Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002325.1 Hibiscus syriacus cultivar Beakdansim tig00004741_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: 69230
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:816 original size:40 final size:35
Alignment explanation
Indices: 754--833 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 35
744 GATAGATGGT
*
754 TTATTATTGTTACTGATGAGTGGTGGAGAAAGTGGAG
1 TTATTATTGTTACTGATGAGTGG-AGAGAAAGT-GAG
*
791 TTATTATTGTTATTGATAAGTAGTGGAGAGAAAGTGAG
1 TTATTATTGTTACTGAT--G-AGTGGAGAGAAAGTGAG
829 -TATTA
1 TTATTA
834 ATTAGTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
37 21 0.55
38 3 0.08
39 9 0.24
40 5 0.13
ACGTcount: A:0.31, C:0.01, G:0.30, T:0.38
Consensus pattern (35 bp):
TTATTATTGTTACTGATGAGTGGAGAGAAAGTGAG
Found at i:3892 original size:26 final size:23
Alignment explanation
Indices: 3862--3924 Score: 63
Period size: 26 Copynumber: 2.6 Consensus size: 23
3852 AATCGATACC
3862 TTTTGCATTTGCATTCACATTTT
1 TTTTGCATTTGCATTCACATTTT
* * **
3885 TACGTTTGTATTTACATTTTCATTTT
1 T---TTTGCATTTGCATTCACATTTT
3911 TTTTGCATTTGCAT
1 TTTTGCATTTGCAT
3925 CTTTGCATAG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
23 12 0.39
26 19 0.61
ACGTcount: A:0.17, C:0.14, G:0.10, T:0.59
Consensus pattern (23 bp):
TTTTGCATTTGCATTCACATTTT
Found at i:6341 original size:9 final size:8
Alignment explanation
Indices: 6323--6423 Score: 93
Period size: 8 Copynumber: 12.2 Consensus size: 8
6313 CTCATCCATT
6323 AAAAAAGA
1 AAAAAAGA
6331 AAAAGAAGA
1 AAAA-AAGA
6340 AAAAAAG-
1 AAAAAAGA
*
6347 -AGAAA-A
1 AAAAAAGA
*
6353 AAAAGAGA
1 AAAAAAGA
6361 AAAAAAGGGAA
1 AAAAAA--G-A
6372 AAAAAGAGA
1 AAAAA-AGA
6381 AAAAAAGA
1 AAAAAAGA
6389 AAAAAAGA
1 AAAAAAGA
6397 AAAAAA-A
1 AAAAAAGA
6404 AAGAAAAGA
1 AA-AAAAGA
6413 AAGAAAAGA
1 AA-AAAAGA
6422 AA
1 AA
6424 TGAAATTGAA
Statistics
Matches: 79, Mismatches: 4, Indels: 19
0.77 0.04 0.19
Matches are distributed among these distances:
6 4 0.05
7 6 0.08
8 34 0.43
9 26 0.33
10 2 0.03
11 6 0.08
12 1 0.01
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:6350 original size:10 final size:10
Alignment explanation
Indices: 6330--6416 Score: 108
Period size: 10 Copynumber: 8.7 Consensus size: 10
6320 ATTAAAAAAG
6330 AAAAAGAAGAA
1 AAAAAG-AGAA
6341 AAAAAGAGAAA
1 AAAAAGAG-AA
6352 AAAAAGAGAA
1 AAAAAGAGAA
*
6362 AAAAAGGGAA
1 AAAAAGAGAA
6372 AAAAAGAG-A
1 AAAAAGAGAA
6381 AAAAA-AGAA
1 AAAAAGAGAA
6390 AAAAAGA-AA
1 AAAAAGAGAA
*
6399 AAAAAAAGAA
1 AAAAAGAGAA
6409 AAGAAAGA
1 AA-AAAGA
6417 AAAGAAATGA
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
8 2 0.03
9 20 0.30
10 25 0.37
11 20 0.30
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAGAGAA
Found at i:6429 original size:5 final size:5
Alignment explanation
Indices: 6325--6428 Score: 64
Period size: 5 Copynumber: 21.6 Consensus size: 5
6315 CATCCATTAA
*
6325 AAAAG AAAA- AGAAG AAAA- AAAGAG AAAA- AAAAG AGAAA- AAAAGG
1 AAAAG AAAAG AAAAG AAAAG AAA-AG AAAAG AAAAG A-AAAG AAAA-G
* *
6369 GAAA- AAAAG AGAAA- AAAAG -AAA- AAAAG AAAAAA AAAAG AAAAG -AAAG
1 AAAAG AAAAG A-AAAG AAAAG AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG
*
6416 AAAAG AAATG AAA
1 AAAAG AAAAG AAA
6429 TTGAATCAAG
Statistics
Matches: 78, Mismatches: 7, Indels: 28
0.69 0.06 0.25
Matches are distributed among these distances:
4 29 0.37
5 33 0.42
6 16 0.21
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:7992 original size:28 final size:28
Alignment explanation
Indices: 7952--8009 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
7942 GTAATCCAAG
7952 TGGGGCATCTTGAAGGCTCACA-TCAGCA
1 TGGGGCATCTTGAAGGCTCACACT-AGCA
7980 TGGGGCATCTTGAAGGCTCACACTAGCA
1 TGGGGCATCTTGAAGGCTCACACTAGCA
8008 TG
1 TG
8010 AAAAGGTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22
Consensus pattern (28 bp):
TGGGGCATCTTGAAGGCTCACACTAGCA
Found at i:9429 original size:23 final size:23
Alignment explanation
Indices: 9354--9422 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
9344 TATCTCATTC
9354 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
*
9377 AAGATT-TTATTTCATT----C--
1 AAGATTGTT-TTTCCTTGAAACAG
9394 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
9417 AAGATT
1 AAGATT
9423 TTATTTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 16
0.67 0.04 0.30
Matches are distributed among these distances:
17 12 0.33
18 2 0.06
19 1 0.03
21 1 0.03
22 2 0.06
23 18 0.50
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (23 bp):
AAGATTGTTTTTCCTTGAAACAG
Found at i:9661 original size:23 final size:23
Alignment explanation
Indices: 9635--9703 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
