Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003705.1 Hibiscus syriacus cultivar Beakdansim tig00007924_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: 206937
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:8976 original size:16 final size:17
Alignment explanation
Indices: 8952--8986 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
8942 ATCTTGAAAC
8952 AAATATATT-ATAAATT
1 AAATATATTCATAAATT
*
8968 AAATCTATTCATAAATT
1 AAATATATTCATAAATT
8985 AA
1 AA
8987 GTTGATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATATTCATAAATT
Found at i:9161 original size:19 final size:20
Alignment explanation
Indices: 9130--9168 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
9120 ATATTTATGG
*
9130 TATTTTTACTTAATATTTAA
1 TATTTTTACTTAAAATTTAA
9150 TATTTTTA-TTAAAATTTAA
1 TATTTTTACTTAAAATTTAA
9169 GTACAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTTTACTTAAAATTTAA
Found at i:10144 original size:23 final size:22
Alignment explanation
Indices: 10113--10156 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
10103 ATTTCTATAA
* *
10113 TATTGAAAATAACTTAATTTTAT
1 TATTAAAAAT-ACATAATTTTAT
10136 TATTAAAAATACATAATTTTA
1 TATTAAAAATACATAATTTTA
10157 GCCATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTAAAAATACATAATTTTAT
Found at i:11048 original size:19 final size:20
Alignment explanation
Indices: 11024--11063 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
11014 TCCTAATAAC
11024 TTTCTT-TCCGAAAAAAAAA
1 TTTCTTGTCCGAAAAAAAAA
* *
11043 TTTCTTGTCCTAAAAGAAAA
1 TTTCTTGTCCGAAAAAAAAA
11063 T
1 T
11064 AATAAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (20 bp):
TTTCTTGTCCGAAAAAAAAA
Found at i:11324 original size:18 final size:18
Alignment explanation
Indices: 11294--11337 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
11284 ACAGCAACTG
*
11294 GACGGCGGCTTTTTCGGT
1 GACGGTGGCTTTTTCGGT
11312 GAC-GTGGCTTTTTCGGT
1 GACGGTGGCTTTTTCGGT
11329 GACGGTGGC
1 GACGGTGGC
11338 GGATACTGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.07, C:0.20, G:0.41, T:0.32
Consensus pattern (18 bp):
GACGGTGGCTTTTTCGGT
Found at i:12702 original size:3 final size:3
Alignment explanation
Indices: 12694--12726 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
12684 ACATTATCCG
12694 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12727 ATCTAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:23544 original size:9 final size:9
Alignment explanation
Indices: 23530--23627 Score: 53
Period size: 9 Copynumber: 10.7 Consensus size: 9
23520 CATGAAGATG
23530 AAAAAAGAA
1 AAAAAAGAA
23539 AAAAAATGAA
1 AAAAAA-GAA
23549 AAATGAAA-AA
1 AAA--AAAGAA
23559 TTAAAAAATGAA
1 --AAAAAA-GAA
*
23571 AAAAATG--
1 AAAAAAGAA
23578 AAAAAA-AA
1 AAAAAAGAA
*
23586 AAATAA-AA
1 AAAAAAGAA
*
23594 AAAAATGAA
1 AAAAAAGAA
*
23603 AAAAAACAA
1 AAAAAAGAA
*
23612 AAAAAACAA
1 AAAAAAGAA
23621 AACAAAA
1 AA-AAAA
23628 ACAAATAAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
7 5 0.07
8 11 0.15
9 27 0.38
10 20 0.28
12 8 0.11
ACGTcount: A:0.83, C:0.03, G:0.06, T:0.08
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:23555 original size:24 final size:23
Alignment explanation
Indices: 23527--23615 Score: 92
Period size: 23 Copynumber: 3.7 Consensus size: 23
23517 TTGCATGAAG
23527 ATGAAAAAAGAAAAAAAATGAAAA
1 ATGAAAAAA-AAAAAAAATGAAAA
**
23551 ATG-AAAAATTAAAAAATGAAAAAA
1 ATGAAAAAAAAAAAAAATG--AAAA
*
23575 ATGAAAAAAAAAAATAAA-AAAAA
1 ATGAAAAAAAAAAA-AAATGAAAA
23598 ATGAAAAAAAACAAAAAA
1 ATGAAAAAAAA-AAAAAA
23616 AACAAAACAA
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
22 8 0.15
23 23 0.42
24 13 0.24
25 8 0.15
26 3 0.05
ACGTcount: A:0.81, C:0.01, G:0.08, T:0.10
Consensus pattern (23 bp):
ATGAAAAAAAAAAAAAATGAAAA
Found at i:23564 original size:22 final size:20
Alignment explanation
Indices: 23537--23594 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 20
23527 ATGAAAAAAG
23537 AAAAAAAATGAAAAATGAAA
1 AAAAAAAATGAAAAATGAAA
23557 AATTAAAAAATGAAAAAAATGAAA
1 AA--AAAAAATG--AAAAATGAAA
23581 AAAAAAAAT-AAAAA
1 AAAAAAAATGAAAAA
23595 AAAATGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 5 0.15
20 2 0.06
22 15 0.44
24 12 0.35
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (20 bp):
AAAAAAAATGAAAAATGAAA
Found at i:23572 original size:6 final size:7
Alignment explanation
Indices: 23540--23605 Score: 52
Period size: 7 Copynumber: 9.7 Consensus size: 7
23530 AAAAAAGAAA
23540 AAAAATG
1 AAAAATG
23547 AAAAATG
1 AAAAATG
*
23554 AAAAATTA
1 AAAAA-TG
23562 AAAAATG
1 AAAAATG
23569 AAAAAAATG
1 --AAAAATG
*
23578 AAAAA-A
1 AAAAATG
23584 AAAAAT-
1 AAAAATG
23590 -AAAA--
1 AAAAATG
23594 AAAAATG
1 AAAAATG
23601 AAAAA
1 AAAAA
23606 AAACAAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
5 8 0.16
6 5 0.10
7 23 0.47
8 6 0.12
9 7 0.14
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:23627 original size:20 final size:19
Alignment explanation
Indices: 23580--23637 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
23570 AAAAAATGAA
*
23580 AAAAAAAAATAAAAAAAA-
1 AAAAAAAAACAAAAAAAAC
23598 ATGAAAAAAAACAAAAAAAAC
1 A--AAAAAAAACAAAAAAAAC
23619 AAAACAAAAACAAATAAAA
1 AAAA-AAAAACAAA-AAAA
23638 GGGGGGTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 1 0.03
19 3 0.09
20 25 0.74
21 5 0.15
ACGTcount: A:0.86, C:0.07, G:0.02, T:0.05
Consensus pattern (19 bp):
AAAAAAAAACAAAAAAAAC
Found at i:25032 original size:53 final size:53
Alignment explanation
Indices: 24959--25683 Score: 1289
Period size: 53 Copynumber: 13.7 Consensus size: 53
24949 GCAACAGAAG
24959 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
25012 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
25065 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
