Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008097.1 Hibiscus syriacus cultivar Beakdansim tig00110621_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3094402
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 12
Found at i:275620 original size:3 final size:3
Alignment explanation
Indices: 275612--275653 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
275602 GACGTAATAT
275612 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
275654 ATTTTCACTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:279595 original size:22 final size:23
Alignment explanation
Indices: 279558--279602 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
279548 TCAATATTTT
* *
279558 TATTTAATGATCTAATTTTATAA
1 TATTTAATGATATAATATTATAA
279581 TATTT-ATGATATAATATTATAA
1 TATTTAATGATATAATATTATAA
279603 ATATATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (23 bp):
TATTTAATGATATAATATTATAA
Found at i:279606 original size:14 final size:14
Alignment explanation
Indices: 279576--279622 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
279566 GATCTAATTT
*
279576 TATAATATTTATGA
1 TATAATATTTATAA
279590 TATAATA-TTATAA
1 TATAATATTTATAA
279603 -ATATATCATTTATAA
1 TATA-AT-ATTTATAA
279618 TATAA
1 TATAA
279623 ACATGTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 3 0.11
13 7 0.25
14 8 0.29
15 7 0.25
16 3 0.11
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (14 bp):
TATAATATTTATAA
Found at i:279656 original size:15 final size:16
Alignment explanation
Indices: 279597--279656 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 16
279587 TGATATAATA
*
279597 TTATAA-ATATATCAT
1 TTATAATATAAATCAT
279612 TTATAATATAAA-CAT
1 TTATAATATAAATCAT
279627 GTTATTAATATATAAATC-T
1 -TTA-T-A-ATATAAATCAT
279646 TTATAATATAA
1 TTATAATATAA
279657 TTTTGGGTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
15 15 0.39
16 8 0.21
17 2 0.05
18 4 0.11
19 8 0.21
20 1 0.03
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (16 bp):
TTATAATATAAATCAT
Found at i:287462 original size:2 final size:2
Alignment explanation
Indices: 287455--287480 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
287445 TTTAATAAAT
287455 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
287481 GTTCGTGTCC
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):
TA
Found at i:288600 original size:14 final size:13
Alignment explanation
Indices: 288576--288622 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
288566 TTTCTTCGAT
*
288576 ATATATAAAAAAA
1 ATATATTAAAAAA
*
288589 ATAATATTAAAATA
1 AT-ATATTAAAAAA
*
288603 ATTTATTAAAAAA
1 ATATATTAAAAAA
288616 A-ATATTA
1 ATATATTA
288623 TTATTATTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 5 0.18
13 12 0.43
14 11 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATATATTAAAAAA
Found at i:288615 original size:15 final size:15
Alignment explanation
Indices: 288581--288625 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
288571 TCGATATATA
*
288581 TAAAAAAAATAATAT
1 TAAAAAAAATATTAT
*
288596 T-AAAATAAT-TTAT
1 TAAAAAAAATATTAT
288609 TAAAAAAAATATTAT
1 TAAAAAAAATATTAT
288624 TA
1 TA
288626 TTATTCATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 4 0.16
14 14 0.56
15 7 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAAAAAATATTAT
Found at i:288695 original size:20 final size:21
Alignment explanation
Indices: 288672--288718 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
288662 AAATTATTTA
288672 AATATATAA-ACAATTAAAAC
1 AATATATAATACAATTAAAAC
* *
288692 AATA-AAAATACAATTAGAAC
1 AATATATAATACAATTAAAAC
288712 AATATAT
1 AATATAT
288719 TTAAAAGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.14
20 18 0.82
21 1 0.05
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
AATATATAATACAATTAAAAC
Found at i:290125 original size:3 final size:3
Alignment explanation
Indices: 290117--290226 Score: 159
Period size: 3 Copynumber: 37.0 Consensus size: 3
290107 TTAATATATT
*
290117 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
290164 TAA TGA TAA TGA TAA TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
290212 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
290227 AATGGATAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
2 2 0.02
3 92 0.98
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:290718 original size:114 final size:113
Alignment explanation
Indices: 290472--291479 Score: 1615
Period size: 114 Copynumber: 8.9 Consensus size: 113
290462 GCTCTTGATG
*
290472 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CT
* * * * *
290536 CTGGTAATGTTGATCCATCAACTGATGAATTCAAGCAACAGGTTGAACA
65 CTGGAAAAGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
* *
290585 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
290650 TGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACA
66 TGGAAAAG-ATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
290699 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * * *
290764 TGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACA
66 TGGAAAAGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
*
290812 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
290877 TGGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGATGATCCATCAA-GTGATGAATTCAAGCAAAAGGTTGAACA
*
290926 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
*
290991 TGGAAAAGAATGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACA
66 TGGAAAAG-ATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
291040 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * * *
291105 TGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACA
66 TGGAAAAGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
*
291153 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
291218 TGGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGATGATCCATCAA-GTGATGAATTCAAGCAAAAGGTTGAACA
*
291267 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * *
291332 TGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTCGAACA
66 TGGAAAAG-ATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
* *
291381 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
*
291446 TGGAAACA-ATGATCCATCAATTTGATGAATTCAA
66 TGGAAA-AGATGATCCATCAA-GTGATGAATTCAA
291480 AATCTTTGCT
Statistics
Matches: 832, Mismatches: 55, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
112 1 0.00
113 309 0.37
114 497 0.60
115 25 0.03
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
Found at i:290867 original size:227 final size:226
Alignment explanation
Indices: 290472--291479 Score: 1615
Period size: 227 Copynumber: 4.4 Consensus size: 226
290462 GCTCTTGATG
*
290472 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CT
* * * * *
290536 CTGGTAATGTTGATCCATCAACTGATGAATTCAAGCAACAGGTTGAACAAATTCTTCTCATTATG
65 CTGGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
290601 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCC
130 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAG-ATGATCC
*
290666 ATCAAGTGATGAATTTAAACAAAAGGTTGAACA
194 ATCAAGTGATGAATTCAAACAAAAGGTTGAACA
290699 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * *
290764 TGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGA
66 TGGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
* *
290829 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAACGATGATCCAT
131 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCAT
* *
290894 CAATTTGATGAATTCAAGCAAAAGGTTGAACA
196 CAA-GTGATGAATTCAAACAAAAGGTTGAACA
*
290926 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * *
290991 TGGAAAAGAATGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAGTTCTTCTCATTATG
66 TGGAAAAG-ATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
*
291056 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCA
130 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCA
* * * ***
291121 CCAAATGATGGATTCAGGTAAAAGGTTGAACA
195 TCAAGTGATGAATTCAAACAAAAGGTTGAACA
*
291153 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * *
291218 TGGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATG
66 TGGAAAAGATGATCCATCAA-ATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
291283 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCC
130 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAG-ATGATCC
* *
291348 ATCAAGTGATGAATTTAAACAAAAGGTCGAACA
194 ATCAAGTGATGAATTCAAACAAAAGGTTGAACA
* *
291381 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
*
291446 TGGAAACA-ATGATCCATCAATTTGATGAATTCAA
66 TGGAAA-AGATGATCCATCAA-ATGATGAATTCAA
291480 AATCTTTGCT
Statistics
Matches: 728, Mismatches: 47, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
226 25 0.03
227 461 0.63
228 242 0.33
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (226 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCAT
CAAGTGATGAATTCAAACAAAAGGTTGAACA
Found at i:291096 original size:341 final size:341
Alignment explanation
Indices: 290474--291461 Score: 1838
Period size: 341 Copynumber: 2.9 Consensus size: 341
290464 TCTTGATGAG
*