9625 TATCTCACTC
9635 AAGATTGTTTTTCCTTGAAATAG
1 AAGATTGTTTTTCCTTGAAATAG
* * * *
9658 AAGA-T-TTTAT-CTCG--CT-C
1 AAGATTGTTTTTCCTTGAAATAG
9675 AAGATTGTTTTTCCTTGAAATAG
1 AAGATTGTTTTTCCTTGAAATAG
9698 AAGATT
1 AAGATT
9704 TTATCTCGCT
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 4 0.12
18 2 0.06
19 4 0.12
20 6 0.19
21 4 0.12
22 2 0.06
23 10 0.31
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (23 bp):
AAGATTGTTTTTCCTTGAAATAG
Found at i:9678 original size:120 final size:120
Alignment explanation
Indices: 9315--9936 Score: 872
Period size: 120 Copynumber: 5.2 Consensus size: 120
9305 ATCTCACAGG
*
9315 AGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAACAGAAG
1 AGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAG
* * * **
9380 ATTTTATTTCATTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATTTCATTCA
66 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGCTCA
* *
9435 AGATTGTTTTTCCTTGAAACAAAATATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAAAAA
1 AGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAAC-AGAA
* *
9500 GATTTTACCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCA
65 GATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGCTCA
* * *
9556 AGAATGTTTTTTCTTGAAACATAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAG
1 AGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAG
*
9621 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAATAGAAGATTTTATCTCGCTCA
66 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGCTCA
* * * * *
9676 AGATTGTTTTTCCTTGAAATAGAAGATTTTATCTCGCTCAAGATTATTTTTCCTTGAAACAGAAT
1 AGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAG
*
9741 ATTTTATCTCGCTCAAGATTGTTTTTCGC-TGAAACAGAAGATTTTATCTCGCTCA
66 ATTTTATCTCACTCAAGATTGTTTTTC-CTTGAAACAGAAGATTTTATCTCGCTCA
* * * *
9796 AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTAAAACAAAAG
1 AGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAG
* ** * * * * * * **
9861 ATTTTATCTCGCTTGATATAG-TTTCCCTCGAAATAAAAGATTTTATCTCGCTTG
66 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGCTCA
* *
9915 AGATAG-TTTCCCTTGAAACAAA
1 AGATTGTTTTTCCTTGAAACAAA
9937 TTTTGTCTCG
Statistics
Matches: 456, Mismatches: 43, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
118 15 0.03
119 30 0.07
120 300 0.66
121 111 0.24
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (120 bp):
AGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAG
ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGCTCA
Found at i:9724 original size:20 final size:20
Alignment explanation
Indices: 9701--9765 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
9691 GAAATAGAAG
9701 ATTTTATCTCGCTCAAGATT
1 ATTTTATCTCGCTCAAGATT
* ** *
9721 ATTTT-TCCTTG-AAACAGAAT
1 ATTTTAT-CTCGCTCA-AGATT
9741 ATTTTATCTCGCTCAAGATT
1 ATTTTATCTCGCTCAAGATT
*
9761 GTTTT
1 ATTTT
9766 TCGCTGAAAC
Statistics
Matches: 32, Mismatches: 9, Indels: 8
0.65 0.18 0.16
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (20 bp):
ATTTTATCTCGCTCAAGATT
Found at i:9873 original size:40 final size:40
Alignment explanation
Indices: 9315--9870 Score: 871
Period size: 40 Copynumber: 13.9 Consensus size: 40
9305 ATCTCACAGG
* *
9315 AGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCATTCA
1 AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCA
* *
9355 AGATTGTTTTTCCTTGAAACAGAAGATTTTATTTCATTCA
1 AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCA
* *
9395 AGATTGTTTTTCCTTGAAACAGAAGATTTTATTTCATTCA
1 AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCA
* *
9435 AGATTGTTTTTCCTTGAAACAAAATATTTTATCTCACTCA
1 AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCA
* *
9475 AGATTGTTTTTCCTTGAAACAAAAAGATTTTACCTCACTCA
1 AGATTGTTTTTCCTTGAAAC-AGAAGATTTTATCTCACTCA
9516 AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCA
1 AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCA
* * *
9556 AGAATGTTTTTTCTTGAAACATAAGATTTTATCTCACTCA
1 AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCA
9596 AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCA
1 AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCA
* *
9636 AGATTGTTTTTCCTTGAAATAGAAGATTTTATCTCGCTCA
1 AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCA
* *
9676 AGATTGTTTTTCCTTGAAATAGAAGATTTTATCTCGCTCA
1 AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCA
* * *
9716 AGATTATTTTTCCTTGAAACAGAATATTTTATCTCGCTCA
1 AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCA
*
9756 AGATTGTTTTTCGC-TGAAACAGAAGATTTTATCTCGCTCA
1 AGATTGTTTTTC-CTTGAAACAGAAGATTTTATCTCACTCA
*
9796 AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGCTCA
1 AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCA
* *
9836 AGATTGTTTTTCCTTAAAACAAAAGATTTTATCTC
1 AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
9871 GCTTGATATA
Statistics
Matches: 488, Mismatches: 25, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
39 1 0.00
40 448 0.92
41 39 0.08
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (40 bp):
AGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCA
Found at i:9910 original size:39 final size:38
Alignment explanation
Indices: 9446--10005 Score: 250
Period size: 40 Copynumber: 14.2 Consensus size: 38
9436 GATTGTTTTT
* * ** * *
9446 CCTTGAAACAAAATATTTTATCTCACTCAAGATTGTTTTT
1 CCTTGAAA-AAAAGATTTTATCTCGCTTGAGATAG-TTTC
* * ** * *
9486 CCTTGAAACAAAAAGATTTTACCTCACTCAAGATTGTTTTT
1 CCTTG-AA-AAAAAGATTTTATCTCGCTTGAGATAG-TTTC
* * ** *
9527 CCTTGAAACAGAAGATTTTATCTCACTCAAGA-ATGTTTTT
1 CCTTGAAA-AAAAGATTTTATCTCGCTTGAGATA-G-TTTC
* * * ** * *
9567 TCTTGAAACATAAGATTTTATCTCACTCAAGATTGTTTTT
1 CCTTGAAA-AAAAGATTTTATCTCGCTTGAGATAG-TTTC
* * ** * *
9607 CCTTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTT
1 CCTTGAAA-AAAAGATTTTATCTCGCTTGAGATAG-TTTC
* ** * *
9647 CCTTGAAATAGAAGATTTTATCTCGCTCAAGATTGTTTTT
1 CCTTGAAA-AAAAGATTTTATCTCGCTTGAGATAG-TTTC
* ** * *
9687 CCTTGAAATAGAAGATTTTATCTCGCTCAAGATTATTTTT
1 CCTTGAAA-AAAAGATTTTATCTCGCTTGAGA-TAGTTTC
* * ** *
9727 CCTTGAAACAGAATATTTTATCTCGCTCAAGATTGTTTTTC
1 CCTTGAAA-AAAAGATTTTATCTCGCTTGAGATAG--TTTC
* * ** * *
9768 GC-TGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTT
1 CCTTGAAA-AAAAGATTTTATCTCGCTTGAGATAG-TTTC
* ** * *
9807 CCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTT
1 CCTTGAAA-AAAAGATTTTATCTCGCTTGAGATAG-TTTC
* *
9847 CCTTAAAACAAAAGATTTTATCTCGCTTGATATAGTTTC
1 CCTTGAAA-AAAAGATTTTATCTCGCTTGAGATAGTTTC
*
9886 CCTCGAAATAAAAGATTTTATCTCGCTTGAGATAGTTTC
1 CCTTGAAA-AAAAGATTTTATCTCGCTTGAGATAGTTTC
* *
9925 CCTTG-AAACAA-ATTTTGTCTCGCTTGAGATAGTTTC
1 CCTTGAAAAAAAGATTTTATCTCGCTTGAGATAGTTTC
* * * * *
9961 CCTTG-AAACAAG-TTTTGTCTCCCTTGAAATAGTTTG
1 CCTTGAAAAAAAGATTTTATCTCGCTTGAGATAGTTTC
*
9997 TCTTGAAAA
1 CCTTGAAAA
10006 TTTTGAGAAC
Statistics
Matches: 468, Mismatches: 41, Indels: 25
0.88 0.08 0.05
Matches are distributed among these distances:
36 60 0.13
37 6 0.01
38 2 0.00
39 49 0.10
40 309 0.66
41 41 0.09
42 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (38 bp):
CCTTGAAAAAAAGATTTTATCTCGCTTGAGATAGTTTC
Found at i:9957 original size:75 final size:78
Alignment explanation
Indices: 9330--9968 Score: 345
Period size: 80 Copynumber: 8.1 Consensus size: 78
9320 GTTTTTCCTT
* ** * * * * *
9330 GAAACAAAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATTTC-ATTC
1 GAAATAAAAGATTTTATCTCGCTCAAGATAGTTTTCCCTTAAAACA-AAGATTTTATCTCGCTT-
* * * *
9394 AAGATTGTTTTTCCTT
64 GAGATAG-TTTCCCTC
* * * ** * * * * * **
9410 GAAACAGAAGATTTTATTTCATTCAAGATTGTTTTTCCTTGAAACAAAATATTTTATCTCACTCA
1 GAAATAAAAGATTTTATCTCGCTCAAGATAGTTTTCCCTTAAAAC-AAAGATTTTATCTCGCTTG
* * *
9475 AGATTGTTTTTCCTT
65 AGATAG-TTTCCCTC
* * * * * * * *
9490 GAAACAAAAAGATTTTACCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
1 GAAA-TAAAAGATTTTATCTCGCTCAAGATAGTTTTCCCTTAAAACA-AAGATTTTATCTCGCTT
* ** *
9555 AAGA-ATGTTTTTTCTT
64 GAGATA-G-TTTCCCTC
* * * * * * * **
9571 GAAACATAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCA
1 GAAATAAAAGATTTTATCTCGCTCAAGATAGTTTTCCCTTAAAACA-AAGATTTTATCTCGCTTG
* * *
9636 AGATTGTTTTTCCTT
65 AGATAG-TTTCCCTC
* * * * * **
9651 GAAATAGAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAATAGAAGATTTTATCTCGCTCA
1 GAAATAAAAGATTTTATCTCGCTCAAGATAGTTTTCCCTTAAAACA-AAGATTTTATCTCGCTTG
* * *
9716 AGATTATTTTTCCTT
65 AGA-TAGTTTCCCTC
* * * * * * *
9731 GAAACAGAATATTTTATCTCGCTCAAGATTGTTTTTCGC-TGAAACAGAAGATTTTATCTCGCTC
1 GAAATAAAAGATTTTATCTCGCTCAAGATAG-TTTTCCCTTAAAACA-AAGATTTTATCTCGCTT
* * * *
9795 AAGATTGTTTTTCCTT
64 GAGATAG-TTTCCCTC
* * * *
9811 GAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTAAAACAAAAGATTTTATCTCGCTTG
1 GAAATAAAAGATTTTATCTCGCTCAAGATAGTTTTCCCTTAAAAC-AAAGATTTTATCTCGCTTG
*
9876 ATATAGTTTCCCTC
65 AGATAGTTTCCCTC
** * *
9890 GAAATAAAAGATTTTATCTCGCTTGAGATAG-TTTCCCTTGAAAC-AA-ATTTTGTCTCGCTTGA
1 GAAATAAAAGATTTTATCTCGCTCAAGATAGTTTTCCCTTAAAACAAAGATTTTATCTCGCTTGA
*
9952 GATAGTTTCCCTT
66 GATAGTTTCCCTC
9965 GAAA
1 GAAA
9969 CAAGTTTTGT
Statistics
Matches: 495, Mismatches: 53, Indels: 27
0.86 0.09 0.05
Matches are distributed among these distances:
75 30 0.06
76 2 0.00
78 11 0.02
79 38 0.08
80 336 0.68
81 78 0.16
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (78 bp):
GAAATAAAAGATTTTATCTCGCTCAAGATAGTTTTCCCTTAAAACAAAGATTTTATCTCGCTTGA
GATAGTTTCCCTC
Found at i:10062 original size:36 final size:36