25119 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
25172 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
25226 ATTGTTCGAGTTCTACTCCCTGAAGAAAT--AGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
25277 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
25330 ATTGTTCGAGTTCTTACTCCCTGAAG-AA-A-AGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
25381 ATTGTTTGAGTTCTACTCCCTGAAGAAATAGAGAGCAGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
25434 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
25488 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
25541 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* * *
25595 ATTGTTTGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAAGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
25648 ATTGTTGGAGTTCTACTCCCTGAAGAAATAGGGAGC
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGC
25684 AGACACGATT
Statistics
Matches: 650, Mismatches: 12, Indels: 20
0.95 0.02 0.03
Matches are distributed among these distances:
50 12 0.02
51 87 0.13
52 2 0.00
53 329 0.51
54 220 0.34
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (53 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:25144 original size:107 final size:106
Alignment explanation
Indices: 24959--25683 Score: 1289
Period size: 107 Copynumber: 6.8 Consensus size: 106
24949 GCAACAGAAG
24959 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
25024 CTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
66 CTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
25065 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
25130 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
65 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
25172 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
25237 TCTACTCCCTGAAGAAAT--AGAGCGGACCCGTAGGAAGATT
65 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
25277 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
25342 CTTACTCCCTGAAG-AA-A-AGAGCGGACCCGTAGGAAGATT
66 C-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
25381 ATTGTTTGAGTTCTACTCCCTGAAGAAATAGAGAGCAGACCCGTAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
25446 CTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
66 C-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
25488 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
*
25553 CTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
66 C-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* * * *
25595 ATTGTTTGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAAGAAGATTATTGTTGGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
*
25660 CTACTCCCTGAAGAAATAGGGAGC
66 CTACTCCCTGAAGAAATAGAGAGC
25684 AGACACGATT
Statistics
Matches: 600, Mismatches: 13, Indels: 12
0.96 0.02 0.02
Matches are distributed among these distances:
104 154 0.26
105 49 0.08
106 35 0.06
107 362 0.60
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (106 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
CTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:25750 original size:54 final size:55
Alignment explanation
Indices: 25661--25765 Score: 149
Period size: 54 Copynumber: 1.9 Consensus size: 55
25651 GTTGGAGTTC
* *
25661 TACTCCCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTA
1 TACTCCCTGAAGAAATAGAGAGCAGACACGATTGTTGAAGATTGTGCGAGTCTTA
* * * *
25716 TACTCTCTGAAG-CATAGAGAGCAGAGACGTTTGTTGAAGATTGTGCGAGT
1 TACTCCCTGAAGAAATAGAGAGCAGACACGATTGTTGAAGATTGTGCGAGT
25766 TTCATGCATC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
54 33 0.75
55 11 0.25
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (55 bp):
TACTCCCTGAAGAAATAGAGAGCAGACACGATTGTTGAAGATTGTGCGAGTCTTA
Found at i:25780 original size:54 final size:54
Alignment explanation
Indices: 25661--25790 Score: 142
Period size: 54 Copynumber: 2.4 Consensus size: 54
25651 GTTGGAGTTC
* *
25661 TACTCCCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTA
1 TACT-CCTGAAGAAATAGAGAGCAGACACGATTGTTGAAGATTGTGCGAGTCTTA
* * *
25716 TACTCTCTGAAG-CATAGAGAGCAGAGACGTTTGTTGAAGATTGTGCGAGT-TTCA
1 TACTC-CTGAAGAAATAGAGAGCAGACACGATTGTTGAAGATTGTGCGAGTCTT-A
*
25770 TGCATCCTGAA-AAATAG-GAGC
1 TAC-TCCTGAAGAAATAGAGAGC
25791 GAACCCGCTG
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
53 6 0.09
54 46 0.72
55 12 0.19
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (54 bp):
TACTCCTGAAGAAATAGAGAGCAGACACGATTGTTGAAGATTGTGCGAGTCTTA
Found at i:30471 original size:67 final size:67
Alignment explanation
Indices: 30363--30497 Score: 225
Period size: 67 Copynumber: 2.0 Consensus size: 67
30353 GGTTAGAAAC
* *
30363 TCAACCAAGAGACTAAAATAGCTACGAATAAATCTGATTGCATCGACAAACGAACCACAAAAGAG
1 TCAACAAAGAGACTAAAATAGATACGAATAAATCTGATTGCATCGACAAACGAACCACAAAAGAG
30428 AA
66 AA
* * *
30430 TCAACAAAGAGACTAAAATATATACGAATAAATCTGATTGCATCGACAAATGAACCACAAAAGGG
1 TCAACAAAGAGACTAAAATAGATACGAATAAATCTGATTGCATCGACAAACGAACCACAAAAGAG
30495 AA
66 AA
30497 T
1 T
30498 TAAGGTATTG
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.17
Consensus pattern (67 bp):
TCAACAAAGAGACTAAAATAGATACGAATAAATCTGATTGCATCGACAAACGAACCACAAAAGAG
AA
Found at i:39275 original size:21 final size:21
Alignment explanation
Indices: 39251--39386 Score: 143
Period size: 21 Copynumber: 6.6 Consensus size: 21
39241 TATCGTAAAT
*
39251 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
39272 TCGCGTTGCGAT-TTTCCAGT
1 TCGCGTTGCGATAGTTGAAAA
39292 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
39313 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
39334 T-GACGTTGCGAT-TTTCCAGT
1 TCG-CGTTGCGATAGTTGAAAA
39354 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
39375 TCGCGTTGCGAT