290474 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCT
* * * * * *
290538 GGTAATGTTGATCCATCAA-CTGATGAATTCAAGCAACAGGTTGAACAAATTCTTCTCATTATGA
65 GGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGA
290602 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCA
130 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCA
290667 TCAAGTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCT
195 TCAAGTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCT
290732 TCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAG
260 TCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAG
290797 GTAAAAGGTTGAACAAA
325 GTAAAAGGTTGAACAAA
290814 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
290879 GAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAA
66 GAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAA
290944 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCAT
131 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCAT
*
291009 CAAGTGATGAATTTAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
196 CAAGTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
291074 CAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGG
261 CAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGG
291139 TAAAAGGTTGAACAAA
326 TAAAAGGTTGAACAAA
291155 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
291220 GAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAA
66 GAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAA
291285 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCAT
131 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCAT
* *
291350 CAAGTGATGAATTTAAACAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTT
196 CAAGTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
*
291415 CAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAACA-ATGATCCA
261 CAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA-AGATGATCCA
291462 TCAATTTGAT
Statistics
Matches: 633, Mismatches: 12, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
339 1 0.00
340 77 0.12
341 554 0.88
342 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (341 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAA
CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCAT
CAAGTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
CAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGG
TAAAAGGTTGAACAAA
Found at i:292159 original size:52 final size:52
Alignment explanation
Indices: 292110--292565 Score: 767
Period size: 52 Copynumber: 8.8 Consensus size: 52
292100 CTATCCAATT
* *
292110 AGATCAGATATCTCAAAGAACACTTCCAGAAAATGCTATGTTCTGTCCAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACC
*
292162 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACC
* * *
292214 AGATCAGATAACTCAAAGAATACTTCTAGAAGATGCTATGTTATGAT-CAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACC
292266 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACC
*
292318 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACC
*
292370 AGATCAGATAACTCAAAGAACGCTTCCAGAAGATGCTATGTTCTGTCCAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACC
*
292422 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACC
292474 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACC
292526 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
292566 AGCACATTCA
Statistics
Matches: 384, Mismatches: 14, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
51 3 0.01
52 378 0.98
53 3 0.01
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (52 bp):
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACC
Found at i:293765 original size:11 final size:11
Alignment explanation
Indices: 293749--293788 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
293739 TCTATATTTA
293749 TTTTTTTTTTC
1 TTTTTTTTTTC
293760 TTTTTTTTTTC
1 TTTTTTTTTTC
*
293771 -TTTCTTTTTC
1 TTTTTTTTTTC
293781 TTTCTTTT
1 TTT-TTTT
293789 CTTCAAGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.36
11 13 0.52
12 3 0.12
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:293780 original size:6 final size:6
Alignment explanation
Indices: 293722--293783 Score: 51
Period size: 6 Copynumber: 10.5 Consensus size: 6
293712 TGACCCTCCT
* *
293722 TTTTTC TTTTTTC CTTTTC TATATTTA TTTTT- TTTTTC TTTTT- TTTTTC
1 TTTTTC -TTTTTC TTTTTC T-T-TTTC TTTTTC TTTTTC TTTTTC TTTTTC
293771 --TTTC TTTTTC TTT
1 TTTTTC TTTTTC TTT
293784 CTTTTCTTCA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
4 4 0.09
5 10 0.22
6 20 0.43
7 8 0.17
8 4 0.09
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:293789 original size:15 final size:14
Alignment explanation
Indices: 293749--293791 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
293739 TCTATATTTA
293749 TTTTTT-TTTTCTT
1 TTTTTTCTTTTCTT
*
293762 TTTTTTTTCTTTCTT
1 TTTTTTCT-TTTCTT
293777 TTTCTTTCTTTTCTT
1 TTT-TTTCTTTTCTT
293792 CAAGCATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 6 0.23
14 1 0.04
15 15 0.58
16 4 0.15
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTCTTTTCTT
Found at i:304925 original size:14 final size:13
Alignment explanation
Indices: 304901--304947 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
304891 TTTCTTCGAT
*
304901 ATATATAAAAAAA
1 ATATATTAAAAAA
*
304914 ATAATATTAAAATA
1 AT-ATATTAAAAAA
*
304928 ATTTATTAAAAAA
1 ATATATTAAAAAA
304941 A-ATATTA
1 ATATATTA
304948 TTTATTATTC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 5 0.18
13 12 0.43
14 11 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATATATTAAAAAA
Found at i:305024 original size:20 final size:21
Alignment explanation
Indices: 305001--305047 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
304991 AAATTATTTA
305001 AATATATAA-ACAATTAAAAC
1 AATATATAATACAATTAAAAC
* * *
305021 AATA-AAAATATAATTAGAAC
1 AATATATAATACAATTAAAAC
305041 AATATAT
1 AATATAT
305048 TTAAAAGTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.14
20 17 0.81
21 1 0.05
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (21 bp):
AATATATAATACAATTAAAAC
Found at i:306452 original size:3 final size:3
Alignment explanation
Indices: 306444--306548 Score: 135
Period size: 3 Copynumber: 36.0 Consensus size: 3
306434 TTAATATATT
*
306444 TAA TAA TAA -AA TAA TAA TAA TAA TAA -AA -AA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
306489 TGA TAA TGA TAA TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
306537 TAA TAA TAA TAA
1 TAA TAA TAA TAA
306549 AATGGATAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
2 6 0.07
3 83 0.93
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:310939 original size:15 final size:15
Alignment explanation
Indices: 310915--310956 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
310905 GTATTATTAA
310915 ATTAAATTATAAACT
1 ATTAAATTATAAACT
* *
310930 ATTTAATTATAAAGT
1 ATTAAATTATAAACT
310945 ATTAAATTATAA
1 ATTAAATTATAA
310957 TTATTAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
ATTAAATTATAAACT
Found at i:310999 original size:16 final size:16
Alignment explanation
Indices: 310978--311015 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
310968 TTAAAAATAT
310978 AAATATAAT-TTTATTA
1 AAATATAATATTTA-TA
310994 AAATATAATATTTATA
1 AAATATAATATTTATA
311010 AAATAT
1 AAATAT
311016 TAGTTTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATAATATTTATA
Found at i:312813 original size:15 final size:15
Alignment explanation
Indices: 312793--312828 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
312783 TAATAATATG
312793 TTTAATACTTTATAA
1 TTTAATACTTTATAA
*
312808 TTTAATATTTTATAA
1 TTTAATACTTTATAA
*
312823 ATTAAT
1 TTTAAT
312829 TTAGTGTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAATACTTTATAA
Found at i:322981 original size:53 final size:54
Alignment explanation
Indices: 322896--323008 Score: 174
Period size: 53 Copynumber: 2.1 Consensus size: 54
322886 AATAGGTCAA
*
322896 GCAAAAAAGTGCAATCACCCCTAGAGAAGGAT-AACATTCTATACAACATAAGT
1 GCAAAAAAGTGCAATCACCCCTAAAGAAGGATAAACATTCTATACAACATAAGT
*
322949 GCAACAAAGTGCAATCACCCCTAAAGAAGGATAACAAACATTCTATACAACATAAGT
1 GCAAAAAAGTGCAATCACCCCTAAAGAAGGAT---AAACATTCTATACAACATAAGT
323006 GCA
1 GCA
323009 TGTAGAGTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
53 30 0.56
57 24 0.44
ACGTcount: A:0.46, C:0.22, G:0.14, T:0.18
Consensus pattern (54 bp):
GCAAAAAAGTGCAATCACCCCTAAAGAAGGATAAACATTCTATACAACATAAGT
Found at i:327072 original size:16 final size:16
Alignment explanation
Indices: 327047--327080 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
327037 TATACTAAAA
*
327047 TAATTATTTTGATTTT
1 TAATTATTTTAATTTT
*
327063 TAATTTTTTTAATTTT
1 TAATTATTTTAATTTT
327079 TA
1 TA
327081 TAAAATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TAATTATTTTAATTTT
Found at i:327536 original size:22 final size:24
Alignment explanation
Indices: 327492--327544 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
327482 TTTTAAAATG
327492 ATTTAATGATCCCTTATATATATT
1 ATTTAATGATCCCTTATATATATT
*
327516 ATTTAATGATCTCTTATATATATT
1 ATTTAATGATCCCTTATATATATT
327540 ATTTA
1 ATTTA