Alignment explanation
Indices: 10008--10122 Score: 106
Period size: 36 Copynumber: 3.2 Consensus size: 36
9998 CTTGAAAATT
*
10008 TTGAGAACA-TTTCCCTTGAAACGAATTTTGTCTCCC
1 TTGAG-ACAGTTTCTCTTGAAACGAATTTTGTCTCCC
*
10044 TTGAGACAGTTTCTCTTGAAACAGAGTTTTGTCTCCC
1 TTGAGACAGTTTCTCTTGAAAC-GAATTTTGTCTCCC
** ** * * * * *
10081 TAAAGATGGTTTTTCTTAAAACCAAATTTGTCTCAC
1 TTGAGACAGTTTCTCTTGAAACGAATTTTGTCTCCC
10117 TTGAGA
1 TTGAGA
10123 TGGTTTTTCT
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
35 3 0.05
36 31 0.49
37 29 0.46
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (36 bp):
TTGAGACAGTTTCTCTTGAAACGAATTTTGTCTCCC
Found at i:10191 original size:28 final size:28
Alignment explanation
Indices: 10145--10252 Score: 148
Period size: 28 Copynumber: 3.8 Consensus size: 28
10135 AAAAACCCTG
10145 GAGACAGTTT-TCCTTTGAAACAAGTTTTT
1 GAGACAGTTTCT-C-TTGAAACAAGTTTTT
*
10174 GAGATAGTTTCTCTTGAAACAAGTTTTT
1 GAGACAGTTTCTCTTGAAACAAGTTTTT
10202 GAGACAGTTTCTCTTGAAACAAGTTTTT
1 GAGACAGTTTCTCTTGAAACAAGTTTTT
*
10230 GAGACAATTT-TCCTTCGAAACAA
1 GAGACAGTTTCT-CTT-GAAACAA
10253 AATTTATCTC
Statistics
Matches: 73, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.01
28 54 0.74
29 17 0.23
30 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.38
Consensus pattern (28 bp):
GAGACAGTTTCTCTTGAAACAAGTTTTT
Found at i:10236 original size:13 final size:13
Alignment explanation
Indices: 10158--10240 Score: 55
Period size: 13 Copynumber: 6.2 Consensus size: 13
10148 ACAGTTTTCC
10158 TTTGAAACAAGTT
1 TTTGAAACAAGTT
* *
10171 TTTGAGA-TAGTTT
1 TTTGAAACAAG-TT
10184 CTCTTGAAACAAGTT
1 -T-TTGAAACAAGTT
*
10199 TTTGAGAC-AGTTT
1 TTTGAAACAAG-TT
10212 CTCTTGAAACAAGTT
1 -T-TTGAAACAAGTT
*
10227 TTTGAGACAA-TT
1 TTTGAAACAAGTT
10239 TT
1 TT
10241 CCTTCGAAAC
Statistics
Matches: 55, Mismatches: 7, Indels: 17
0.70 0.09 0.22
Matches are distributed among these distances:
12 8 0.15
13 24 0.44
14 4 0.07
15 15 0.27
16 4 0.07
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (13 bp):
TTTGAAACAAGTT
Found at i:10360 original size:24 final size:24
Alignment explanation
Indices: 10326--10371 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
10316 TTTATCTCAA
* *
10326 TTGAGATGGTTTTTCTTAAAACCC
1 TTGAGACGGTTTTCCTTAAAACCC
*
10350 TTGAGACGGTTTTCCTTGAAAC
1 TTGAGACGGTTTTCCTTAAAAC
10372 AAAATTTATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTGAGACGGTTTTCCTTAAAACCC
Found at i:10466 original size:120 final size:122
Alignment explanation
Indices: 10228--10467 Score: 360
Period size: 120 Copynumber: 2.0 Consensus size: 122
10218 AAACAAGTTT
*
10228 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGA
1 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTAA
* * * *
10293 GACAGTTTTCCTTTGAAACAAAATTTATCTCAATTGAGATGGTTTTTCTTAAAACCC
66 GACAATTTTCCTTCGAAACAAAATTTATCTCAATTGAGATGGCTTCTCTTAAAACCC
** *
10350 TTGAGACGGTTTTCCTT-GAAACAAAATTTATCTCATTTGAGATGGTTTTTCTTAAAA-CCTTAA
1 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTAA
* *
10413 GACAATTTTCCTTCGAAGCAAAATTTATCTCACTTGAGA-GAGCTTCTCTTAAAAC
66 GACAATTTTCCTTCGAAACAAAATTTATCTCAATTGAGATG-GCTTCTCTTAAAAC
10468 AAGTTTCTTA
Statistics
Matches: 107, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
119 1 0.01
120 52 0.49
121 39 0.36
122 15 0.14
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (122 bp):
TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTAA
GACAATTTTCCTTCGAAACAAAATTTATCTCAATTGAGATGGCTTCTCTTAAAACCC
Found at i:10467 original size:60 final size:61
Alignment explanation
Indices: 10228--10451 Score: 362
Period size: 61 Copynumber: 3.7 Consensus size: 61
10218 AAACAAGTTT
10228 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCC
1 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCC
* * *
10289 TTGAGACAGTTTTCCTTTGAAACAAAATTTATCTCAATTGAGATGGTTTTTCTTAAAACCC
1 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCC
** *
10350 TTGAGACGGTTTTCCTT-GAAACAAAATTTATCTCATTTGAGATGGTTTTTCTTAAAA-CC
1 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCC
* *
10409 TTAAGACAATTTTCCTTCGAAGCAAAATTTATCTCACTTGAGA
1 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGA
10452 GAGCTTCTCT
Statistics
Matches: 152, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
59 16 0.11
60 62 0.41
61 74 0.49
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (61 bp):
TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCC
Found at i:10788 original size:20 final size:20
Alignment explanation
Indices: 10725--10788 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
10715 TCCAGTATAG
*
10725 AGTTTATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* * **