1 TCGCGTTGCGAT
39387 TTTCCAGTTC
Statistics
Matches: 91, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
20 29 0.32
21 62 0.68
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:39348 original size:62 final size:62
Alignment explanation
Indices: 39251--39386 Score: 247
Period size: 62 Copynumber: 2.2 Consensus size: 62
39241 TATCGTAAAT
39251 TCGCGTTGCGATAATTGAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
*
39313 TCGCGTTGCGATAGTTGAAAAT-GACGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAATCG-CGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
39375 TCGCGTTGCGAT
1 TCGCGTTGCGAT
39387 TTTCCAGTTC
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
61 1 0.01
62 71 0.99
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (62 bp):
TCGCGTTGCGATAATTGAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
Found at i:39358 original size:41 final size:41
Alignment explanation
Indices: 39313--39409 Score: 169
Period size: 41 Copynumber: 2.4 Consensus size: 41
39303 TAGTTGAAAA
39313 TCGCGTTGCGATAGTTGAAAAT-GACGTTGCGATTTTCCAGT
1 TCGCGTTGCGATAGTTGAAAATCG-CGTTGCGATTTTCCAGT
39354 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
*
39395 TCGCGTTGGGATAGT
1 TCGCGTTGCGATAGT
39410 CTACAGTTGT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
41 53 0.98
42 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.34
Consensus pattern (41 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
Found at i:39443 original size:41 final size:41
Alignment explanation
Indices: 39337--39470 Score: 148
Period size: 41 Copynumber: 3.2 Consensus size: 41
39327 TTGAAAATGA
* * * *
39337 CGTTGCGATTTTCCAGTTCGCGTTGCGATAGT-TGAAAATCG-
1 CGTTGCGATTTTCCAATTC-CGTTGCGATAGTCT-ACAGTTGT
* *
39378 CGTTGCGATTTTCCAGTTCGCGTTGGGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAATTC-CGTTGCGATAGTCTACAGTTGT
39420 CGTTGCGATTTTCCAAATT-CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCC-AATTCCGTTGCGATAGTCTACAGTTGT
*
39461 TGTTGCGATT
1 CGTTGCGATT
39471 GTCTACAGTT
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
41 65 0.78
42 15 0.18
43 3 0.04
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTTCCAATTCCGTTGCGATAGTCTACAGTTGT
Found at i:39492 original size:22 final size:22
Alignment explanation
Indices: 39378--39497 Score: 108
Period size: 22 Copynumber: 5.7 Consensus size: 22
39368 TTGAAAATCG
*
39378 CGTTGCGATT-T-TCCAGTTCG-
1 CGTTGCGATTGTCTACAGTT-GT
* *
39398 CGTTGGGATAGTCTACAGTTGT
1 CGTTGCGATTGTCTACAGTTGT
* **
39420 CGTTGCGATT-T-TCCAAAT-T
1 CGTTGCGATTGTCTACAGTTGT
*
39439 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTGTCTACAGTTGT
*
39461 TGTTGCGATTGTCTACAGTTGT
1 CGTTGCGATTGTCTACAGTTGT
*
39483 CGTTGCGATTTTCTA
1 CGTTGCGATTGTCTA
39498 AATTTGTTGC
Statistics
Matches: 78, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
19 10 0.13
20 13 0.17
21 7 0.09
22 48 0.62
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (22 bp):
CGTTGCGATTGTCTACAGTTGT
Found at i:39508 original size:19 final size:20
Alignment explanation
Indices: 39421--39509 Score: 65
Period size: 22 Copynumber: 4.3 Consensus size: 20
39411 TACAGTTGTC
* * *
39421 GTTGCGATTTTCCA-AATTC
1 GTTGCGATTGTCTACAATTT
* *
39440 GTTGCGATAGTCTACAGTTGTT
1 GTTGCGATTGTCTACA-AT-TT
*
39462 GTTGCGATTGTCTACAGTTGT
1 GTTGCGATTGTCTACAATT-T
*
39483 CGTTGCGATTTTCTA-AATTT
1 -GTTGCGATTGTCTACAATTT
39503 GTTGCGA
1 GTTGCGA
39510 AAATTCGTTG
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
19 18 0.32
20 3 0.05
21 6 0.11
22 29 0.52
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.43
Consensus pattern (20 bp):
GTTGCGATTGTCTACAATTT
Found at i:39613 original size:6 final size:6
Alignment explanation
Indices: 39602--39627 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39592 AGACACGTAT
39602 GACCAC GACCAC GACCAC GACCAC GA
1 GACCAC GACCAC GACCAC GACCAC GA
39628 GACGAGACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.46, G:0.19, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:40167 original size:6 final size:6
Alignment explanation
Indices: 40123--40170 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
40113 TCTCATCTCG
*
40123 GGTCG- GGTCG- GGTCG- GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
40168 GGT
1 GGT
40171 AATACGTGTC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
5 15 0.37
6 26 0.63
ACGTcount: A:0.00, C:0.17, G:0.56, T:0.27
Consensus pattern (6 bp):
GGTCGT
Found at i:40300 original size:22 final size:22
Alignment explanation
Indices: 40275--40324 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
40265 TGGAAAATCG
* *
40275 CAACGACAACTGTAGACTTTCA
1 CAACGACAACCGTAGACTATCA
* *
40297 CAACAACAACCGTAGACTATCG
1 CAACGACAACCGTAGACTATCA
40319 CAACGA
1 CAACGA
40325 ATTTGGAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.30, G:0.14, T:0.16
Consensus pattern (22 bp):
CAACGACAACCGTAGACTATCA
Found at i:40415 original size:21 final size:21
Alignment explanation
Indices: 40352--40415 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
40342 GACATTGTAG
*
40352 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
40373 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
40393 ACTATTGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
40414 AC
1 AC
40416 GCGAATTTGC
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:41487 original size:17 final size:17
Alignment explanation
Indices: 41461--41498 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
41451 TCTATGAAAT
41461 TTTTAAATTTTCT-TATA
1 TTTTAAATTTT-TATATA
*
41478 TTTTAGATTTTTATATA
1 TTTTAAATTTTTATATA
41495 TTTT
1 TTTT
41499 CTATTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTAAATTTTTATATA
Found at i:48347 original size:3 final size:3