327545 TTTCATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (24 bp):
ATTTAATGATCCCTTATATATATT
Found at i:328890 original size:16 final size:16
Alignment explanation
Indices: 328869--328901 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
328859 AATTTTATTT
328869 TTTTAATA-CAATATCA
1 TTTTAATATC-ATATCA
328885 TTTTAATATCATATCA
1 TTTTAATATCATATCA
328901 T
1 T
328902 ATATTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTAATATCATATCA
Found at i:329494 original size:29 final size:29
Alignment explanation
Indices: 329462--329561 Score: 182
Period size: 29 Copynumber: 3.4 Consensus size: 29
329452 ATGCATGGAT
**
329462 TGCATGGCGACCTGGTAGGTCGTTGGGCG
1 TGCATGGCGACCTGGTAGGTCACTGGGCG
329491 TGCATGGCGACCTGGTAGGTCACTGGGCG
1 TGCATGGCGACCTGGTAGGTCACTGGGCG
329520 TGCATGGCGACCTGGTAGGTCACTGGGCG
1 TGCATGGCGACCTGGTAGGTCACTGGGCG
329549 TGCATGGCGACCT
1 TGCATGGCGACCT
329562 ATCCCATCTA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 69 1.00
ACGTcount: A:0.13, C:0.24, G:0.41, T:0.22
Consensus pattern (29 bp):
TGCATGGCGACCTGGTAGGTCACTGGGCG
Found at i:337694 original size:16 final size:15
Alignment explanation
Indices: 337673--337706 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
337663 TATAAAATAC
*
337673 AAATTAAACATAACAT
1 AAATTAAA-ATAAAAT
337689 AAATTAAAATAAAAT
1 AAATTAAAATAAAAT
337704 AAA
1 AAA
337707 GTAATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATTAAAATAAAAT
Found at i:340932 original size:18 final size:19
Alignment explanation
Indices: 340896--340944 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
340886 CAGTCCTTTA
*
340896 ATTA-ATATTTATTTATTT
1 ATTACATATGTATTTATTT
340914 ATTACATATGTATTT-TTT
1 ATTACATATGTATTTATTT
340932 ATGTACA-ATGTAT
1 AT-TACATATGTAT
340945 CATTTTAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (19 bp):
ATTACATATGTATTTATTT
Found at i:344829 original size:23 final size:23
Alignment explanation
Indices: 344783--344831 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
344773 ATAATTTTTT
* *
344783 TAATAAATTTAAGGATTATTTTA
1 TAATAAATTTAAGGATCATCTTA
*
344806 TAATAAATTTAATGATCATCTTA
1 TAATAAATTTAAGGATCATCTTA
344829 TAA
1 TAA
344832 CAATTTGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (23 bp):
TAATAAATTTAAGGATCATCTTA
Found at i:347919 original size:176 final size:178
Alignment explanation
Indices: 347625--347975 Score: 679
Period size: 176 Copynumber: 2.0 Consensus size: 178
347615 TTGCTAGTGG
347625 AAATGACTGACCTAATGAGTCTCATTAATCTGAACAATGGTTGCCAAAGTGAAGCATTGCTTCTG
1 AAATGACTGACCTAATGAGTCTCATTAATCTGAACAATGGTTGCCAAAGTGAAGCATTGCTTCTG
347690 TAATAAAGACTAATGTGCTAACTTGGGACTAGATAGATCAATCTAACTTCGCAAAAGAAAATCGC
66 TAATAAAGACTAATGTGCTAACTTGGGACTAGATAGATCAATCTAACTTCGCAAAAGAAAATCGC
347755 ACCCTTTTCC-T-ATATGTGTATATATTTTAATGTCTTTAGTTTTATC
131 ACCCTTTTCCATGATATGTGTATATATTTTAATGTCTTTAGTTTTATC
347801 AAATGACTGACCTAATGAGTCTCATTAATCTGAACAATGGTTGCCAAAGTGAAGCATTGCTTCTG
1 AAATGACTGACCTAATGAGTCTCATTAATCTGAACAATGGTTGCCAAAGTGAAGCATTGCTTCTG
347866 TAATAAAGACTAATGTGCTAACTTGGGACTAGATAGATCAATCTAACTTCGCAAAAGAAAATCGC
66 TAATAAAGACTAATGTGCTAACTTGGGACTAGATAGATCAATCTAACTTCGCAAAAGAAAATCGC
347931 ACCCTTTTCCTATGATATGTGTATATATTTTAATGTCTTTAGTTT
131 ACCCTTTTCC-ATGATATGTGTATATATTTTAATGTCTTTAGTTT
347976 ATCCTTCCTA
Statistics
Matches: 172, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
176 140 0.81
178 1 0.01
179 31 0.18
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (178 bp):
AAATGACTGACCTAATGAGTCTCATTAATCTGAACAATGGTTGCCAAAGTGAAGCATTGCTTCTG
TAATAAAGACTAATGTGCTAACTTGGGACTAGATAGATCAATCTAACTTCGCAAAAGAAAATCGC
ACCCTTTTCCATGATATGTGTATATATTTTAATGTCTTTAGTTTTATC
Found at i:353304 original size:15 final size:15
Alignment explanation
Indices: 353271--353305 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
353261 GTAAATATTA
353271 ATTTATTTTTTAAAT
1 ATTTATTTTTTAAAT
353286 -TTTATTTTTTAAAT
1 ATTTATTTTTTAAAT
353300 ATTTAT
1 ATTTAT
353306 AATTCGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTATTTTTTAAAT
Found at i:354140 original size:30 final size:30
Alignment explanation
Indices: 354106--354164 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
354096 AGTGACCACC
* * *
354106 ATAGGTCTCAATGAACACATGGTGACCTAG
1 ATAGGTCTCAAGGAACACACGGCGACCTAG
*
354136 ATAGGTCTCCAGGAACACACGGCGACCTA
1 ATAGGTCTCAAGGAACACACGGCGACCTA
354165 TGGAGCACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (30 bp):
ATAGGTCTCAAGGAACACACGGCGACCTAG
Found at i:354179 original size:19 final size:19
Alignment explanation
Indices: 354155--354206 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
354145 CAGGAACACA
*
354155 CGGCGACCTATGGAGCACT
1 CGGCGACCTATGGAGCAAT
*
354174 CGGCGACCTATGAAGCAAT
1 CGGCGACCTATGGAGCAAT
*
354193 TGGCGACCTATGGA
1 CGGCGACCTATGGA
354207 ACTGCAACAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.31, T:0.17
Consensus pattern (19 bp):
CGGCGACCTATGGAGCAAT
Found at i:355134 original size:76 final size:76
Alignment explanation
Indices: 355044--355195 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
355034 TGAAGAATAG
355044 TGATTTTTATTTATAGTATACACGAGAATTGATATGATACATGGCTTACTTGCATAAACAATTAT
1 TGATTTTTATTTATAGTATACACGAGAATTGATATGATACATGGCTTACTTGCATAAACAATTAT
355109 TGTTGATGCAT
66 TGTTGATGCAT
355120 TGATTTTTATTTATAGTATACACGAGAATTGATATGATACATGGCTTACTTGCATAAACAATTAT
1 TGATTTTTATTTATAGTATACACGAGAATTGATATGATACATGGCTTACTTGCATAAACAATTAT
355185 TGTTGATGCAT
66 TGTTGATGCAT
355196 ACACACCTTC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.41
Consensus pattern (76 bp):
TGATTTTTATTTATAGTATACACGAGAATTGATATGATACATGGCTTACTTGCATAAACAATTAT
TGTTGATGCAT
Found at i:373254 original size:175 final size:175
Alignment explanation
Indices: 372963--373325 Score: 586
Period size: 175 Copynumber: 2.1 Consensus size: 175
372953 ATAAAAATTA
** *
372963 AATATTTTTTAATTAAAAAAATGGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAA
1 AATA-TTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAA
* *
373028 TTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTA
65 TTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGAATATTAAATTA
373093 TTAATTAGGTTTTAAATGG-TTGGGCTT-AGCCTATATGTTATATAT
130 TTAATTAGGTTTTAAATGGTTTGGG-TTAAGCCTATATGTTATATAT
*
373138 AATATTTTTAATTCAAAAAACCAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAA
1 AATATTTTTAATT-AAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAA
* *
373203 TTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGAATATTAAATTA
65 TTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGAATATTAAATTA
* *
373268 TTAATTGGGTTTTAAATGGTTTGGGTTAATCCTATATGTTATATAT
130 TTAATTAGGTTTTAAATGGTTTGGGTTAAGCCTATATGTTATATAT
*
373314 AATATATTTAAT
1 AATATTTTTAAT
373326 ATTTAAAATT
Statistics
Matches: 174, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
174 9 0.05
175 132 0.76
176 33 0.19
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.47
Consensus pattern (175 bp):
AATATTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAT
TTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGAATATTAAATTAT
TAATTAGGTTTTAAATGGTTTGGGTTAAGCCTATATGTTATATAT
Found at i:373357 original size:9 final size:9
Alignment explanation
Indices: 373335--373368 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
373325 TATTTAAAAT
*
373335 TTAATTTCGG
1 TTAA-TTCGA
373345 TTAATTCGA
1 TTAATTCGA
373354 TTAATTCGA
1 TTAATTCGA
373363 TTAATT
1 TTAATT
373369 AACTGATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50
Consensus pattern (9 bp):
TTAATTCGA
Found at i:377867 original size:40 final size:41
Alignment explanation
Indices: 377811--377894 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 41
377801 AAAAGATGTA
*
377811 ATTGAAGTTACCCATATA-TTCTACCGTAATAGAAAAATAT
1 ATTGAAATTACCCATATATTTCTACCGTAATAGAAAAATAT
* * *
377851 ATTGAAATTACGCATATATTTTCTACTGTAATAGAAAACTAT
1 ATTGAAATTACCCATATA-TTTCTACCGTAATAGAAAAATAT
377893 AT
1 AT
377895 AATCTAACTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 16 0.42
42 22 0.58
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.36
Consensus pattern (41 bp):
ATTGAAATTACCCATATATTTCTACCGTAATAGAAAAATAT
Found at i:379310 original size:23 final size:23
Alignment explanation
Indices: 379265--379310 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
379255 CGACTATTGA
* **
379265 TATTTTTTATTATCATTTTATTT
1 TATTTTTTATTATCAATAAATTT
*
379288 TATTTTTTATTTTCAATAAATTT
1 TATTTTTTATTATCAATAAATTT
379311 GTCTATATGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTTTTTATTATCAATAAATTT
Found at i:381357 original size:82 final size:82
Alignment explanation
Indices: 381212--381428 Score: 328
Period size: 82 Copynumber: 2.6 Consensus size: 82
381202 CCAGAACCGC
* * * *
381212 GTCCATAGGGCTTACCTTAAGCACAC-GACAAAAAGGAAACCAACCTAAGGATAGGCTTTGGGGC
1 GTCCATAGGGCTTACCCTAAGCACACAG-C--AAAGGGAGCCAACCTAAGGATAGGCTTCGGGGC
* *
381276 CTATATCTTTAAGTCCGTAA
63 CTATACCCTTAAGTCCGTAA
*
381296 GTCCATAGGGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAAGGATAGGCTTCGGGGCCTG
1 GTCCATAGGGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAAGGATAGGCTTCGGGGCCTA
381361 TACCCTTAAGTCCGTAA
66 TACCCTTAAGTCCGTAA
381378 GTCCATAGGGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAATGGAT
1 GTCCATAGGGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAA-GGAT
381429 CATCTTGGGG
Statistics
Matches: 124, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
82 93 0.75
83 4 0.03
84 26 0.21
85 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.19
Consensus pattern (82 bp):
GTCCATAGGGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAAGGATAGGCTTCGGGGCCTA
TACCCTTAAGTCCGTAA
Found at i:385791 original size:23 final size:24
Alignment explanation
Indices: 385739--385799 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
385729 ATTATTAACT
* *
385739 AACATATTCATTTAATGTTCACGA
1 AACATGTTCATTTAGTGTTCACGA
*
385763 AA-ATGTTCATTTAGTGTTCA-TA
1 AACATGTTCATTTAGTGTTCACGA
*
385785 AACATGTTCGTTTAG
1 AACATGTTCATTTAG
385800 CATTCGTGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 3 0.09
23 27 0.84
24 2 0.06
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (24 bp):
AACATGTTCATTTAGTGTTCACGA
Found at i:392909 original size:25 final size:25
Alignment explanation
Indices: 392871--392926 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
392861 TTTGTGCATG
**
392871 GTTTTTTCAATTGAATGATTACTTGT
1 GTTTTTTCAATTGAATGAACAC-TGT
* *
392897 GTTTTTTC-CTTGAGTGAACACTGT
1 GTTTTTTCAATTGAATGAACACTGT
392921 GTTTTT
1 GTTTTT
392927 GTCATGTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 9 0.35
25 9 0.35
26 8 0.31
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.54
Consensus pattern (25 bp):
GTTTTTTCAATTGAATGAACACTGT
Found at i:402216 original size:21 final size:20
Alignment explanation
Indices: 402157--402216 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 20
402147 TTAAGTGCCT
*
402157 TTTTCTATATTTATTATTATAT
1 TTTT-TATATTTATT-TTATAC
402179 TTTGTTATAGTTT-TTTTATAAC
1 TTT-TTATA-TTTATTTTAT-AC
402201 TTTTTATATTTATTTT
1 TTTTTATATTTATTTT
402217 TTCAATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
20 3 0.09
21 13 0.39
22 13 0.39
23 4 0.12
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTTTATATTTATTTTATAC
Found at i:404857 original size:7 final size:7
Alignment explanation
Indices: 404845--404871 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
404835 AAATTATAAA
404845 ATTTACG
1 ATTTACG
404852 ATTTACG
1 ATTTACG
404859 ATTTACG
1 ATTTACG
404866 ATTTAC
1 ATTTAC
404872 CGAAAGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (7 bp):
ATTTACG
Found at i:407506 original size:3 final size:3
Alignment explanation
Indices: 407500--407526 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
407490 CTTGATGATG
407500 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
407527 TGATCATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:413086 original size:19 final size:19
Alignment explanation
Indices: 413062--413099 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
413052 AAATTTATTG
413062 TCGAAATTTACTGGGGGAA
1 TCGAAATTTACTGGGGGAA
413081 TCGAAATTTACTGGGGGAA
1 TCGAAATTTACTGGGGGAA
413100 ATTTCAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.26
Consensus pattern (19 bp):
TCGAAATTTACTGGGGGAA
Found at i:413923 original size:18 final size:18
Alignment explanation
Indices: 413900--413936 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
413890 ACTTTAAGTT
413900 ATAAAATCTTGAATAACA
1 ATAAAATCTTGAATAACA
413918 ATAAAATCTTGAATAACA
1 ATAAAATCTTGAATAACA
413936 A
1 A
413937 GAAAGCATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (18 bp):
ATAAAATCTTGAATAACA
Found at i:415807 original size:2 final size:2
Alignment explanation
Indices: 415800--415830 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
415790 TTCCTTCTTG
415800 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
415831 TGTTTTAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:419843 original size:13 final size:13
Alignment explanation
Indices: 419827--419858 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
419817 GCCCCGATTA
419827 CCCGATTACCCGC
1 CCCGATTACCCGC
*
419840 CCCGATTACCCTC
1 CCCGATTACCCGC
419853 CCCGAT
1 CCCGAT
419859 AAATATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.53, G:0.12, T:0.19
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:419989 original size:12 final size:12
Alignment explanation
Indices: 419974--420008 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
419964 CGATTCTCGG
419974 CCCAATACCCGA
1 CCCAATACCCGA
*
419986 CCCAATACCCGG
1 CCCAATACCCGA
419998 CCCAATACCCG
1 CCCAATACCCG
420009 TTTAAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:430679 original size:20 final size:20
Alignment explanation
Indices: 430654--430697 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
430644 ATATAGTATT
430654 GATAATGTAAGAACAATATC
1 GATAATGTAAGAACAATATC
*
430674 GATAATGTAAGAACAGTATC
1 GATAATGTAAGAACAATATC
430694 GATA
1 GATA
430698 CTACATACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (20 bp):
GATAATGTAAGAACAATATC
Found at i:434701 original size:88 final size:89
Alignment explanation
Indices: 434551--434728 Score: 313
Period size: 88 Copynumber: 2.0 Consensus size: 89
434541 CTACGGCCAA
** * *
434551 CACAAGAGAGAGATGCCAAGAGTGGAGAAACGTCTGCTTATGACTGAAGTGTGAACTAAGGATGA
1 CACAAGAGAGAGATGCCAAGAGACGAGAAACGTCTGCTTATGACGGAAGTGTGAACCAAGGATGA
434616 AGATAGCTGAAAATGCTGAAAACC
66 AGATAGCTGAAAATGCTGAAAACC
434640 CACAAGAGAGAGATGCCAAGA-ACGAGAAACGTCTGCTTATGACGGAAGTGTGAACCAAGGATGA
1 CACAAGAGAGAGATGCCAAGAGACGAGAAACGTCTGCTTATGACGGAAGTGTGAACCAAGGATGA
434704 AGATAGCTGAAAATGCTGAAAACC
66 AGATAGCTGAAAATGCTGAAAACC
434728 C
1 C
434729 TATCTCTCTC
Statistics
Matches: 85, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
88 64 0.75
89 21 0.25
ACGTcount: A:0.40, C:0.16, G:0.28, T:0.16
Consensus pattern (89 bp):
CACAAGAGAGAGATGCCAAGAGACGAGAAACGTCTGCTTATGACGGAAGTGTGAACCAAGGATGA
AGATAGCTGAAAATGCTGAAAACC
Found at i:435716 original size:22 final size:23
Alignment explanation
Indices: 435691--435749 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
435681 ATTAAAAAGG
* *
435691 ATTTATTATTAAATTTAA-TTTA
1 ATTTATTATAAAATATAATTTTA
435713 ATTTAATT-TAAAATATAATTTTA
1 ATTT-ATTATAAAATATAATTTTA
* *
435736 TTTTATTACAAAAT
1 ATTTATTATAAAAT
435750 TAGAAATGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 15 0.50
23 15 0.50
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTTATTATAAAATATAATTTTA
Found at i:436668 original size:29 final size:29
Alignment explanation
Indices: 436590--436671 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
436580 CAGTAGCCGT
* ** *
436590 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACTCCCGGCGACCAACG
* *
436619 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACTCCCGGCGACCAACG
*
436648 AGGTCGCCATGCACTCGCGGCGAC
1 AGGTCGCCATGCACTCCCGGCGAC
436672 ATCCCCTGCT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.18, C:0.40, G:0.29, T:0.12
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCGGCGACCAACG
Found at i:436792 original size:36 final size:36
Alignment explanation
Indices: 436752--436848 Score: 194
Period size: 36 Copynumber: 2.7 Consensus size: 36
436742 CCCTATTCTT
436752 CCCATGCATGAACCGATCCTTGGTCGCCCCGAGTGC
1 CCCATGCATGAACCGATCCTTGGTCGCCCCGAGTGC
436788 CCCATGCATGAACCGATCCTTGGTCGCCCCGAGTGC
1 CCCATGCATGAACCGATCCTTGGTCGCCCCGAGTGC
436824 CCCATGCATGAACCGATCCTTGGTC
1 CCCATGCATGAACCGATCCTTGGTC
436849 ATCCTTGGTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.18, C:0.38, G:0.24, T:0.21
Consensus pattern (36 bp):
CCCATGCATGAACCGATCCTTGGTCGCCCCGAGTGC
Found at i:437010 original size:29 final size:29
Alignment explanation
Indices: 436927--437010 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
436917 ATGAATCCTT
** * **
436927 GGTCGCCTCGAGTGCATGGCGACCTCCTT
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
* *
436956 GGTCGCCGGGCGTGCATGGCGACCTAGGA
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
*
436985 GGTCGCTGGGAGTGCATGGCGACCTA
1 GGTCGCCGGGAGTGCATGGCGACCTA
437011 TGGTTGGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.13, C:0.29, G:0.39, T:0.19
Consensus pattern (29 bp):
GGTCGCCGGGAGTGCATGGCGACCTACGA
Found at i:437962 original size:23 final size:23
Alignment explanation
Indices: 437915--437977 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
437905 AAGGTAAAAG
*
437915 AAAATGCGTCATAAAAATTAAAGA
1 AAAATGTGTCATAAAAATT-AAGA
437939 AAAATGTGTCATAAAAATGT-AGA
1 AAAATGTGTCATAAAAAT-TAAGA
* *
437962 AAAATATATCATAAAA
1 AAAATGTGTCATAAAA
437978 GTATATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.49
24 17 0.49
25 1 0.03
ACGTcount: A:0.59, C:0.06, G:0.11, T:0.24
Consensus pattern (23 bp):
AAAATGTGTCATAAAAATTAAGA
Found at i:437965 original size:24 final size:24
Alignment explanation
Indices: 437911--437956 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
437901 TCAAAAGGTA
437911 AAAG-AAAATGCGTCATAAAAATT
1 AAAGAAAAATGCGTCATAAAAATT
*
437934 AAAGAAAAATGTGTCATAAAAAT
1 AAAGAAAAATGCGTCATAAAAAT
437957 GTAGAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.59, C:0.07, G:0.13, T:0.22