10745 CG-TC-TAACGAGGAAGAAGA
1 AGTTCATAATGA-GAAGAACT
10764 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
10784 TGTTC
1 AGTTC
10789 GACCTCGCAT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
18 5 0.16
19 8 0.26
20 13 0.42
21 5 0.16
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:11061 original size:136 final size:136
Alignment explanation
Indices: 10804--11283 Score: 790
Period size: 136 Copynumber: 3.6 Consensus size: 136
10794 CGCATTAGTG
*
10804 TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
**
10869 AAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACATCTCGCTTGAGGGA
66 AAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGA
10934 TTAACA
131 TTAACA
*
10940 TTTCTAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
*
11005 AAGAGCTTGTTCGACCTATCACTCAATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGA
66 AAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGA
11070 TTAACA
131 TTAACA
11076 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
* * * *
11141 AAGAGCTTGTTTGACTTATCACTCGATTCACGATATTTTGAATCAGTGACGCCTCGCTTGAGGGA
66 AAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGA
*
11206 TTGACA
131 TTAACA
* * * *
11212 TTTCTAATTAAGAGTTCATAATGAGAAGAACTCGTCCTA-A-AGGG-G-A-AAGTTCATAATGAG
1 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
*
11272 AAGAACTTGTTC
66 AAGAGCTTGTTC
11284 CTTTCAAGTC
Statistics
Matches: 326, Mismatches: 18, Indels: 5
0.93 0.05 0.01
Matches are distributed among these distances:
131 24 0.07
132 1 0.00
133 1 0.00
134 4 0.01
135 1 0.00
136 295 0.90
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (136 bp):
TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
AAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGA
TTAACA
Found at i:11458 original size:117 final size:111
Alignment explanation
Indices: 11221--11513 Score: 353
Period size: 117 Copynumber: 2.6 Consensus size: 111
11211 ATTTCTAATT
* *
11221 AAGAGTTCATAATGAGAAGAACTCGTCCTAAAGG--GGAAAGTTCATAATGAGAAGAACTTGTT-
1 AAGAGTTCATAATGAGAAGAACTCATCC-AAAGGAAGAAAAGTTCATAATGAGAAGAACTTGTTC
11283 --CCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
65 AACCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
* *
11328 GAGAGTTCATAATGAGAAGAACTCATCGAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AAGAGTTCATAATGAGAAGAACTCATCCAA--AGGAAGAA-AAGTTCATAATGAGAAGAACTTGT
** * * * *
11393 TCAACCTTGGTTTGATTCCATCACAGAAGGAGGTGGATCAATATTTTCAGTG
63 TCAACC-T--TTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
* *
11445 AAGAGTTCATAATGAGAAGAACTCATCCAACAAGAGAGAAAAAGTTCATAATTAGAAGAACTTGT
1 AAGAGTTCATAATGAGAAGAACTCATCCAA-AGGA-AG-AAAAGTTCATAATGAGAAGAACTTGT
11510 TCAA
63 TCAA
11514 TCCAAAGCTT
Statistics
Matches: 158, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
106 2 0.01
107 25 0.16
108 3 0.02
110 2 0.01
111 25 0.16
114 2 0.01
115 1 0.01
116 3 0.02
117 93 0.59
118 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (111 bp):
AAGAGTTCATAATGAGAAGAACTCATCCAAAGGAAGAAAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
Found at i:33335 original size:149 final size:153
Alignment explanation
Indices: 33166--33471 Score: 530
Period size: 156 Copynumber: 2.0 Consensus size: 153
33156 AAAATTATAA
33166 AAAAATCAAATTAAAATTTGCTCATAGTTGTTTATATCA-TTTTTTAAAGG-AAACA-T-ATAAT
1 AAAAATCAAATTAAAATTTGCTCATAGTTGTTTATATCATTTTTTTAAAGGAAAACATTAATAAT
* *
33227 ATTTTATTTATTGTTTTGGCTCAAAATTTAAACTTGAAATAATTTTAAAAACTCAAACACACCTA
66 ATTTTATTTATTGTTTTGGCTCAAAATTTAAACTTGAAATAATTTTAAAAACTCAAAAACACATA
33292 TATCTTATAAATTTTGAAGCACG
131 TATCTTATAAATTTTGAAGCACG
33315 AAAAATCAAATTAAAATTTGCTCATAGTTGTTTATATCATTTTTTTAAAGGAAAACATTGTCAAT
1 AAAAATCAAATTAAAATTTGCTCATAGTTGTTTATATCATTTTTTTAAAGGAAAACA-T-T-AAT
33380 AATATTTTATTTATTGTTTTGGCTCAAAATTTAAACTTGAAATAATTTTAAAAACTCAAAAACAC
63 AATATTTTATTTATTGTTTTGGCTCAAAATTTAAACTTGAAATAATTTTAAAAACTCAAAAACAC
*
33445 ATATATCTTTTAAATTTTGAAGCACG
128 ATATATCTTATAAATTTTGAAGCACG
33471 A
1 A
33472 TTTTGAAATC
Statistics
Matches: 147, Mismatches: 3, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
149 39 0.27
150 11 0.07
151 5 0.03
154 1 0.01
156 91 0.62
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (153 bp):
AAAAATCAAATTAAAATTTGCTCATAGTTGTTTATATCATTTTTTTAAAGGAAAACATTAATAAT
ATTTTATTTATTGTTTTGGCTCAAAATTTAAACTTGAAATAATTTTAAAAACTCAAAAACACATA
TATCTTATAAATTTTGAAGCACG
Found at i:35384 original size:18 final size:18
Alignment explanation
Indices: 35353--35391 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
35343 TTGACCAACA
* *
35353 CGACCCGTTGACCCGACC
1 CGACCAGTTAACCCGACC
35371 CGACCAGTTAACCCGACC
1 CGACCAGTTAACCCGACC
35389 CGA
1 CGA