Alignment explanation
Indices: 48339--48373 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
48329 TTTTCATCCC
*
48339 ATT ATT ATT ATT ATT ATT ATT ATT -TT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
48374 GTTTTTTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:48382 original size:17 final size:17
Alignment explanation
Indices: 48339--48373 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
48329 TTTTCATCCC
*
48339 ATTATTATTATTATTATT
1 ATTATT-TTATCATTATT
48357 ATTATTTTATCATTATT
1 ATTATTTTATCATTATT
48374 GTTTTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTATTTTATCATTATT
Found at i:58506 original size:37 final size:37
Alignment explanation
Indices: 58452--58570 Score: 161
Period size: 36 Copynumber: 3.2 Consensus size: 37
58442 ATGAGATTGG
* *
58452 AGCAAAGTCAATTTTAAGCCTTCACCGAAAAGGAGTGA
1 AGCAAA-TCAATCTTAAGCCTTCACCGAAAAGTAGTGA
58490 AGCAAATCAATCTTAAGCCTTCACC-AAAGAGTAGTGA
1 AGCAAATCAATCTTAAGCCTTCACCGAAA-AGTAGTGA
* * *
58527 AGTAAA-CCATCTTAAGCCTTCACCGAAGAGTAGTGA
1 AGCAAATCAATCTTAAGCCTTCACCGAAAAGTAGTGA
58563 AGCAAATC
1 AGCAAATC
58571 CATCCATAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
36 33 0.46
37 33 0.46
38 6 0.08
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (37 bp):
AGCAAATCAATCTTAAGCCTTCACCGAAAAGTAGTGA
Found at i:64309 original size:20 final size:22
Alignment explanation
Indices: 64272--64331 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
64262 TTTGATGTAT
* *
64272 AGGGAATCGA-TCCCCCCTTG-
1 AGGGAACCGATTCCCCCTTTGA
*
64292 AGGGAACCGATTCTCCCTTTGA
1 AGGGAACCGATTCCCCCTTTGA
64314 AGGGGAACCGATTCCCCC
1 A-GGGAACCGATTCCCCC
64332 CACAGGGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 9 0.27
21 8 0.24
22 1 0.03
23 15 0.45
ACGTcount: A:0.22, C:0.33, G:0.25, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATTCCCCCTTTGA
Found at i:66662 original size:29 final size:29
Alignment explanation
Indices: 66629--66686 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
66619 TTTTAAATGA
66629 TAAATGGGAGAAGTGTTAAAGTAAGGGGG
1 TAAATGGGAGAAGTGTTAAAGTAAGGGGG
66658 TAAATGGGAGAAGTGTTAAAGTAAGGGGG
1 TAAATGGGAGAAGTGTTAAAGTAAGGGGG
66687 AGTAATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.41, T:0.21
Consensus pattern (29 bp):
TAAATGGGAGAAGTGTTAAAGTAAGGGGG
Found at i:68245 original size:214 final size:213
Alignment explanation
Indices: 67726--68274 Score: 875
Period size: 213 Copynumber: 2.6 Consensus size: 213
67716 TAAATCAACA
* * *
67726 AAGATGAAATTTTTTAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATATGTCCTTCGGG
1 AAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGG
* *
67791 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATACTTCGGGTCATCTATAAGCCTTTAGAGCAA
66 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATTTATAAGCCTTTAGAGCAA
* *
67856 GATGATAAGTTCTTCGGGCGATCCATAAAACCTTCAGGTAGGATGTTCACAAGAATTTGAAAATG
131 GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCAGGTAGGATGTTCACAAGAATTTGAAAATG
67921 AAAAAATGACGTTTTAAG
196 AAAAAATGACGTTTTAAG
* *
67939 AAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTTCTTCGGG
1 AAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGG
*
68004 CCATCAGTAAGTCTTTCGAGCATGATGCTGAAATCCTTCGGGTCATTTATAAGCCTTTAGAGCAA
66 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATTTATAAGCCTTTAGAGCAA
* * *
68069 GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATATTTTCACATGAATTTGAAAA
131 GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCAGGTAGG--ATGTTCACAAGAATTTGAAAA
*
68134 TG-AAAAATGATGTTTTAAG
194 TGAAAAAATGACGTTTTAAG
* * * **
68153 AAGATGGAATTTTTGAAAACGAAGAATGTGATATTCAAAATTTCACAATTTATAAGTCCTTTAGG
1 AAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGG
* * *
68218 CCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTAATTTTTAAGCCTT
66 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATTTATAAGCCTT
68275 CATAAGAGAG
Statistics
Matches: 309, Mismatches: 25, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
213 161 0.52
214 127 0.41
215 21 0.07
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (213 bp):
AAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGG
CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATTTATAAGCCTTTAGAGCAA
GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCAGGTAGGATGTTCACAAGAATTTGAAAATG
AAAAAATGACGTTTTAAG
Found at i:75953 original size:36 final size:37
Alignment explanation
Indices: 75843--75961 Score: 125
Period size: 37 Copynumber: 3.2 Consensus size: 37
75833 AAAGAATTGG
* * *
75843 AGCAAAGTCAATTTTAAGCCTTCACCGAAAAGGAGTGA
1 AGCAAA-TCAATCTTAAGCCTTCACCGAAGAGCAGTGA
* **
75881 AGCAAATCAATCTTAAGCCTTTA-TTAAGGAGCAGTGA
1 AGCAAATCAATCTTAAGCCTTCACCGAA-GAGCAGTGA
* * *
75918 AGTAAA-CCATCTTAAGCCTTCACCGAAGAGTAGTGA
1 AGCAAATCAATCTTAAGCCTTCACCGAAGAGCAGTGA
75954 AGCAAATC
1 AGCAAATC
75962 CGTCCATAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
36 29 0.45
37 30 0.46
38 6 0.09
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (37 bp):
AGCAAATCAATCTTAAGCCTTCACCGAAGAGCAGTGA
Found at i:76156 original size:42 final size:39
Alignment explanation
Indices: 76079--76185 Score: 106
Period size: 42 Copynumber: 2.6 Consensus size: 39
76069 TTCACGATTT
* * * *
76079 ATAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGC-ATCA-TAAGCCTTTAGAGCAAGATG
*
76120 CTTAAATCCTTCGGGTCATCTATAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGG-CATC-ATAAGCCTTTAGAGCAAGATG
76162 ATAAATCCTTCGGGCCATCCATAA
1 ATAAATCCTTCGGG-CAT-CATAA
76186 AATCTTCAGG
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
41 20 0.36
42 33 0.60
43 2 0.04
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (39 bp):
ATAAATCCTTCGGGCATCATAAGCCTTTAGAGCAAGATG