Consensus pattern (24 bp):
AAAGAAAAATGCGTCATAAAAATT
Found at i:445136 original size:21 final size:21
Alignment explanation
Indices: 445112--445155 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
445102 CAATCGCTCC
445112 TTTTAAAAATTTTAAATTTTT
1 TTTTAAAAATTTTAAATTTTT
* *
445133 TTTTATATATTTTAAATTTTT
1 TTTTAAAAATTTTAAATTTTT
445154 TT
1 TT
445156 ATTTAAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTAAAAATTTTAAATTTTT
Found at i:448355 original size:37 final size:37
Alignment explanation
Indices: 448279--448355 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 37
448269 TTTTTATATT
* * *
448279 TTTAATTTTATAAAAGAAATTGTATAAATATTATGAA
1 TTTAATTTTATAAAAGAAAATATATAAATATTATCAA
* *
448316 TTTAATTTT-TTAAAGAAAATATATAAATATTTTACAA
1 TTTAATTTTATAAAAGAAAATATATAAATATTAT-CAA
448353 TTT
1 TTT
448356 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 20 0.59
37 14 0.41
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (37 bp):
TTTAATTTTATAAAAGAAAATATATAAATATTATCAA
Found at i:449380 original size:2 final size:2
Alignment explanation
Indices: 449373--449418 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
449363 AAAAAGTGAG
449373 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
449415 AT AT
1 AT AT
449419 TAATTTAACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:456669 original size:2 final size:2
Alignment explanation
Indices: 456662--456692 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
456652 CCCTTACCCC
456662 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
456693 GAGAAAGAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:456800 original size:67 final size:67
Alignment explanation
Indices: 456692--456827 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 67
456682 ATTATATATA
456692 TGAGAAAGAGGGACAATCATTTATTTTATTAGTGCTTAGGGGAGAGAGAAGATTTGAGAATGGTG
1 TGAGAAAGAGGGACAATCATTTATTTTATTAGTGCTTAGGGGAGAGAGAAGATTTGAGAATGGTG
456757 TT
66 TT
*
456759 TGAGAAAGAGGGACAGTCATTTATTTTATTAGTGCTTAGGGGAGAGAGAAGATTTGAGAATGGTG
1 TGAGAAAGAGGGACAATCATTTATTTTATTAGTGCTTAGGGGAGAGAGAAGATTTGAGAATGGTG
456824 TT
66 TT
456826 TG
1 TG
456828 GGGGGGGGGG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.32
Consensus pattern (67 bp):
TGAGAAAGAGGGACAATCATTTATTTTATTAGTGCTTAGGGGAGAGAGAAGATTTGAGAATGGTG
TT
Found at i:484131 original size:22 final size:23
Alignment explanation
Indices: 484092--484134 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
484082 TTTATTTGAA
*
484092 AATGGTAATATTTTTTTATGTTT
1 AATGGTAATATTTATTTATGTTT
484115 AATGGTAA-ATTTATTTATGT
1 AATGGTAATATTTATTTATGT
484135 CGATGTCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (23 bp):
AATGGTAATATTTATTTATGTTT
Found at i:491784 original size:20 final size:20
Alignment explanation
Indices: 491765--491945 Score: 134
Period size: 20 Copynumber: 8.9 Consensus size: 20
491755 AACGTAATTT
* *
491765 TGACTATCGCATTGCGATTT
1 TGACTATCGCAATGCGATTA
*
491785 TCCGACTATCACAATGCGAATATA
1 T--GACTATCGCAATGCG-AT-TA
*
491809 T-A-AATCGCAATGCGATTA
1 TGACTATCGCAATGCGATTA
*
491827 TGACTATCGCAACGCGATTA
1 TGACTATCGCAATGCGATTA
* * * *
491847 TGACTAGCGCAACGAGATTC
1 TGACTATCGCAATGCGATTA
**
491867 TGACTATCGCAACACGATTA
1 TGACTATCGCAATGCGATTA
* * **
491887 TGAAC-GTCGCAACGCGATGC
1 TG-ACTATCGCAATGCGATTA
* **
491907 TGACTATCGCAACGCGATGC
1 TGACTATCGCAATGCGATTA
491927 TGACTATCGCAATGCGATT
1 TGACTATCGCAATGCGATT
491946 TTCAAAGCAC
Statistics
Matches: 132, Mismatches: 21, Indels: 16
0.78 0.12 0.09
Matches are distributed among these distances:
18 3 0.02
19 5 0.04
20 104 0.79
21 3 0.02
22 13 0.10
23 2 0.02
24 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (20 bp):
TGACTATCGCAATGCGATTA
Found at i:491858 original size:40 final size:40
Alignment explanation
Indices: 491814--491945 Score: 151
Period size: 40 Copynumber: 3.3 Consensus size: 40
491804 ATATATAAAT
* *
491814 CGCAATGCGATTATGACTATCGCAACGCGATTATGACTAG
1 CGCAACGCGATTCTGACTATCGCAACGCGATTATGACTAG
* *
491854 CGCAACGAGATTCTGACTATCGCAACACGATTATGA--ACG
1 CGCAACGCGATTCTGACTATCGCAACGCGATTATGACTA-G
* ** *
491893 TCGCAACGCGATGCTGACTATCGCAACGCGATGCTGACTAT
1 -CGCAACGCGATTCTGACTATCGCAACGCGATTATGACTAG
*
491934 CGCAATGCGATT
1 CGCAACGCGATT
491946 TTCAAAGCAC
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 73 0.96
42 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (40 bp):
CGCAACGCGATTCTGACTATCGCAACGCGATTATGACTAG
Found at i:491945 original size:60 final size:60
Alignment explanation
Indices: 491812--491945 Score: 180
Period size: 60 Copynumber: 2.2 Consensus size: 60
491802 GAATATATAA
* *
491812 ATCGCAATGCGATTATGACTATCGCAACGCGATTATGACTAGCGCAACGAGATTCTGACT
1 ATCGCAATGCGATTATGACTATCGCAACGCGATGATGACTAGCGCAACGAGATGCTGACT
** * * * *
491872 ATCGCAACACGATTATGAAC-GTCGCAACGCGATGCTGACTATCGCAACGCGATGCTGACT
1 ATCGCAATGCGATTATG-ACTATCGCAACGCGATGATGACTAGCGCAACGAGATGCTGACT
491932 ATCGCAATGCGATT
1 ATCGCAATGCGATT
491946 TTCAAAGCAC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 61 0.97
61 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.23
Consensus pattern (60 bp):
ATCGCAATGCGATTATGACTATCGCAACGCGATGATGACTAGCGCAACGAGATGCTGACT
Found at i:492163 original size:22 final size:22
Alignment explanation
Indices: 492122--492164 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
492112 GGCGACATCC
*
492122 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACAAAATCA
492144 GTCCCCATCTCCGGA-AAAATC
1 GTCCCCATCTCC-GACAAAATC
492165 CGTCTATCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.28, C:0.40, G:0.14, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACAAAATCA
Found at i:492574 original size:19 final size:20
Alignment explanation
Indices: 492552--492604 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
492542 AATCGCAATA
492552 CGATTTT-AGTTTCGCGTTG
1 CGATTTTAAGTTTCGCGTTG
* * *
492571 CGATTTTCATTTTCGTGTTG
1 CGATTTTAAGTTTCGCGTTG
492591 CGATTTTAAGTTTC
1 CGATTTTAAGTTTC
492605 AGAAACTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (20 bp):
CGATTTTAAGTTTCGCGTTG
Found at i:494614 original size:18 final size:19
Alignment explanation
Indices: 494572--494618 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
494562 GCGATTCTCT
494572 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
494592 CGTTGCGATAGTCA-TTCG
1 CGTTGCGATAGTCATTTCG
*
494610 TGTTGCGAT
1 CGTTGCGAT
494619 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
20 14 0.54
ACGTcount: A:0.15, C:0.19, G:0.28, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:495136 original size:21 final size:21
Alignment explanation
Indices: 495110--495163 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
495100 CTCACCTGTC
495110 ATCGTTCAAGAGGCCTCCCAT
1 ATCGTTCAAGAGGCCTCCCAT
495131 ATCGTTCAAGAGGCCTCCCAT
1 ATCGTTCAAGAGGCCTCCCAT
495152 ATCGTTCAAGAG
1 ATCGTTCAAGAG
495164 ACCCCTATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCTCCCAT
Found at i:496677 original size:14 final size:14
Alignment explanation
Indices: 496640--496701 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
496630 TTGCTTGTTT
*
496640 AATTGATTTATAAA
1 AATTGATTTGTAAA
496654 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
496668 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
496683 TATTGATGTGTAAA
1 AATTGATTTGTAAA
496697 TAATT
1 -AATT
496702 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:496853 original size:20 final size:20
Alignment explanation
Indices: 496800--496853 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
496790 AGGTACACTT
* **
496800 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCAAAAGACAAAA
* *
496820 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCAAAAGACAAAA
*
496840 TCTCAACGCAAAAG
1 TCGCAACGCAAAAG
496854 TCAATTCGCG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (20 bp):
TCGCAACGCAAAAGACAAAA
Found at i:496889 original size:20 final size:20
Alignment explanation
Indices: 496852--497132 Score: 344
Period size: 20 Copynumber: 14.4 Consensus size: 20
496842 TCAACGCAAA
496852 AGTC-AATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* * *
496871 AGTCTAATACGCTTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
496891 --T----TTCTCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* *
496905 AGTCAAATACCCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* * *
496925 AATCAAATTCACATTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
496945 ACTCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
496965 AGTCAAA-TAGTCGTTGCGAT
1 AGTCAAATTCG-CGTTGCGAT
*
496985 AATCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
497005 AGTCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
497025 AGACAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
497045 AGACAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
497065 AGTCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* *
497085 AATCAAATTCGCATTGCGAT
1 AGTCAAATTCGCGTTGCGAT
497105 AGTCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
497125 ATTCAAAT
1 AGTCAAAT
497133 GAATGTGTAA
