:48560133 original size:114 final size:109
Alignment explanation
Indices: 48559933--48560245 Score: 427
Period size: 114 Copynumber: 2.9 Consensus size: 109
48559923 NNNNNNNNNN
48559933 GCATAGGAGCAGGTGGTGGTGCAGGTGGTGGCGCTGGAGGCGGTGCTGGTGGTGGTTTTGGAGGT
1 GCATAGGAGCAGGTGGTGGTGC-GGTGGTGGCGCTGGAGGCGGTGCTGGTGGTGGTTTTGGAGGT
48559998 GGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGTGGTGGAAAAGGTGGAG
65 GGAAAAGGTGGAGGGATAGGAGGTGG-GCTGGTGGTGG---AGGTGGAG
*
48560047 GCATAGGAGCAGGTGGTGGTGCCGGTGGTGGCGTTGGAGGCGGTGCTGGTGGTGGTTTTGGAGGT
1 GCATAGGAGCAGGTGGTGGTG-CGGTGGTGGCGCTGGAGGCGGTGCTGGTGGTGGTTTTGGAGGT
48560112 GGAAAAGGTGGAGGGATAGGAGGT-GG-T-GT--TGGAGGTGGAG
65 GGAAAAGGTGGAGGGATAGGAGGTGGGCTGGTGGTGGAGGTGGAG
* * *
48560152 G--T-GG-G--GTTGGTGGT--GGTGGTGGCGCTGGAGGGGGTGCTGGTGGTGGCTTTGGAGGTG
1 GCATAGGAGCAGGTGGTGGTGCGGTGGTGGCGCTGGAGGCGGTGCTGGTGGTGGTTTTGGAGGTG
*
48560209 GAAAAGGTGGAGGGATAGGAGGTGGTGCTGGCGGTGG
66 GAAAAGGTGGAGGGATAGGAGGTGG-GCTGGTGGTGG
48560246 TTTTGGAGGT
Statistics
Matches: 186, Mismatches: 6, Indels: 26
0.85 0.03 0.12
Matches are distributed among these distances:
96 63 0.34
97 1 0.01
98 1 0.01
99 9 0.05
100 1 0.01
101 1 0.01
102 5 0.03
103 1 0.01
105 9 0.05
108 3 0.02
110 2 0.01
111 1 0.01
112 1 0.01
113 1 0.01
114 86 0.46
115 1 0.01
ACGTcount: A:0.15, C:0.07, G:0.56, T:0.22
Consensus pattern (109 bp):
GCATAGGAGCAGGTGGTGGTGCGGTGGTGGCGCTGGAGGCGGTGCTGGTGGTGGTTTTGGAGGTG
GAAAAGGTGGAGGGATAGGAGGTGGGCTGGTGGTGGAGGTGGAG
Found at i:48560134 original size:48 final size:48
Alignment explanation
Indices: 48560082--48560293 Score: 212
Period size: 48 Copynumber: 4.4 Consensus size: 48
48560072 TGGTGGCGTT
*
48560082 GGAGGCGGTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATA
1 GGAGGTGGTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATA
* * *** **** * *
48560130 GGAGGTGGTGTTGGAGGTGGAGGTGG-GGTTGGTGGTGGTGGTGGCGCT-
1 GGAGGTGGTGCTGGTGGTGGTTTTGGAGG-TGGAAAAGGTGGAGG-GATA
* *
48560178 GGAGGGGGTGCTGGTGGTGGCTTTGGAGGTGGAAAAGGTGGAGGGATA
1 GGAGGTGGTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATA
* * * *
48560226 GGAGGTGGTGCTGGCGGTGGTTTTGGAGGTGGACAAGGCGGAGGTATA
1 GGAGGTGGTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATA
* *
48560274 GGAGGTGGAGTTGGTGGTGG
1 GGAGGTGGTGCTGGTGGTGG
48560294 AGGAGGTGCT
Statistics
Matches: 127, Mismatches: 33, Indels: 8
0.76 0.20 0.05
Matches are distributed among these distances:
47 4 0.03
48 119 0.94
49 4 0.03
ACGTcount: A:0.15, C:0.05, G:0.57, T:0.24
Consensus pattern (48 bp):
GGAGGTGGTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATA
Found at i:48560151 original size:18 final size:18
Alignment explanation
Indices: 48560130--48560173 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
48560120 TGGAGGGATA
*
48560130 GGAGGTGGTGTTGGAGGT
1 GGAGGTGGGGTTGGAGGT
*
48560148 GGAGGTGGGGTTGGTGGT
1 GGAGGTGGGGTTGGAGGT
*
48560166 GGTGGTGG
1 GGAGGTGG
48560174 CGCTGGAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.07, C:0.00, G:0.66, T:0.27
Consensus pattern (18 bp):
GGAGGTGGGGTTGGAGGT
Found at i:48560169 original size:30 final size:30
Alignment explanation
Indices: 48560133--48560210 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
48560123 AGGGATAGGA
*
48560133 GGTGGTGTTGGAGGTGGAGGTGGG-GTTGGT
1 GGTGGTGTTGGAGGTGGAGG-GGGTGCTGGT
* * *
48560163 GGTGGTGGTGGCGCTGGAGGGGGTGCTGGT
1 GGTGGTGTTGGAGGTGGAGGGGGTGCTGGT
48560193 GGTGGCT-TTGGAGGTGGA
1 GGTGG-TGTTGGAGGTGGA
48560211 AAAGGTGGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 3 0.08
30 35 0.90