Found at i:76337 original size:216 final size:214
Alignment explanation
Indices: 75964--76563 Score: 954
Period size: 216 Copynumber: 2.8 Consensus size: 214
75954 AGCAAATCCG
* *
75964 TCCATAAAACTTTCGGGTAGGATATTTTCACATGAATTTGAAAATGAAAAAATAATGTTTTAAGA
1 TCCATAAAAC-TTCGGGTAGGATATTTTCACAAGAATTTGAAAATGAAAAAATGATGTTTTAAGA
* *
76029 AGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTCGGGC
65 AGATGGAATTTTTGAAAACGAAGAATGCTATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGC
*
76094 TATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTAGAGCAAG
130 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTAGAGCAAG
76159 ATGATAAATCCTTCGGGCCA
195 ATGATAAATCCTTCGGGCCA
* * **
76179 TCCATAAAATCTTCAGGTAGGATGTTTTCACAAGAATTTGAAAATGAAAAAATGGCGTTTTAAGA
1 TCCATAAAA-CTTCGGGTAGGATATTTTCACAAGAATTTGAAAATGAAAAAATGATGTTTTAAGA
* * *
76244 AGAT-GAATTTTTTTTAAAACTAAGAATGCTATTTTCAAAATTTCACAATTTATAAGTTCTTCGG
65 AGATGGAA--TTTTTGAAAACGAAGAATGCTATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
* *
76308 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTAAGCCTTTAGAGCA
128 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTAGAGCA
*
76373 AGATGATAAGTCCTTCGGGCCA
193 AGATGATAAATCCTTCGGGCCA
*
76395 TCCATAAAACCTTCGGGTAGGATATTTTCACATA-AATTTGAAAATGAAAAAATGATGTTTTAAA
1 TCCATAAAA-CTTCGGGTAGGATATTTTCACA-AGAATTTGAAAATGAAAAAATGATGTTTTAAG
76459 AAGATGGAATTTTTGAAAACGAAGAATG-TGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
64 AAGATGGAATTTTTGAAAACGAAGAATGCT-ATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
* *
76523 GCCATCAATAAGTATTTCGAGCATGATGCTTAAATCCTTCG
128 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCG
76564 AGTAATTTTT
Statistics
Matches: 352, Mismatches: 27, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
214 4 0.01
215 149 0.42
216 195 0.55
217 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (214 bp):
TCCATAAAACTTCGGGTAGGATATTTTCACAAGAATTTGAAAATGAAAAAATGATGTTTTAAGAA
GATGGAATTTTTGAAAACGAAGAATGCTATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCC
ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTAGAGCAAGA
TGATAAATCCTTCGGGCCA
Found at i:84834 original size:18 final size:18
Alignment explanation
Indices: 84813--84861 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
84803 GTTGTTTTTG
84813 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* * *
84831 AAATAAAAGAAAAATATTT
1 AAATAAAA-AATAAGAATT
84850 AAATAAACAAAT
1 AAATAAA-AAAT
84862 TAAATAGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 8 0.32
19 16 0.64
20 1 0.04
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:86678 original size:11 final size:11
Alignment explanation
Indices: 86662--86711 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
86652 AGTTTGCTAA
86662 AAAAATAAAAT
1 AAAAATAAAAT
86673 AAAAATAAAA-
1 AAAAATAAAAT
* *
86683 CAAAATAAAAC
1 AAAAATAAAAT
*
86694 GAAAATAAAAT
1 AAAAATAAAAT
*
86705 GAAAATA
1 AAAAATA
86712 GAAACACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
10 9 0.26
11 26 0.74
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:86689 original size:21 final size:21
Alignment explanation
Indices: 86663--86724 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 21
86653 GTTTGCTAAA
*
86663 AAAATAAAATAAAAATAAAAC
1 AAAATAAAACAAAAATAAAAC
* *
86684 AAAATAAAACGAAAATAAAATG
1 AAAATAAAACAAAAATAAAA-C
86706 AAAATAGAAACACAAAATA
1 AAAATA-AAACA-AAAATA
86725 TAAAGAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.53
22 6 0.18
23 4 0.12
24 6 0.18
ACGTcount: A:0.76, C:0.06, G:0.05, T:0.13
Consensus pattern (21 bp):
AAAATAAAACAAAAATAAAAC
Found at i:86709 original size:6 final size:5
Alignment explanation
Indices: 86663--86711 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
86653 GTTTGCTAAA
* *
86663 AAAAT AAAAT AAAAAT AAAAC AAAAT AAAACG AAAAT AAAAT GAAAAT
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT -AAAAT
86711 A
1 A
86712 GAAACACAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 23 0.62
6 14 0.38
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:91363 original size:19 final size:18
Alignment explanation
Indices: 91344--91392 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
91334 GTTATTTTTA
91344 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* *
91362 AAATAAAAGAAAAATAATT
1 AAATAAAA-AATAAGAATT
91381 AAATAAATAAAT
1 AAATAAA-AAAT
91393 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:91847 original size:65 final size:63
Alignment explanation
Indices: 91730--91937 Score: 208
Period size: 65 Copynumber: 3.2 Consensus size: 63
91720 TATCAAAGTG
* * *
91730 ATGCACCGATGCACCAATCCATGCATCGATGCAC-C-ATGAATTAAATTG-AACATCAAATGCAT
1 ATGCATCGATGCA-CAA-CCATGCATCGATGCACTCGACGAATT---TTGAAACATCGAATGCAT
*
91792 TTC
61 TTA
* *
91795 ATGCATCGATGCACATACCATGCATCGATGCACT-GAGGATTTTATGAAAACATCGAATGCATTT
1 ATGCATCGATGCACA-ACCATGCATCGATGCACTCGACGAATTT-TG-AAACATCGAATGCATTT
91859 A
63 A
* * * * *
91860 ATGCATCGATGCACCAGCCATGCATCGATGCACTCTACTAATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCA-CAACCATGCATCGATGCACTCGACGAATTTTGAAACATCGAATGCATTTA
91924 ATGCATCGATGCAC
1 ATGCATCGATGCAC
91938 TCTTAGTGCA
Statistics
Matches: 123, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 47 0.38
65 65 0.53
66 7 0.06
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCGATGCACTCGACGAATTTTGAAACATCGAATGCATTTA
Found at i:91937 original size:17 final size:19
Alignment explanation
Indices: 91909--91957 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
91899 AATTTTGAAA
91909 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
91927 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
91946 CACCGATGCACT
1 CATCGATGCACT