Statistics
Matches: 227, Mismatches: 26, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
14 10 0.04
16 1 0.00
18 1 0.00
19 6 0.03
20 207 0.91
21 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (20 bp):
AGTCAAATTCGCGTTGCGAT
Found at i:497355 original size:140 final size:140
Alignment explanation
Indices: 497103--497372 Score: 504
Period size: 140 Copynumber: 1.9 Consensus size: 140
497093 TCGCATTGCG
*
497103 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAGCTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
* * *
497168 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACTCATAA
66 TAGCAATATTCAAACTCAAATTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
497233 AATACACATA
131 AATACACATA
497243 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
497308 TAGCAATATTCAAACTCAAATTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATATTCAAACTCAAATTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
497373 TACAACGTTT
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 126 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
TAGCAATATTCAAACTCAAATTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:499498 original size:14 final size:14
Alignment explanation
Indices: 499479--499515 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
499469 TCCTATGGCA
499479 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
499493 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
499507 TTCTTCTTC
1 TT-TTCTTC
499516 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:499739 original size:24 final size:24
Alignment explanation
Indices: 499705--499758 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
499695 CTGAAACATC
499705 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
499729 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
499753 ATCAAA
1 ATCAAA
499759 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:500605 original size:20 final size:20
Alignment explanation
Indices: 500580--500637 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
500570 GAAATTCAGT
*
500580 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
500600 GTTGCGATAGTCAGAATCTC
1 GTTGCGATAGTCAGAATCGC
*
500620 ATTGCGATAGTCAGAATC
1 GTTGCGATAGTCAGAATC
500638 ATATTGCGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:500643 original size:20 final size:19
Alignment explanation
Indices: 500581--500647 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 19
500571 AAATTCAGTG
* **
500581 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATC-TA
500601 TTGCGATAGTCAGAATCTCA
1 TTGCGATAGTCAGAATCT-A
500621 TTGCGATAGTCAGAATCATA
1 TTGCGATAGTCAGAATC-TA
500641 TTGCGAT
1 TTGCGAT
500648 TTACATATTC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 41 0.98
21 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (19 bp):
TTGCGATAGTCAGAATCTA
Found at i:510623 original size:22 final size:22
Alignment explanation
Indices: 510580--510623 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
510570 AAATTTACAT
*
510580 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
510602 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
510624 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:512814 original size:3 final size:3
Alignment explanation
Indices: 512806--512848 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
512796 ACTTGTAATT
* *
512806 TAA TAA TAA GAA TAA TAA -AA TAA TAG TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
512849 ATAGATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:512827 original size:17 final size:16
Alignment explanation
Indices: 512807--512860 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
512797 CTTGTAATTT
512807 AATAATAAGAATAATAA
1 AATAAT-AGAATAATAA
512824 AATAATAGTAATAATAA
1 AATAATAG-AATAATAA
*
512841 TATAATA-AATAGATAA
1 AATAATAGAATA-ATAA
512857 AATA
1 AATA
512861 TAAACAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
15 4 0.12
16 9 0.27
17 20 0.61
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (16 bp):
AATAATAGAATAATAA
Found at i:512839 original size:20 final size:20
Alignment explanation
Indices: 512806--512848 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
512796 ACTTGTAATT
512806 TAATAATAAGAATAATAAAA
1 TAATAATAAGAATAATAAAA
* * *
512826 TAATAGTAATAATAATATAA
1 TAATAATAAGAATAATAAAA
512846 TAA
1 TAA
512849 ATAGATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
TAATAATAAGAATAATAAAA
Found at i:512859 original size:9 final size:8
Alignment explanation
Indices: 512807--512874 Score: 59
Period size: 9 Copynumber: 8.2 Consensus size: 8
512797 CTTGTAATTT
512807 AATAATAA
1 AATAATAA
512815 GAATAATAA
1 -AATAATAA
*
512824 AATAATAGT
1 AATAATA-A
512833 AATAATAA
1 AATAATAA
*
512841 TATAAT-A
1 AATAATAA
512848 AATAGATAA
1 AATA-ATAA
512857 AAT-ATAA
1 AATAATAA
*
512864 ACAAAATAA
1 A-ATAATAA
512873 AA
1 AA
512875 AAGACCCGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
7 9 0.18
8 16 0.33
9 24 0.49
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (8 bp):
AATAATAA
Found at i:513234 original size:43 final size:40
Alignment explanation
Indices: 513161--513273 Score: 104
Period size: 40 Copynumber: 2.8 Consensus size: 40
513151 AAGAGCGATA
* *
513161 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAGGGG-TG
1 ACACGGCTCCTACGTGATGAAGACGGCTGG---TC-AGGGGATG
* *
513204 ACACGGCTCCTACGTGATGAAGA-GATCTGGTCGGGGGATG
1 ACACGGCTCCTACGTGATGAAGACG-GCTGGTCAGGGGATG
* * *
513244 ACACGACTCATACGTGATGAAGACGACTGG
1 ACACGGCTCCTACGTGATGAAGACGGCTGG
513274 CCATCTCTAG
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
39 4 0.07
40 29 0.48
41 1 0.02
42 1 0.02
43 25 0.42
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.21
Consensus pattern (40 bp):
ACACGGCTCCTACGTGATGAAGACGGCTGGTCAGGGGATG
Found at i:513659 original size:35 final size:36
Alignment explanation
Indices: 513618--513714 Score: 110
Period size: 36 Copynumber: 2.7 Consensus size: 36
513608 GACAAAATTC
**
513618 ATTTCAAGAGAAACAATCTCAAAGAT-GTTTATTTT
1 ATTTCAAGAGAAACAATCTCAAAGATGGTAAATTTT
*
513653 ATTTCAAGGGAAACAGAT-TCAAAGATGGTAAATTTT
1 ATTTCAAGAGAAACA-ATCTCAAAGATGGTAAATTTT
* *
513689 GTTTCCAA-AGAAACAAACTCAAAGAT
1 ATTT-CAAGAGAAACAATCTCAAAGAT
513715 TTTTCAAAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
35 23 0.44
36 26 0.50
37 3 0.06
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (36 bp):
ATTTCAAGAGAAACAATCTCAAAGATGGTAAATTTT
Found at i:514545 original size:30 final size:30
Alignment explanation
Indices: 514482--514544 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
514472 AGAGACAAAA
*
514482 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCCAAAAAAACAAACTCAAAGAT
*
514512 TTTTGTTT-CAAAAAAACAATCTCAAAGAT
1 TTTTGTTTCCAAAAAAACAAACTCAAAGAT
514541 TTTT
1 TTTT
514545 TCACGAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (30 bp):
TTTTGTTTCCAAAAAAACAAACTCAAAGAT
Found at i:514605 original size:52 final size:53
Alignment explanation
Indices: 514532--514634 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 53
514522 AAAAAACAAT
*
514532 CTCAAAGATTTTTTCACGAAATTGTCTCAAGAGAGACAACACTTTGTTTCAGA
1 CTCAAAGATTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
514585 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
514635 AAATAAATAG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 41 0.84
53 8 0.16
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:514678 original size:26 final size:28
Alignment explanation
Indices: 514630--514752 Score: 137
Period size: 29 Copynumber: 4.5 Consensus size: 28
514620 CAAAACTTTG
* * *
514630 TTTCAAAATAAATAGACTCAAAGA-TTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
514657 TTTCAAAAGAAAC-AACTCAAAGA-TTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
* *
514683 ATTCAAAAGGAACAAACTTC-AAGATTTT
1 TTTCAAAAGAAACAAAC-TCAAAGATTTT
*
514711 TATTCAAAAGGAACAAACTCAAAGATTTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTT
*
514740 TTTCAAGAGAAAC
1 TTTCAAAAGAAAC
514753 TGTCTCAAGA
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
26 23 0.28
27 18 0.22
28 17 0.20
29 25 0.30
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (28 bp):
TTTCAAAAGAAACAAACTCAAAGATTTT
Found at i:514719 original size:29 final size:27
Alignment explanation
Indices: 514645--514741 Score: 135
Period size: 26 Copynumber: 3.6 Consensus size: 27
514635 AAATAAATAG
*
514645 ACTCAAAGATTTTTTCAAAAGAAAC-A
1 ACTCAAAGATTTTTTCAAAAGGAACAA
*
514671 ACTCAAAGATTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTTCAAAAGGAACAA
514698 ACTTC-AAGATTTTTATTCAAAAGGAACAA
1 AC-TCAAAGA-TTTT-TTCAAAAGGAACAA
514727 ACTCAAAGATTTTTT
1 ACTCAAAGATTTTTT
514742 TCAAGAGAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
26 23 0.37
27 9 0.14
28 11 0.17
29 20 0.32
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.30
Consensus pattern (27 bp):
ACTCAAAGATTTTTTCAAAAGGAACAA
Found at i:515071 original size:36 final size:36
Alignment explanation
Indices: 514987--515089 Score: 108
Period size: 36 Copynumber: 3.0 Consensus size: 36