35392 TTATAATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.46, G:0.21, T:0.10
Consensus pattern (18 bp):
CGACCAGTTAACCCGACC
Found at i:35438 original size:29 final size:29
Alignment explanation
Indices: 35398--35534 Score: 195
Period size: 29 Copynumber: 4.7 Consensus size: 29
35388 CCGATTATAA
35398 TTTGGTAATTATTTTTAAAACGGTGATAT
1 TTTGGTAATTATTTTTAAAACGGTGATAT
* *
35427 TTTGGTAATTATTGTTAAAACGATGATAT
1 TTTGGTAATTATTTTTAAAACGGTGATAT
* *
35456 TTTAGTAATTATTTTTAAAATGGTGATAT
1 TTTGGTAATTATTTTTAAAACGGTGATAT
*
35485 TTTGAG-AATTATTTTTAAAAAGGTGATAT
1 TTTG-GTAATTATTTTTAAAACGGTGATAT
*
35514 TTTGGTAAATATTTTTTAAAA
1 TTTGGTAATTA-TTTTTAAAA
35535 AATGCTATTT
Statistics
Matches: 96, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
28 1 0.01
29 85 0.89
30 10 0.10
ACGTcount: A:0.35, C:0.01, G:0.15, T:0.48
Consensus pattern (29 bp):
TTTGGTAATTATTTTTAAAACGGTGATAT
Found at i:42336 original size:7 final size:7
Alignment explanation
Indices: 42319--42413 Score: 183
Period size: 7 Copynumber: 13.7 Consensus size: 7
42309 GCTCAATTTC
42319 CCTTC-T
1 CCTTCAT
42325 CCTTCAT
1 CCTTCAT
42332 CCTTCAT
1 CCTTCAT
42339 CCTTCAT
1 CCTTCAT
42346 CCTTCAT
1 CCTTCAT
42353 CCTTCAT
1 CCTTCAT
42360 CCTTCAT
1 CCTTCAT
42367 CCTTCAT
1 CCTTCAT
42374 CCTTCAT
1 CCTTCAT
42381 CCTTCAT
1 CCTTCAT
42388 CCTTCAT
1 CCTTCAT
42395 CCTTCAT
1 CCTTCAT
42402 CCTTCAT
1 CCTTCAT
42409 CCTTC
1 CCTTC
42414 TTTCAAGTCT
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
6 5 0.06
7 83 0.94
ACGTcount: A:0.13, C:0.44, G:0.00, T:0.43
Consensus pattern (7 bp):
CCTTCAT
Found at i:43014 original size:29 final size:29
Alignment explanation
Indices: 42970--43106 Score: 177
Period size: 29 Copynumber: 4.7 Consensus size: 29
42960 GACCCGACCC
42970 GGTGATATTTTGGTAATTATTGTTAAAAT
1 GGTGATATTTTGGTAATTATTGTTAAAAT
*
42999 GGTGATATTTTAGTAATTATTGTTAAAAT
1 GGTGATATTTTGGTAATTATTGTTAAAAT
* * *
43028 GGTGATATTTTAGTAATTATTTTTAAAAC
1 GGTGATATTTTGGTAATTATTGTTAAAAT
* * *
43057 AGTGATATTTTGGGAATTATT-TATAAAAA
1 GGTGATATTTTGGTAATTATTGT-TAAAAT
* *
43086 GGTGCTATTTTGGTAAATATT
1 GGTGATATTTTGGTAATTATT
43107 TTTTTAAAAT
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
28 1 0.01
29 95 0.99
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (29 bp):
GGTGATATTTTGGTAATTATTGTTAAAAT
Found at i:43062 original size:58 final size:58
Alignment explanation
Indices: 42970--43127 Score: 192
Period size: 58 Copynumber: 2.7 Consensus size: 58
42960 GACCCGACCC
* * * *
42970 GGTGATATTTTGGTAATTATTGTTAAAATGGTGATATTTTAGTAATTATTGT-TAAAAT
1 GGTGATATTTTGGTAATTATTTTTAAAATAGTGATATTTTAGGAATTATT-TATAAAAA
* * *
43028 GGTGATATTTTAGTAATTATTTTTAAAACAGTGATATTTTGGGAATTATTTATAAAAA
1 GGTGATATTTTGGTAATTATTTTTAAAATAGTGATATTTTAGGAATTATTTATAAAAA
* * *
43086 GGTGCTATTTTGGTAAATATTTTTTTAAAATAGTGCTATTTT
1 GGTGATATTTTGGT-AAT-TATTTTTAAAATAGTGATATTTT
43128 CATAATATTG
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
57 1 0.01
58 61 0.72
59 3 0.04
60 20 0.24
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (58 bp):
GGTGATATTTTGGTAATTATTTTTAAAATAGTGATATTTTAGGAATTATTTATAAAAA
Found at i:45413 original size:3 final size:3
Alignment explanation
Indices: 45407--45481 Score: 105
Period size: 3 Copynumber: 25.0 Consensus size: 3
45397 TATATGTATT
* * *
45407 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
45455 TAA TAA TAA TTA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
45482 ATAAATTAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:46061 original size:113 final size:114
Alignment explanation
Indices: 45811--46599 Score: 1121
Period size: 113 Copynumber: 7.0 Consensus size: 114
45801 ATAGAATTAT
* *
45811 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * *
45876 ATTATGAAC-TTCTCTGGAAATGATGATCCATCAATTGAT-GAATTCAT
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAG
* *
45923 GTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCCTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
45988 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA-
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAG
* * *
46036 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
46101 ATTATGAACTTTCTCTGGAAAAGCTGATCCATC--ATTATGGA-TTCAA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAG
* * *
46147 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTTTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
46212 ATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA-
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAG
* * *
46260 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
46325 ATTATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGAT-GAATTCAG