91958 AAGGGTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:97768 original size:24 final size:24
Alignment explanation
Indices: 97736--97813 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 24
97726 ACACTTAACA
97736 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
97760 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
97782 -TGCACCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
97804 GTGCATCGAT
1 GTGCATCGAT
97814 TAACAGGGCT
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
20 3 0.07
21 11 0.26
22 1 0.02
23 11 0.26
24 16 0.38
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.31
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:99763 original size:14 final size:15
Alignment explanation
Indices: 99738--99766 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
99728 TTGTTTTTTA
99738 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
99753 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
99767 AAATGCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.28, T:0.62
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:100551 original size:64 final size:63
Alignment explanation
Indices: 100430--100638 Score: 192
Period size: 64 Copynumber: 3.3 Consensus size: 63
100420 TTTATCAAAG
* * * * *
100430 TGATGCACCGATGCACCGATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGA
1 TGATGCATCGATGCA-C-AACCATGCATCGATGCACTCAGGATATT---TTGAAAAATCGAATGC
100492 ATT
61 ATT
* *
100495 TCATGCATCGATGCACATACCATGCATCGATGCACTGAGGAT-TTTATGAAAAATCGAATGCATT
1 TGATGCATCGATGCACA-ACCATGCATCGATGCACTCAGGATATTT-TGAAAAATCGAATGCATT
* * * * * * *
100559 TGATACATTGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAAAATCGAATGCATT
100623 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
100639 TCTTAGTGCA
Statistics
Matches: 119, Mismatches: 18, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 91 0.76
65 23 0.19
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAAAATCGAATGCATT
Found at i:100638 original size:17 final size:19
Alignment explanation
Indices: 100610--100658 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
100600 TATTTTGAAA
100610 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
100628 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
100647 CACCGATGCACT
1 CATCGATGCACT
100659 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:100737 original size:29 final size:29
Alignment explanation
Indices: 100695--100762 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
100685 ATTTTACACT
*
100695 GATGCACCGATGCACCATGAGTATGCATC
1 GATGCACTGATGCACCATGAGTATGCATC
* *
100724 GATGTACTGATGCACCATGGGTATGCATC
1 GATGCACTGATGCACCATGAGTATGCATC
100753 GATGCACTGA
1 GATGCACTGA
100763 CGCTCCCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (29 bp):
GATGCACTGATGCACCATGAGTATGCATC
Found at i:108103 original size:74 final size:74
Alignment explanation
Indices: 108018--108315 Score: 224
Period size: 74 Copynumber: 4.0 Consensus size: 74
108008 GTCCCAAAAC
* * ** * *
108018 AGAAAATAGAAATCAAGATGAAGATGTTACCCTCATAAGAGGAACTTGAGTTAACCTTTAAAGAG
1 AGAAAACAGAAAACAAGATGAAGATGTTACCCTCCGAAGAGGAACCTGAGTTAACCTTCAAAGAG
108083 GAACTCAAA
66 GAACTCAAA
* * * ** *
108092 AGAAAACAGAAAACATGATG-AGAATGTTGCCCTCCGAAGAGGATCCCAAGTTAACCTTCAGAGA
1 AGAAAACAGAAAACAAGATGAAG-ATGTTACCCTCCGAAGAGGAACCTGAGTTAACCTTCAAAGA
*** *
108156 TTTACTCAAC
65 GGAACTCAAA
* * * * * * * * *
108166 AGAAATCAGAAGACATGATGGAGATATTATCCTCCGAAGAGGATCCTGAGTTAACCTCCGAAGA-
1 AGAAAACAGAAAACAAGATGAAGATGTTACCCTCCGAAGAGGAACCTGAGTTAACCTTCAAAGAG
108230 GACACTCAAA
66 GA-ACTCAAA
* * * * * * * ** *
108240 CAGAGATCATAAAACAAGATGAGGATGTTACCCTCCTAAAACG-ATTTCGAGTTAACCTTCAAAT
1 -AGAAAACAGAAAACAAGATGAAGATGTTACCCTCCGAAGAGGAACCT-GAGTTAACCTTCAAAG
108304 AGGAACTCAAA
64 AGGAACTCAAA
108315 A
1 A
108316 AGAATTTTAT
Statistics
Matches: 172, Mismatches: 46, Indels: 12
0.75 0.20 0.05
Matches are distributed among these distances:
73 2 0.01
74 114 0.66
75 54 0.31
76 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (74 bp):
AGAAAACAGAAAACAAGATGAAGATGTTACCCTCCGAAGAGGAACCTGAGTTAACCTTCAAAGAG
GAACTCAAA
Found at i:120980 original size:45 final size:45
Alignment explanation
Indices: 120931--121040 Score: 220
Period size: 45 Copynumber: 2.4 Consensus size: 45
120921 ACACGTTGCA
120931 GTTCCAGCAGCTTCCAGCAAACGATGGCAGCCCCTCTACGTCCCC
1 GTTCCAGCAGCTTCCAGCAAACGATGGCAGCCCCTCTACGTCCCC
120976 GTTCCAGCAGCTTCCAGCAAACGATGGCAGCCCCTCTACGTCCCC
1 GTTCCAGCAGCTTCCAGCAAACGATGGCAGCCCCTCTACGTCCCC
121021 GTTCCAGCAGCTTCCAGCAA
1 GTTCCAGCAGCTTCCAGCAA
121041 GCATATCAAC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.21, C:0.41, G:0.20, T:0.18
Consensus pattern (45 bp):
GTTCCAGCAGCTTCCAGCAAACGATGGCAGCCCCTCTACGTCCCC
Found at i:122440 original size:2 final size:2
Alignment explanation
Indices: 122433--122470 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
122423 AATTTTAAGA
122433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
122471 TTTCTTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:124541 original size:6 final size:7
Alignment explanation
Indices: 124507--124547 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
124497 TTTTCGTACA
124507 TGCA-TT
1 TGCATTT
124513 TGCATTT
1 TGCATTT
124520 TGCATCTT
1 TGCAT-TT
124528 TGCATTT
1 TGCATTT
124535 T-CATTT
1 TGCATTT
*
124541 TGTATTT
1 TGCATTT
124548 GTTATTTGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
6 10 0.32
7 14 0.45
8 7 0.23
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:124633 original size:18 final size:19
Alignment explanation
Indices: 124610--124647 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
124600 CACATCTTTG
124610 CATTTGCA-TTTTCATTTT
1 CATTTGCACTTTTCATTTT
124628 CATTTGCATCTTTTCATTTT