514977 GAGAAAATGA
* * * *
514987 TGTCTCAAGCGAGACGAACTTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
515021 AGTCTC-A-CTGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGC-GAGACAAAATTTGTTTTTAGAGAAAT
*
515056 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
515090 ACGATCTCAA
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
32 1 0.02
33 12 0.21
34 9 0.16
35 16 0.28
36 18 0.32
37 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:515098 original size:36 final size:36
Alignment explanation
Indices: 515030--515100 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
515020 TAGTCTCACT
**
515030 GAGACAAAATTTGTTTTTAGAGAAATTGTCTCAAGC
1 GAGACAAAATTTGTTTTTAGAGAAAACGTCTCAAGC
*
515066 GAGACAAAGTTTGTTTTT-GAGAAAACGATCTCAAG
1 GAGACAAAATTTGTTTTTAGAGAAAACG-TCTCAAG
515101 TGATCAACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 7 0.23
36 24 0.77
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (36 bp):
GAGACAAAATTTGTTTTTAGAGAAAACGTCTCAAGC
Found at i:515177 original size:98 final size:103
Alignment explanation
Indices: 515057--515284 Score: 251
Period size: 103 Copynumber: 2.3 Consensus size: 103
515047 TAGAGAAATT
*
515057 GTCTCAAGCGAGAC-AAAGTTTGTTTTTG-AGAAA-ACG-ATCTCAA-GT-GATCAACTTTGTTT
1 GTCTCAAGCGAGACGAAA-TTTGTTTTTGAAGAAACAAGAATCT-AAGGTAGAT-AACTTTGTTT
*
515116 A-ATGTGAA-CAAATTCGAAATTTGGATATCAAAGG-AAAAG
63 ATA-GTGAATCAAATTCAAAATTTGGATATCAAAGGAAAAAG
* * *
515155 GTCTCAAGCGAGACGAAATTTG-TTTTGAAAGAAACAAGAATCTAAGGTGAGATTATTTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTTG-AAGAAACAAGAATCTAAGGT-AGATAACTTTGTTTA
* * *
515219 TAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
64 TAGTGAATCAAATTCAAAATTTGGATATCAAAGGAAAAAG
*
515259 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
515285 AAAATTCTCA
Statistics
Matches: 109, Mismatches: 9, Indels: 17
0.81 0.07 0.13
Matches are distributed among these distances:
97 5 0.05
98 18 0.17
99 8 0.07
100 4 0.04
101 6 0.06
102 13 0.12
103 27 0.25
104 25 0.23
105 3 0.03
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (103 bp):
GTCTCAAGCGAGACGAAATTTGTTTTTGAAGAAACAAGAATCTAAGGTAGATAACTTTGTTTATA
GTGAATCAAATTCAAAATTTGGATATCAAAGGAAAAAG
Found at i:515766 original size:4 final size:4
Alignment explanation
Indices: 515757--515796 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
515747 TTTATGTATC
* *
515757 ATGT ATGT ATGT ATGT ATGT GTAT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
515797 GTATACTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:515785 original size:20 final size:20
Alignment explanation
Indices: 515760--515801 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
515750 ATGTATCATG
515760 TATGTATGTATGTATGTGTA
1 TATGTATGTATGTATGTGTA
515780 TATGTATGTATGTATGTGTA
1 TATGTATGTATGTATGTGTA
515800 TA
1 TA
515802 CTTTTCTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (20 bp):
TATGTATGTATGTATGTGTA
Found at i:516814 original size:11 final size:11
Alignment explanation
Indices: 516798--516840 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
516788 CCTCTTTTTG
516798 TTCTTTGCTTT
1 TTCTTTGCTTT
516809 TTCTTTGCTTT
1 TTCTTTGCTTT
*
516820 TTGCTTTGATTT
1 TT-CTTTGCTTT
*
516832 CTCTTTGCT
1 TTCTTTGCT
516841 CTTTGTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.02, C:0.19, G:0.12, T:0.67
Consensus pattern (11 bp):
TTCTTTGCTTT
Found at i:516826 original size:23 final size:24
Alignment explanation
Indices: 516791--516846 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
516781 GTTCTTTCCT
* *
516791 CTTTTTGTTCTTTGCTTTTTCTTTG
1 CTTTTTG-TCTTTGATTTCTCTTTG
516816 CTTTTTG-CTTTGATTTCTCTTTG
1 CTTTTTGTCTTTGATTTCTCTTTG
*
516839 CTCTTTGT
1 CTTTTTGT
516847 TTTTTCTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 20 0.74
25 7 0.26
ACGTcount: A:0.02, C:0.18, G:0.12, T:0.68
Consensus pattern (24 bp):
CTTTTTGTCTTTGATTTCTCTTTG
Found at i:516867 original size:30 final size:30
Alignment explanation
Indices: 516810--516869 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
516800 CTTTGCTTTT
*
516810 TCTTTGCTTTTTGCTTTGATTTCTCTTTGC
1 TCTTTGCTTTTTGCTTTGATTTATCTTTGC
* *
516840 TCTTTG-TTTTTTCTTTGGTTTGATCTTTGC
1 TCTTTGCTTTTTGCTTTGATTT-ATCTTTGC
516870 ACTCTGCGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.03, C:0.17, G:0.15, T:0.65
Consensus pattern (30 bp):
TCTTTGCTTTTTGCTTTGATTTATCTTTGC
Found at i:517521 original size:45 final size:45
Alignment explanation
Indices: 517430--517521 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
517420 ATAAATACAG
* * *
517430 TGTTTCAAGGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTCGAAAAAATATTTCAAGGTCTCAAAGAGAGAGAA
*
517475 TGTTTCAAGGTCGAAAAAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGTCGAAAAAATATTTCAAGGTCTCAAAGAGAGAGAA
517520 TG
1 TG
517522 CCAAAAATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.26
Consensus pattern (45 bp):
TGTTTCAAGGTCGAAAAAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:518879 original size:30 final size:32
Alignment explanation
Indices: 518825--518885 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
518815 TGACAAAATG
518825 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
518857 ACACAAACAAAAGAG-A-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
518886 CATGTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 13 0.45
31 1 0.03
32 15 0.52
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:520392 original size:22 final size:22
Alignment explanation
Indices: 520349--520392 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
520339 AAATTTACAT
*
520349 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
520371 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
520393 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:522585 original size:3 final size:3
Alignment explanation
Indices: 522577--522634 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
522567 ACTTGTAATT
* * *
522577 TAA TAA TAA GAA TAA TAA -AA TAA TAG TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
522624 TAGA TAA -AA TA
1 TA-A TAA TAA TA
522635 TAAACAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:522592 original size:9 final size:8
Alignment explanation
Indices: 522578--522648 Score: 54
Period size: 9 Copynumber: 8.2 Consensus size: 8
522568 CTTGTAATTT
522578 AATAATAA
1 AATAATAA
522586 GAATAATAA
1 -AATAATAA
*
522595 AATAATAGT
1 AATAATA-A
522604 AATAATAA
1 AATAATAA
*
522612 TTATAATAA
1 -AATAATAA
522621 TAATAGATAA
1 -AATA-ATAA
522631 AAT-ATAA
1 AATAATAA
*
522638 ACAAAATAA
1 A-ATAATAA
522647 AA
1 AA
522649 AAGACCCGGA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
7 5 0.10
8 9 0.17
9 34 0.65
10 4 0.08
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (8 bp):
AATAATAA
Found at i:529614 original size:15 final size:15
Alignment explanation
Indices: 529594--529625 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
529584 GACGAAGCGA
*
529594 TTAAAATTTCCCCCT
1 TTAAAATTTCACCCT
529609 TTAAAATTTCACCCT
1 TTAAAATTTCACCCT
529624 TT
1 TT
529626 TGTACTCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAAAATTTCACCCT
Found at i:529891 original size:41 final size:41
Alignment explanation
Indices: 529835--530119 Score: 327
Period size: 41 Copynumber: 7.0 Consensus size: 41
529825 ATTTATTCTA
*
529835 AAAAACGCCACTAAAGTACGAGTCTTTGGCGGCGTTTGTAT
1 AAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGTAT
* * *
529876 AAAAATGCCATTAAAGTACGGGTCTTTGGCGACGTTTGTAT
1 AAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGTAT
* *
529917 AAAAACACCACTAAAGTACGGGTCTTTGGTGGCGTTTGTAT
1 AAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGTAT
* * * *
529958 TAAAACACCACTAAAGTACAGGTCTTTGGCGACGTTTGTAT
1 AAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGTAT
* * **
529999 AAAAACACCACTAAAGTACGGGTATTTGGCGTTGTTTGTAT
1 AAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGTAT
* * * *** * *
530040 AGAAACGACACTAAAGTCCGGGTAAGTAGCGGCATTTGTAT
1 AAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGTAT
* * ** *
530081 AGAAACGCCACTAAAGTACGAGAATTTAGCGGCGTTTGT
1 AAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGT
530120 GCTTACAATG
Statistics
Matches: 209, Mismatches: 35, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 209 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (41 bp):
AAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGTAT
Found at i:530152 original size:82 final size:82
Alignment explanation
Indices: 530066--530262 Score: 279
Period size: 82 Copynumber: 2.4 Consensus size: 82
530056 TCCGGGTAAG
* * * *
530066 TAGCGGCATTTGTATAGAAACGCCACTAAAGTACGAGAATTTAGCGGCGTTTGTGCTT-ACAATG
1 TAGCGGCATTTATACAAAAACGCCACTAAAGTACGAGAATTTAGCGGCGTTTGTGCTTCA-AACG
*
530130 CCACTAAAGTACAATATT
65 ACACTAAAGTACAATATT
* * * * *
530148 TAGCGGCATTTATACACAAACGCCGCTAAAATATGAGCATTTAGCGGCGTTTGTGCTTCAAACGA
1 TAGCGGCATTTATACAAAAACGCCACTAAAGTACGAGAATTTAGCGGCGTTTGTGCTTCAAACGA
*
530213 CACTAAAGTACATTATT
66 CACTAAAGTACAATATT
530230 TAGCGGCATTTATACAAAAACGCCACTAAAGTA
1 TAGCGGCATTTATACAAAAACGCCACTAAAGTA