31 1 0.03
ACGTcount: A:0.06, C:0.05, G:0.62, T:0.27
Consensus pattern (30 bp):
GGTGGTGTTGGAGGTGGAGGGGGTGCTGGT
Found at i:48560203 original size:96 final size:96
Alignment explanation
Indices: 48560070--48560245 Score: 307
Period size: 96 Copynumber: 1.8 Consensus size: 96
48560060 TGGTGGTGCC
* *
48560070 GGTGGTGGCGTTGGAGGCGGTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGG
1 GGTGGTGGCGCTGGAGGCGGTGCTGGTGGTGGCTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGG
*
48560135 TGGTGTTGGAGGTGGAGGTGGGGTTGGTGGT
66 TGGTGCTGGAGGTGGAGGTGGGGTTGGTGGT
*
48560166 GGTGGTGGCGCTGGAGGGGGTGCTGGTGGTGGCTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGG
1 GGTGGTGGCGCTGGAGGCGGTGCTGGTGGTGGCTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGG
*
48560231 TGGTGCTGGCGGTGG
66 TGGTGCTGGAGGTGG
48560246 TTTTGGAGGT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 75 1.00
ACGTcount: A:0.12, C:0.05, G:0.59, T:0.24
Consensus pattern (96 bp):
GGTGGTGGCGCTGGAGGCGGTGCTGGTGGTGGCTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGG
TGGTGCTGGAGGTGGAGGTGGGGTTGGTGGT
Found at i:48560278 original size:96 final size:96
Alignment explanation
Indices: 48560076--48560269 Score: 237
Period size: 96 Copynumber: 2.0 Consensus size: 96
48560066 TGCCGGTGGT
* * *
48560076 GGCGTTGGAGGCGGTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGTGT
1 GGCGATGGAGGCGGTGCTGGTGGTGGCTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGTGC
**** * *
48560141 TGGAGGTGGAGGTGGGGTTGGTGGTGGTGGT
66 TGGAGGTGGAGGTGGGGTTGGACAAGGCGGA
* *
48560172 GGCGCTGGAGGGGGTGCTGGTGGTGGCTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGTGC
1 GGCGATGGAGGCGGTGCTGGTGGTGGCTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGTGC
* ***
48560237 TGGCGGTGGTTTTGGAGG-TGGACAAGGCGGA
66 TGGAGGTGGAGGTGG-GGTTGGACAAGGCGGA
48560268 GG
1 GG
48560270 TATAGGAGGT
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
96 81 0.98
97 2 0.02
ACGTcount: A:0.14, C:0.06, G:0.57, T:0.23
Consensus pattern (96 bp):
GGCGATGGAGGCGGTGCTGGTGGTGGCTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGTGC
TGGAGGTGGAGGTGGGGTTGGACAAGGCGGA
Found at i:48560298 original size:15 final size:15
Alignment explanation
Indices: 48560288--48560342 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
48560278 GTGGAGTTGG
48560288 TGGTGGAGGAGGTGC
1 TGGTGGAGGAGGTGC
* *
48560303 TGGTGGTGGCGGTGGC
1 TGGTGGAGGAGGT-GC
* *
48560319 T-TTGGAGGTGGTGC
1 TGGTGGAGGAGGTGC
48560333 TGGTGGAGGA
1 TGGTGGAGGA
48560343 ATTGGAGGAG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
14 3 0.10
15 25 0.81
16 3 0.10
ACGTcount: A:0.09, C:0.07, G:0.58, T:0.25
Consensus pattern (15 bp):
TGGTGGAGGAGGTGC
Found at i:48560311 original size:30 final size:30
Alignment explanation
Indices: 48560277--48560347 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
48560267 AGGTATAGGA
48560277 GGTGGAGTTGG-TGGTGGAGGAGGTGCTGGT
1 GGTGGAGTTGGCT-GTGGAGGAGGTGCTGGT
* * * *
48560307 GGTGGCGGTGGCTTTGGAGGTGGTGCTGGT
1 GGTGGAGTTGGCTGTGGAGGAGGTGCTGGT
* *
48560337 GGAGGAATTGG
1 GGTGGAGTTGG
48560348 AGGAGGATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.10, C:0.06, G:0.58, T:0.27
Consensus pattern (30 bp):
GGTGGAGTTGGCTGTGGAGGAGGTGCTGGT
Found at i:48563503 original size:14 final size:13
Alignment explanation
Indices: 48563470--48563510 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
48563460 GTTACATATA
48563470 ATTATAATTATTT
1 ATTATAATTATTT
48563483 ATTATAATTATGTT
1 ATTATAATTAT-TT
* *
48563497 TTTATAATTGTTT
1 ATTATAATTATTT