1 CATTTGCA-CTTTTCATTTT
124648 TTATGTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.16, C:0.18, G:0.05, T:0.61
Consensus pattern (19 bp):
CATTTGCACTTTTCATTTT
Found at i:127903 original size:8 final size:8
Alignment explanation
Indices: 127885--127917 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
127875 AAAAAAAAGG
127885 AAAGG-AA
1 AAAGGAAA
127892 AAAGGAAA
1 AAAGGAAA
*
127900 AAAGAAAA
1 AAAGGAAA
127908 AAAGGAAA
1 AAAGGAAA
127916 AA
1 AA
127918 TTGAATCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 5 0.22
8 18 0.78
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAGGAAA
Found at i:132202 original size:54 final size:54
Alignment explanation
Indices: 132120--132270 Score: 169
Period size: 54 Copynumber: 2.8 Consensus size: 54
132110 GAAATATATG
* * *
132120 CAGAAACCAC-AGAAAATGATTAATGTGTTGTCAAATGCTTTACGAACATCTGGC
1 CAGAAGCCACAAGAAAA-GATGAATGTGTTGTCAAATGCTTTACGAAAATCTGGC
* * * * *
132174 CAGAAGCCACAAGAAAGGGTGAATGTGTTATCAAAAGCTTTACGAAAATCTGGG
1 CAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATGCTTTACGAAAATCTGGC
* * * * *
132228 CAGAAGCCACGAGAAAATATGAATGTATTGTCACATGTTTTAC
1 CAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATGCTTTAC
132271 AAACCAGTGA
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
54 74 0.94
55 5 0.06
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (54 bp):
CAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATGCTTTACGAAAATCTGGC
Found at i:132668 original size:22 final size:22
Alignment explanation
Indices: 132640--132718 Score: 95
Period size: 22 Copynumber: 3.6 Consensus size: 22
132630 ACATCTACAT
*
132640 TCTTCAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
132662 TCTTCAAAGATGATAGATTTTC
1 TCTTCAAAGATGATAGATTCTC
* * *
132684 TATTCAAATATGATAGTTTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
132706 TTTTCAAATATGA
1 TCTTCAAAGATGA
132719 AAGCTTTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:133267 original size:113 final size:112
Alignment explanation
Indices: 133070--133522 Score: 592
Period size: 113 Copynumber: 4.0 Consensus size: 112
133060 TAGCAAAGAT
* ** **
133070 TCGAATCCATCACTCAATGGATCAACA-TGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCGAATTCATCACTTGATGGATCAGTATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
* * *
133134 AGAAGGAAGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 A-AAAGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
133182 TCGAATTCATCACTTGATGGATCGGTATTGCCAGGTAGAGTTCATAATGAGAATAACTCATCTGA
1 TCGAATTCATCACTTGATGGATCAGTATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
* *
133247 AAAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTAC
66 AAAA-GAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
133295 TCGAATTCATCACTTGATGGATCAGCATTGTCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCGAATTCATCACTTGATGGATCAGTATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
* *
133360 AGAAGAATGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAAAGAA-GAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * * *
133408 TTGAATTCATCACTCGATGGATCAACT-TTTCCAGAGGA-AGTTCATAATAAGAAGAACTCATCT
1 TCGAATTCATCACTTGATGGATC-AGTATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCT
* * *
133471 GAAGATA-AAGAA-AAGTTCATAATGAGAAGAACTTGTTAAACCTTTTGC
64 GAA-AAAGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
133519 TCGA
1 TCGA
133523 CTCTATCGTA
Statistics
Matches: 303, Mismatches: 32, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
111 36 0.12
112 29 0.10
113 234 0.77
114 4 0.01
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (112 bp):
TCGAATTCATCACTTGATGGATCAGTATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
AAAAGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:135112 original size:22 final size:22
Alignment explanation
Indices: 135068--135112 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
135058 ATTTTAGTCA
* *
135068 TTATTTATTTATTTTTATATGT
1 TTATATATTTATTATTATATGT
135090 TTATATATTTAATTATTAT-TGT
1 TTATATATTT-ATTATTATATGT
135112 T
1 T
135113 ATTATTATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (22 bp):
TTATATATTTATTATTATATGT
Found at i:136566 original size:2 final size:2
Alignment explanation
Indices: 136559--136623 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
136549 AAGGCACATC
136559 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
136601 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
136624 TCAACATAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:141837 original size:22 final size:20
Alignment explanation
Indices: 141799--141838 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
141789 TCGGTCAAAA
*
141799 TATAATTTTAAATTTAATCT
1 TATAATTTTAAAATTAATCT
141819 TATAATTGTATAAAATTAAT
1 TATAATT-T-TAAAATTAAT
141839 ATAAAATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 1 0.06
22 9 0.53
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
TATAATTTTAAAATTAATCT
Found at i:143134 original size:2 final size:2
Alignment explanation
Indices: 143127--143156 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
143117 GATGTCTCTG
143127 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
143157 GAAAAGGGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:143420 original size:72 final size:75
Alignment explanation
Indices: 143340--143490 Score: 236
Period size: 77 Copynumber: 2.0 Consensus size: 75
143330 GCACAATCGT
* *
143340 ATGGCAATTAGCATAACACAACAC-CA-CA-TTACCCACATCTACTCTATCAAGGCACCAAATTT
1 ATGGCAATTAGCACAACACAACACACACCACTTACCCACACCTACTCTATCAAGGCACCAAATTT
*
143402 ATAAAATAGA
66 AAAAAATAGA
143412 ATGGCAATTAGCACAACACAACACAACACCACCTTACCCACACCTACTCTATCAAGGCACCAAAT