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAA-ATGATGGATTTGAG
* * * *
46374 GTAAAAGGTTGAACAAATTCTTCTCTTTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
46439 ATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATAGAATT-AG
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAG
* *
46487 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
46552 ATTATGAACTTTCTCTGGAAATG-TCAATCCATCAAATGATAGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCT-GATCCATCAAATGATGGATTTGA
46600 ATCTTTGCTA
Statistics
Matches: 611, Mismatches: 55, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
110 3 0.00
111 98 0.16
112 71 0.12
113 331 0.54
114 108 0.18
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (114 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAG
Found at i:46216 original size:224 final size:226
Alignment explanation
Indices: 45811--46572 Score: 1246
Period size: 224 Copynumber: 3.4 Consensus size: 226
45801 ATAGAATTAT
* * * *
45811 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
45876 ATTATGAAC-TTCTCTGGAAATGATGATCCATCAATTGATGAATTCATGTAAAAGGTTGAACAAG
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAATTGATGAATTCAAGTAAAAGGTTGAACAAA
* * *
45940 TTCTTCTCATTATGAACTTCTTCTTCCTTCCTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
131 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
46005 GAAAAGCTGATCCATCAAATGATGGATTTGA
196 GAAAAGCTGATCCATCAAATGATGGATTTGA
*
46036 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
46101 ATTATGAACTTTCTCTGGAAAAGCTGATCCATC-ATT-ATGGATTCAAGCAAAAGGTTGAACAAA
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAATTGATGAATTCAAGTAAAAGGTTGAACAAA
*
46164 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTTTCATTATGAACCTTCTCTG
131 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
46229 GAAAAGCTGATCCATCAAATGATGGATTTGA
196 GAAAAGCTGATCCATCAAATGATGGATTTGA
*
46260 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
46325 ATTATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAA
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAA-TTGATGAATTCAAGTAAAAGGTTGAACAA
*
46390 ATTCTTCTCTTTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCT
130 ATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCT
* * *
46455 GGAAAAGCTGATCCATCAAGTGATAGAATT-A
195 GGAAAAGCTGATCCATCAAATGATGGATTTGA
**
46486 GGCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 -GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAGTTCTTC
46550 TCATTATGAACTTTCTCTGGAAA
64 TCATTATGAACTTTCTCTGGAAA
46573 TGTCAATCCA
Statistics
Matches: 503, Mismatches: 28, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
224 211 0.42
225 73 0.15
226 27 0.05
227 192 0.38
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (226 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGATGATCCATCAATTGATGAATTCAAGTAAAAGGTTGAACAAA
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
GAAAAGCTGATCCATCAAATGATGGATTTGA
Found at i:47530 original size:83 final size:83
Alignment explanation
Indices: 47391--47797 Score: 710
Period size: 83 Copynumber: 4.9 Consensus size: 83
47381 TTTCTACTAT
*
47391 TTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
* *
47456 GAAGATGCTATTG-GCAAA
66 GAAGATGCTA-TGAACACA
* *
47474 TTCATCTTTTAAATTCAATGATTGGTTCAGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
47539 GAAGATGCTATGAACACA
66 GAAGATGCTATGAACACA
* *
47557 TTCATCTTCTAAATTTAATGATTGGTTCTGCCAAACCAGATCAAATAACTCAAAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
*
47622 GTAGATGCTATGAACACA
66 GAAGATGCTATGAACACA
*
47640 TTCATCTTCTAAATTCAATGATTTGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
47705 GAAGATGCTATGAACACA
66 GAAGATGCTATGAACACA
47723 TTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCA-ATAACTCAAAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
47787 GAAGATGCTAT
66 GAAGATGCTAT
47798 TGGCAAATTC
Statistics
Matches: 308, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
82 34 0.11
83 274 0.89
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
TTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
GAAGATGCTATGAACACA
Found at i:48953 original size:1 final size:1
Alignment explanation
Indices: 48949--49024 Score: 71
Period size: 1 Copynumber: 76.0 Consensus size: 1
48939 TTTACCCCCC
* * * * * * * *
48949 TTTTTTTTTTTCTTTTTTTTCTTTTTTTTCTTTTTTTCTTTTTCTTTTTCTTTTTTTTCTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
49014 TTTTCTTTTTT
1 TTTTTTTTTTT
49025 CTTCAAGCAT
Statistics
Matches: 57, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:48966 original size:9 final size:9
Alignment explanation