48563510 A
1 A
48563511 GGTAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (13 bp):
ATTATAATTATTT
Found at i:48565781 original size:24 final size:24
Alignment explanation
Indices: 48565716--48565782 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
48565706 TTATAAGTTG
*
48565716 AAATAATATT-GATGATAAATCTAA
1 AAATAATATTAGAT-TTAAATCTAA
* *
48565740 AAATAATATTAAACTTAAA-CATAA
1 AAATAATATTAGATTTAAATC-TAA
48565764 AAATAATATTAGATTTAAA
1 AAATAATATTAGATTTAAA
48565783 ATTAAATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 34 0.94
25 1 0.03
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAATATTAGATTTAAATCTAA
Found at i:48567533 original size:44 final size:44
Alignment explanation
Indices: 48567438--48567814 Score: 246
Period size: 44 Copynumber: 8.5 Consensus size: 44
48567428 TCTGTTTTAT
* * * *
48567438 TGCAACTTTAGGGAAATAAGATTTGTTATCTTCAGTCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGA-TTGCTATCTTCAATCTGCTCCAC
* * *
48567483 TCCAACTTCAGGGAGATAAGACTTG-TAACTTCAATCCGCTCCAC
1 TGCAACTTCAGGGAGATAAGA-TTGCTATCTTCAATCTGCTCCAC
* * * ** * *
48567527 TACAACTTTAGGGAGATAGGATTAG-TGGCTTTAACCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATT-GCTATCTTCAATCTGCTCCAC
* * * * * *
48567571 TGCAACTTTAGGGAGATACGATTCGCCATCTTTAGTCTGCCCCAC
1 TGCAACTTCAGGGAGATAAGATT-GCTATCTTCAATCTGCTCCAC
** * * *
48567616 TGCAACTTCAGGG-GATAAGACTTG-TGGCCTCAATCTACCCCAC
1 TGCAACTTCAGGGAGATAAGA-TTGCTATCTTCAATCTGCTCCAC
* * *
48567659 TACAACTTCAAGGG-GATAATATTGATATCTTCAA-CTTGCTCCAC
1 TGCAACTTC-AGGGAGATAAGATTGCTATCTTCAATC-TGCTCCAC
* * * * *
48567703 TGCAACTTCAGGGAGATAAGGTACGCTAACTTCAGTCTACTCCAC
1 TGCAACTTCAGGGAGATAAGAT-TGCTATCTTCAATCTGCTCCAC
* * *** * *
48567748 TGCAGCTTCAGGGAGATAGGATCATTGA-CTTTAATCTGCTCCAT
1 TGCAACTTCAGGGAGATAAGATTGCT-ATCTTCAATCTGCTCCAC
**
48567792 TGCAACTTCAATGAGATAAGATT
1 TGCAACTTCAGGGAGATAAGATT
48567815 TGCCATGATC
Statistics
Matches: 260, Mismatches: 62, Indels: 21
0.76 0.18 0.06
Matches are distributed among these distances:
43 30 0.12
44 146 0.56
45 83 0.32
46 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
TGCAACTTCAGGGAGATAAGATTGCTATCTTCAATCTGCTCCAC
Found at i:48567706 original size:132 final size:133
Alignment explanation
Indices: 48567438--48567765 Score: 374
Period size: 132 Copynumber: 2.5 Consensus size: 133
48567428 TCTGTTTTAT
* * * *
48567438 TGCAACTTTAGGGAAATAAGATTTGTTATCTTCAGTCTGCTCCACTCCAACTTCAGGGAGATAAG
1 TGCAACTTTAGGGAGATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
* * * * * * *
48567503 ACTTGTAACTTCAATCCGCTCCACTACAACTTTAGGGAGATAGGATTAGTGGCTTTAACCTGCTC
66 ACTTGTAACCTCAATCCACCCCACTACAACTTAAGGGAGATAAGATTAGTAGCTTCAACCTGCTC
48567568 CAC
131 CAC
* * * *
48567571 TGCAACTTTAGGGAGATACGATTCGCCATCTTTAGTCTGCCCCACTGCAACTTCAGGG-GATAAG
1 TGCAACTTTAGGGAGATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
** * * * *
48567635 ACTTGTGGCCTCAATCTACCCCACTACAACTTCAAGGG-GATAATATT-GATATCTTCAACTTGC
66 ACTTGTAACCTCAATCCACCCCACTACAACTT-AAGGGAGATAAGATTAG-TAGCTTCAACCTGC
48567698 TCCAC
129 TCCAC
* * * * * *
48567703 TGCAACTTCAGGGAGATAAGGTACGCTAACTTCAGTCTACTCCACTGCAGCTTCAGGGAGATA
1 TGCAACTTTAGGGAGATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATA
48567766 GGATCATTGA
Statistics
Matches: 161, Mismatches: 31, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
131 1 0.01
132 102 0.63
133 58 0.36
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (133 bp):
TGCAACTTTAGGGAGATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
ACTTGTAACCTCAATCCACCCCACTACAACTTAAGGGAGATAAGATTAGTAGCTTCAACCTGCTC