530263 TAGTATTTAT
Statistics
Matches: 101, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
82 100 0.99
83 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (82 bp):
TAGCGGCATTTATACAAAAACGCCACTAAAGTACGAGAATTTAGCGGCGTTTGTGCTTCAAACGA
CACTAAAGTACAATATT
Found at i:530257 original size:40 final size:41
Alignment explanation
Indices: 529820--530300 Score: 240
Period size: 41 Copynumber: 11.7 Consensus size: 41
529810 CTGATAAATT
* * *
529820 GCGGCATTTATTCTAAAAAACGCCACTAAAGTACGAGTCTTTG
1 GCGGCATTTATACT-AAAAACGCCACTAAAGTAC-AGTATTTA
* * * * * * *
529863 GCGGCGTTTGTA-TAAAAATGCCATTAAAGTACGGGTCTTTG
1 GCGGCATTTATACTAAAAACGCCACTAAAGTAC-AGTATTTA
* * * * * * *
529904 GCGACGTTTGTA-TAAAAACACCACTAAAGTACGGGTCTTTG
1 GCGGCATTTATACTAAAAACGCCACTAAAGTAC-AGTATTTA
* * * * * * *
529945 GTGGCGTTTGTA-TTAAAACACCACTAAAGTACAGGTCTTTG
1 GCGGCATTTATACTAAAAACGCCACTAAAGTACA-GTATTTA
* * * * * *
529986 GCGACGTTTGTA-TAAAAACACCACTAAAGTACGGGTATTTG
1 GCGGCATTTATACTAAAAACGCCACTAAAGTAC-AGTATTTA
*** * * * * * **
530027 GCGTTGTTTGTA-TAGAAACGACACTAAAGTCCGGGTAAGTA
1 GCGGCATTTATACTAAAAACGCCACTAAAGTAC-AGTATTTA
* * *
530068 GCGGCATTTGTA-TAGAAACGCCACTAAAGTACGAGAATTTA
1 GCGGCATTTATACTAAAAACGCCACTAAAGTAC-AGTATTTA
* * * * * * *
530109 GCGGCGTTTGTGCTTACAATGCCACTAAAGTACAATATTTA
1 GCGGCATTTATACTAAAAACGCCACTAAAGTACAGTATTTA
* * * * *
530150 GCGGCATTTATAC-ACAAACGCCGCTAAAATATGAGCATTTA
1 GCGGCATTTATACTAAAAACGCCACTAAAGTA-CAGTATTTA
* * * ** * *
530191 GCGGCGTTTGTGCTTCAAACGACACTAAAGTACATTATTTA
1 GCGGCATTTATACTAAAAACGCCACTAAAGTACAGTATTTA
*
530232 GCGGCATTTATAC-AAAAACGCCACTAAAGTATAGTATTTA
1 GCGGCATTTATACTAAAAACGCCACTAAAGTACAGTATTTA
* *
530272 TCGGCATTTATACAAAAAACGCCACTAAA
1 GCGGCATTTATACTAAAAACGCCACTAAA
530301 TCACAATTAT
Statistics
Matches: 356, Mismatches: 76, Indels: 14
0.80 0.17 0.03
Matches are distributed among these distances:
40 46 0.13
41 270 0.76
42 31 0.09
43 9 0.03
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (41 bp):
GCGGCATTTATACTAAAAACGCCACTAAAGTACAGTATTTA
Found at i:530310 original size:82 final size:82
Alignment explanation
Indices: 530066--530313 Score: 277
Period size: 82 Copynumber: 3.0 Consensus size: 82
530056 TCCGGGTAAG
* * * * * *
530066 TAGCGGCATTTGTATAGAAACGCCACTAAAGTACGAGAATTTAGCGGCGTTTGTGCTTACAATGC
1 TAGCGGCATTTATACAAAAACGCCACTAAAGTA-TAGAATTTAGCGGCGTTTGTGCTTAAAACGC
530131 CACTAAAGTACAA-TATT
65 CACTAAAGTACAATTATT
* * * * * *
530148 TAGCGGCATTTATACACAAACGCCGCTAAAATATGAGCATTTAGCGGCGTTTGTGCTTCAAACGA
1 TAGCGGCATTTATACAAAAACGCCACTAAAGTAT-AGAATTTAGCGGCGTTTGTGCTTAAAACGC
530213 CACTAAAGTAC-ATTATT
65 CACTAAAGTACAATTATT
* * * * * **
530230 TAGCGGCATTTATACAAAAACGCCACTAAAGTATAGTATTTATCGGCATTTATACAAAAAACGCC
1 TAGCGGCATTTATACAAAAACGCCACTAAAGTATAGAATTTAGCGGCGTTTGTGCTTAAAACGCC
530295 ACTAAA-TCACAATTATT
66 ACTAAAGT-ACAATTATT
530312 TA
1 TA
530314 TCAGCGTTTA
Statistics
Matches: 139, Mismatches: 23, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
80 1 0.01
81 31 0.22
82 107 0.77
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (82 bp):
TAGCGGCATTTATACAAAAACGCCACTAAAGTATAGAATTTAGCGGCGTTTGTGCTTAAAACGCC
ACTAAAGTACAATTATT
Found at i:535920 original size:14 final size:14
Alignment explanation
Indices: 535903--535936 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
535893 TTTATTTTAA
*
535903 TAAATATAGAAGAG
1 TAAAAATAGAAGAG
*
535917 TAAAAATATAAGAG
1 TAAAAATAGAAGAG
535931 TAAAAA
1 TAAAAA
535937 ATTTAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.21
Consensus pattern (14 bp):
TAAAAATAGAAGAG
Found at i:536804 original size:31 final size:30
Alignment explanation
Indices: 536769--536853 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 30
536759 GGAGTACCTT
*
536769 GGGGCCTGAGAGCCTACCCAAG-ACAATTCTC
1 GGGGCC-GAGAGCCTACCCAAGAAAAATT-TC
*
536800 GGGGCC-ACGGAGGCTTACCCAAGAAAAATTTC
1 GGGGCCGA--GA-GCCTACCCAAGAAAAATTTC
536832 GGGGCCGCAGAGCCTACCCAAG
1 GGGGCCG-AGAGCCTACCCAAG
536854 GGTCGCCTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
29 1 0.02
31 18 0.40
32 20 0.44
33 5 0.11
34 1 0.02
ACGTcount: A:0.27, C:0.31, G:0.29, T:0.13
Consensus pattern (30 bp):
GGGGCCGAGAGCCTACCCAAGAAAAATTTC
Found at i:544109 original size:19 final size:19
Alignment explanation
Indices: 544082--544126 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
544072 TAAATGTTCT
*
544082 TGATTTTTATAATAAACTG
1 TGATATTTATAATAAACTG
* *
544101 TGATATTTATAGTAAATTG
1 TGATATTTATAATAAACTG
544120 TGATATT
1 TGATATT
544127 GATTACTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (19 bp):
TGATATTTATAATAAACTG
Found at i:547758 original size:31 final size:31
Alignment explanation
Indices: 547723--547781 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
547713 TGCTTTTCTT
547723 CGCAACGAAGAAGTTATCTTTGCTCTTTCCA
1 CGCAACGAAGAAGTTATCTTTGCTCTTTCCA
547754 CGCAACGAAGAAGTTATCTTTGCTCTTT
1 CGCAACGAAGAAGTTATCTTTGCTCTTT
547782 GCTCTTCACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (31 bp):
CGCAACGAAGAAGTTATCTTTGCTCTTTCCA
Found at i:550077 original size:34 final size:34
Alignment explanation
Indices: 550039--550128 Score: 144
Period size: 34 Copynumber: 2.6 Consensus size: 34
550029 TAAGGAAACA
*
550039 TCTTGGGGCTTGAGAGCCTACCAAAGAGAGAGTT
1 TCTTGGGGCCTGAGAGCCTACCAAAGAGAGAGTT
* *
550073 TCTTGAGGCCTGAGAGCCTACCATAGAGAGAGTT
1 TCTTGGGGCCTGAGAGCCTACCAAAGAGAGAGTT
*
550107 TCTTGGGGCCTAAGAGCCTACC
1 TCTTGGGGCCTGAGAGCCTACC
550129 CAAGGGTCAC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.23
Consensus pattern (34 bp):
TCTTGGGGCCTGAGAGCCTACCAAAGAGAGAGTT
Found at i:551258 original size:27 final size:28
Alignment explanation
Indices: 551211--551271 Score: 97
Period size: 27 Copynumber: 2.2 Consensus size: 28
551201 AGGGCTTGGT
*
551211 GGTATTTTGGATCATTTTACACTTCAGG
1 GGTATTTTGGATCATTTTACACTTCAAG
*
551239 GGTATTTTGG-TCATTTTACAGTTCAAG
1 GGTATTTTGGATCATTTTACACTTCAAG
551266 GGTATT
1 GGTATT
551272 CAAATCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 21 0.68
28 10 0.32
ACGTcount: A:0.21, C:0.11, G:0.23, T:0.44
Consensus pattern (28 bp):
GGTATTTTGGATCATTTTACACTTCAAG
Found at i:551279 original size:27 final size:27
Alignment explanation
Indices: 551221--551281 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
551211 GGTATTTTGG
* ***
551221 ATCATTTTACACTTCAGGGGTATTTTG
1 ATCATTTTACACTTCAAGGGTATTCAA
* *
551248 GTCATTTTACAGTTCAAGGGTATTCAA
1 ATCATTTTACACTTCAAGGGTATTCAA
551275 ATCATTT
1 ATCATTT
551282 CCTTTCGTCC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (27 bp):
ATCATTTTACACTTCAAGGGTATTCAA
Found at i:553702 original size:36 final size:37
Alignment explanation
Indices: 553632--553716 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
553622 ATCCCATTAT
*
553632 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
553668 TATTTTTCAAAGAAACATTTACCAAACTTT-AAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
553704 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
553717 TTGATTACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 14 0.33
37 29 0.67
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.33
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:556482 original size:19 final size:17
Alignment explanation
Indices: 556439--556485 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
556429 TTAATTGAAA
556439 CATCGAATGCATTCTATG
1 CATCG-ATGCATTCTATG
*
556457 CACCGATGCATTCTCCATG
1 CATCGATGCATTCT--ATG
556476 CATCGATGCA
1 CATCGATGCA
556486 CTCTGAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 9 0.36
18 4 0.16
19 12 0.48
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (17 bp):
CATCGATGCATTCTATG
Found at i:556614 original size:64 final size:65
Alignment explanation
Indices: 556436--556599 Score: 224
Period size: 65 Copynumber: 2.5 Consensus size: 65
556426 GAATTAATTG
* ** *
556436 AAACATCGAATGCA-TTCTATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTC
1 AAACATCGAATGCATTTC-ATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTC
556500 A
65 A
* ** **
556501 AAACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTC-
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
556565 AAACATCGAATGCATTTCATGCATCGATGCACACT
1 AAACATCGAATGCATTTCATGCATCGATGCACACT
556600 TGGTGCACCG
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 32 0.37
65 52 0.60
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:563766 original size:20 final size:21
Alignment explanation
Indices: 563729--563768 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
563719 AAATTAAGTT
563729 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
563750 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
563769 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:564160 original size:19 final size:19
Alignment explanation
Indices: 564133--564169 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
564123 ATGCATTTCA
*
564133 TGCATCGATGCACACTTGG
1 TGCACCGATGCACACTTGG
*
564152 TGCACCGATGCATACTTG
1 TGCACCGATGCACACTTG
564170 ATCATGCATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (19 bp):
TGCACCGATGCACACTTGG
Done.