Indices: 48952--49024 Score: 101
Period size: 9 Copynumber: 7.7 Consensus size: 9
48942 ACCCCCCTTT
48952 TTTTTTTTC
1 TTTTTTTTC
48961 TTTTTTTTC
1 TTTTTTTTC
48970 TTTTTTTTC
1 TTTTTTTTC
*
48979 TTTTTTTCTT
1 TTTTTTT-TC
48989 TTTCTTTTTC
1 TTT-TTTTTC
48999 TTTTTTTTC
1 TTTTTTTTC
49008 TTTCTTTTTTC
1 -TT-TTTTTTC
49019 TTTTTT
1 TTTTTT
49025 CTTCAAGCAT
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
9 35 0.60
10 12 0.21
11 11 0.19
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:48973 original size:20 final size:20
Alignment explanation
Indices: 48950--49024 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
48940 TTACCCCCCT
48950 TTTTTTTTTTCTTTTTTTTC
1 TTTTTTTTTTCTTTTTTTTC
48970 --TTTTTTTTC-TTTTTTTC
1 TTTTTTTTTTCTTTTTTTTC
48987 TTTTTCTTTTTCTTTTTTTTC
1 TTTTT-TTTTTCTTTTTTTTC
*
49008 TTTCTTTTTTCTTTTTT
1 TTTTTTTTTTCTTTTTT
49025 CTTCAAGCAT
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
17 8 0.16
18 9 0.18
19 3 0.06
20 18 0.36
21 12 0.24
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (20 bp):
TTTTTTTTTTCTTTTTTTTC
Found at i:48990 original size:38 final size:40
Alignment explanation
Indices: 48948--49024 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 40
48938 CTTTACCCCC
*
48948 CTTTTTTTTTTTCTTTTTTTTC-TT-TTTTTTCTTTTTTT
1 CTTTTTCTTTTTCTTTTTTTTCTTTCTTTTTTCTTTTTTT
48986 CTTTTTCTTTTTCTTTTTTTTCTTTCTTTTTTCTTTTTT
1 CTTTTTCTTTTTCTTTTTTTTCTTTCTTTTTTCTTTTTT
49025 CTTCAAGCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 21 0.58
39 2 0.06
40 13 0.36
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (40 bp):
CTTTTTCTTTTTCTTTTTTTTCTTTCTTTTTTCTTTTTTT
Found at i:48991 original size:32 final size:32
Alignment explanation
Indices: 48948--49023 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 32
48938 CTTTACCCCC
48948 CTTTTTT-TTTTTCTTTTT-TTTCTTTTT-TTT
1 CTTTTTTCTTTTTCTTTTTCTTT-TTTTTCTTT
48978 CTTTTTTTCTTTTTCTTTTTCTTTTTTTTCTTT
1 C-TTTTTTCTTTTTCTTTTTCTTTTTTTTCTTT
49011 CTTTTTTCTTTTT
1 CTTTTTTCTTTTT
49024 TCTTCAAGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
30 1 0.02
31 6 0.14
32 28 0.67
33 7 0.17
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (32 bp):
CTTTTTTCTTTTTCTTTTTCTTTTTTTTCTTT
Found at i:60311 original size:13 final size:15
Alignment explanation
Indices: 60279--60312 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
60269 AAAATATTTA
60279 AAAATATAAACAAGT
1 AAAATATAAACAAGT
60294 AAAAT-TAAACAA-T
1 AAAATATAAACAAGT
60307 AAAATA
1 AAAATA
60313 CAACTAGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.33
14 7 0.39
15 5 0.28
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAATATAAACAAGT
Found at i:61626 original size:3 final size:3
Alignment explanation
Indices: 61620--61694 Score: 87
Period size: 3 Copynumber: 25.0 Consensus size: 3
61610 TATATGTATT
* * * * *
61620 TAA TAA TAA TAA TAA TAA TTA TAA TTA TAA TAA TAT TTA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
61668 TAA TAA TAA TTA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
61695 ATAAATTAAT
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:61649 original size:18 final size:18
Alignment explanation
Indices: 61622--61694 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
61612 TATGTATTTA
*
61622 ATAATAATAATAATAATT
1 ATAATTATAATAATAATT
*
61640 ATAATTATAATAATATTTATA
1 ATAATTATAATAATA---ATT
61661 ATAATTATAATAATAATT
1 ATAATTATAATAATAATT
61679 ATAATTATAATAATAA
1 ATAATTATAATAATAA
61695 ATAAATTAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
18 32 0.65
21 17 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATTATAATAATAATT
Found at i:61704 original size:21 final size:20
Alignment explanation
Indices: 61619--61704 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 20
61609 ATATATGTAT
* *
61619 TTAATAATAATAATAATAAT
1 TTAATTATAATAATAATAAA
*
61639 TATAATTATAATAATATTTATAA
1 T-TAATTATAATAATA-ATA-AA
*
61662 -TAATTATAATAATAAT-TA
1 TTAATTATAATAATAATAAA
61680 -TAATTATAATAATAAATAAA
1 TTAATTATAATAAT-AATAAA
61700 TTAAT
1 TTAAT
61705 ATGGGTAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
18 14 0.26
19 3 0.06
20 3 0.06
21 31 0.57
22 2 0.04
23 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAATTATAATAATAATAAA
Found at i:65625 original size:15 final size:15
Alignment explanation
Indices: 65605--65642 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
65595 AACTTAAGGC
65605 TATTTTCATCATTA-T
1 TATTTTCAT-ATTATT
65620 TATTTTCA-ATTATT
1 TATTTTCATATTATT
65634 TATTTTCAT
1 TATTTTCAT
65643 TCTTTGTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.19
14 9 0.43
15 8 0.38
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTTTCATATTATT
Done.