CAC
Found at i:48570482 original size:15 final size:15
Alignment explanation
Indices: 48570462--48570491 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48570452 TATAAATTTA
48570462 TTATTATTAATAAAT
1 TTATTATTAATAAAT
*
48570477 TTATTATTATTAAAT
1 TTATTATTAATAAAT
48570492 CATTTAATTT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTATTAATAAAT
Found at i:48570497 original size:18 final size:18
Alignment explanation
Indices: 48570448--48570489 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
48570438 GATTAGCTAA
48570448 ATTATATAAATTTATTATT
1 ATTA-ATAAATTTATTATT
48570467 ATTAATAAATTTATTATT
1 ATTAATAAATTTATTATT
48570485 ATTAA
1 ATTAA
48570490 ATCATTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTAATAAATTTATTATT
Found at i:48573569 original size:11 final size:11
Alignment explanation
Indices: 48573551--48573586 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
48573541 CCTTGGCCTC
48573551 TCCTTTTTCTTT
1 TCCTTTTT-TTT
48573563 TCCTTTTTTTT
1 TCCTTTTTTTT
*
48573574 TTCTTTTTTTT
1 TCCTTTTTTTT
48573585 TC
1 TC
48573587 ATCATTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TCCTTTTTTTT
Found at i:48580235 original size:8 final size:8
Alignment explanation
Indices: 48580211--48580242 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
48580201 TCAATTTTGG
48580211 ATTTCAAA
1 ATTTCAAA
48580219 A-TT-AAA
1 ATTTCAAA
48580225 ATTTCAAA
1 ATTTCAAA
48580233 ATTTCAAA
1 ATTTCAAA
48580241 AT
1 AT
48580243 CCAAGATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 4 0.18
7 4 0.18
8 14 0.64
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (8 bp):
ATTTCAAA
Found at i:48581157 original size:7 final size:7
Alignment explanation
Indices: 48581147--48581184 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
48581137 AATAAATTCA
48581147 TAAATTT
1 TAAATTT
48581154 TAAATTT
1 TAAATTT
48581161 TAAATTT
1 TAAATTT
48581168 TAAA-TT
1 TAAATTT
*
48581174 AAAATTT
1 TAAATTT
48581181 TAAA
1 TAAA
48581185 ATGTAAATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
TAAATTT
Found at i:48581166 original size:14 final size:13
Alignment explanation
Indices: 48581147--48581184 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
48581137 AATAAATTCA
48581147 TAAATTTTAAATTT
1 TAAATTTTAAA-TT
48581161 TAAATTTTAAATT
1 TAAATTTTAAATT
*
48581174 AAAATTTTAAA
1 TAAATTTTAAA
48581185 ATGTAAATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAAATTTTAAATT
Found at i:48581180 original size:13 final size:14
Alignment explanation
Indices: 48581125--48581184 Score: 59
Period size: 15 Copynumber: 4.2 Consensus size: 14
48581115 AATTCTCAAA
**
48581125 AAATTTAAAAATAAT
1 AAATTT-AAAATTTT
*
48581140 AAATTCATAAATTTT
1 AAATTTA-AAATTTT
*
48581155 AAATTTTAAATTTT
1 AAATTTAAAATTTT
48581169 AAA-TTAAAATTTT
1 AAATTTAAAATTTT
48581182 AAA
1 AAA
48581185 ATGTAAATCC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
13 12 0.32
14 11 0.29
15 15 0.39
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTTAAAATTTT
Found at i:48581186 original size:14 final size:14
Alignment explanation
Indices: 48581148--48581191 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
48581138 ATAAATTCAT
* *
48581148 AAATTTTAAATTTT
1 AAATTTTAAAATTA
48581162 AAATTTT-AAATTA
1 AAATTTTAAAATTA
48581175 AAATTTTAAAATGTA
1 AAATTTTAAAAT-TA
48581190 AA
1 AA
48581192 TCCAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 11 0.42
14 11 0.42
15 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
AAATTTTAAAATTA
Done.