1 ATGGCAATTAGCACAACACAACAC-ACACCA-CTTACCCACACCTACTCTATCAAGGCACCAAAT
143477 TTAAAAAATAGA
64 TTAAAAAATAGA
143489 AT
1 AT
143491 CATTGCACAC
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
72 23 0.32
74 2 0.03
75 2 0.03
77 44 0.62
ACGTcount: A:0.44, C:0.28, G:0.08, T:0.20
Consensus pattern (75 bp):
ATGGCAATTAGCACAACACAACACACACCACTTACCCACACCTACTCTATCAAGGCACCAAATTT
AAAAAATAGA
Found at i:145182 original size:19 final size:18
Alignment explanation
Indices: 145154--145193 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
145144 GAACAGAATG
*
145154 TTTAAAAGTATCGATACT
1 TTTAAAAGTATCGAAACT
145172 TTTATAAAGTATCGAAACT
1 TTTA-AAAGTATCGAAACT
145191 TTT
1 TTT
145194 GCCTAGGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (18 bp):
TTTAAAAGTATCGAAACT
Found at i:146827 original size:24 final size:24
Alignment explanation
Indices: 146800--146850 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
146790 CAAATCAGTT
*
146800 GTCGCAGTAAGAATGACAGTCGTG
1 GTCGCAGCAAGAATGACAGTCGTG
146824 GTCGCAGCAAGAATGACAGTCGTG
1 GTCGCAGCAAGAATGACAGTCGTG
146848 GTC
1 GTC
146851 ACATCCACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.20
Consensus pattern (24 bp):
GTCGCAGCAAGAATGACAGTCGTG
Found at i:156314 original size:96 final size:97
Alignment explanation
Indices: 156198--156380 Score: 269
Period size: 97 Copynumber: 1.9 Consensus size: 97
156188 GACCCCTTTA
* * **
156198 TTTCGAGATTTGATATTCCCTGAGTAA-AGTGGAACAAATCAAACTCGATTCAATCTTCCCTGTA
1 TTTCAAGATTTGATAATCCCTGAGTAACAGTGGAACAAATCAAACTCGATTCAATCTTCCCTAAA
*
156262 GAATAGTGGAATTAATCAACGTTTCCAGATCT
66 GAATAGTGGAATGAATCAACGTTTCCAGATCT
* ** * *
156294 TTTCAAGATTTGATAATCCCTGAGTAACAGTGGAACAAGTTTACCTCGATTTAATCTTCCCTAAA
1 TTTCAAGATTTGATAATCCCTGAGTAACAGTGGAACAAATCAAACTCGATTCAATCTTCCCTAAA
156359 GAATAGTGGAATGAATCAACGT
66 GAATAGTGGAATGAATCAACGT
156381 CCCTATATCC
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
96 25 0.33
97 51 0.67
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (97 bp):
TTTCAAGATTTGATAATCCCTGAGTAACAGTGGAACAAATCAAACTCGATTCAATCTTCCCTAAA
GAATAGTGGAATGAATCAACGTTTCCAGATCT
Found at i:156440 original size:134 final size:133
Alignment explanation
Indices: 156294--156678 Score: 475
Period size: 134 Copynumber: 2.9 Consensus size: 133
156284 TTCCAGATCT
* * * *
156294 TTTCAAGATTTGATAATCCCTGAGTAACAGTGGAACAAGTTTACCTCGATTTAATCTTCCCTAAA
1 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCCTGAA
* * * * *
156359 GAATAGTGGAATGAATCAACGTCCCTATATCCGATTTTCCCTCAAGAAAAAG-AGGAACATATCC
66 GAACAGTGGAATGAATCAACGTCCC-AGATCTGATTTTCCCTCAAGAAAAAGTA-GAACAAAACC
156423 CTCTC
129 CTCTC
* *
156428 TTTCAAGATTTGATATTCCCTGAGTAACAGCGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAA
1 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCCTGAA
** * * * ** *
156493 GAACAGTGGAAAAAATCAACATTTCCAGATCTGATTCTCCCTCAAGAAGTAGTAGAAGAAAACCC
66 GAACAGTGGAATGAATCAAC-GTCCCAGATCTGATTTTCCCTCAAGAAAAAGTAGAACAAAACCC
156558 TCTC
130 TCTC
** * * * * * *
156562 TTTCAAGATTTGATATTATCTTAGTAATATTAGAACAAGTCAACCTCGATTCAATCTTCCATGAA
1 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCCTGAA
*
156627 GACCAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAAAAG
66 GAACAGTGGAATGAATCAACGT-CCCAGATCTGATTTTCCCTCAAGAAAAAG
156679 CATAACAAGT
Statistics
Matches: 211, Mismatches: 37, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
133 1 0.00
134 206 0.98
135 4 0.02
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.28
Consensus pattern (133 bp):
TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCCTGAA
GAACAGTGGAATGAATCAACGTCCCAGATCTGATTTTCCCTCAAGAAAAAGTAGAACAAAACCCT
CTC
Found at i:156512 original size:231 final size:231
Alignment explanation
Indices: 156107--156524 Score: 563
Period size: 231 Copynumber: 1.8 Consensus size: 231
156097 GCAAATCAAA
* * *
156107 CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACACCCCCATATATGATTTTTCCCTT
1 CTCGATTCAATCTTCCCTAAGTAACAGTGGAATGAATCAACACCCCCATATACGATTTTTCCCTA
* * * *
156172 AGAAAGAAGCGGAACAGACCCCTTTATTTCGAGATTTGATATTCCCTGAGTAAAGTGGAACAAAT
66 AGAAAGAAGAGGAACAGACCCCTCTATTTCAAGATTTGATATTCCCTGAGTAAAGCGGAACAAAT
* * ** *
156237 CAAACTCGATTCAATCTTCCCTGTAGAATAGTGGAATTAATCAACGTTTCCAGATCTTTTCAAGA
131 CAAACTCGATTCAATCTTCCCTGAAGAACAGTGGAAAAAATCAACATTTCCAGATCTTTTCAAGA
156302 TTTGATAATCCCTGAGTAACAGTGGAACAAGTTTAC
196 TTTGATAATCCCTGAGTAACAGTGGAACAAGTTTAC
* * ** * *
156338 CTCGATTTAATCTTCCCTAAAG-AATAGTGGAATGAATCAACGTCCCTATATCCGA-TTTTCCCT
1 CTCGATTCAATCTTCCCT-AAGTAACAGTGGAATGAATCAACACCCCCATATACGATTTTTCCCT
* * *
156401 CAAGAAA-AAGAGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGCGGAACA
65 -AAGAAAGAAGAGGAACAGACCCCTCTATTTCAAGATTTGATATTCCCTGAGTAA-AGCGGAACA
* ***
156465 AGTCTGCCTCGATTCAATCTTCCCTGAAGAACAGTGGAAAAAATCAACATTTCCAGATCT
128 AATCAAACTCGATTCAATCTTCCCTGAAGAACAGTGGAAAAAATCAACATTTCCAGATCT
156525 GATTCTCCCT
Statistics
Matches: 159, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
230 49 0.31
231 108 0.68
232 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (231 bp):
CTCGATTCAATCTTCCCTAAGTAACAGTGGAATGAATCAACACCCCCATATACGATTTTTCCCTA
AGAAAGAAGAGGAACAGACCCCTCTATTTCAAGATTTGATATTCCCTGAGTAAAGCGGAACAAAT
CAAACTCGATTCAATCTTCCCTGAAGAACAGTGGAAAAAATCAACATTTCCAGATCTTTTCAAGA
TTTGATAATCCCTGAGTAACAGTGGAACAAGTTTAC
Found at i:156745 original size:87 final size:87
Alignment explanation
Indices: 156595--156762 Score: 203
Period size: 87 Copynumber: 1.9 Consensus size: 87
156585 GTAATATTAG
* * *
156595 AACAAGTCAACCTCGATTCAATCTTCCATGAAGACCAGTGGAATGAATCAACGTCCCCAGATCTG
1 AACAAGTCAACCTCGATTCAATCTTCCATAAAGAACAGTAGAATGAATCAACGTCCCCAGATCTG
* *
156660 ATTTTCCCTCAAGAAAAAGCAT
66 ATCTACCCTCAAGAAAAAGCAT
** * * * * *
156682 AACAAGTGTACCTCGATTCATTCTTCCCTAAAGAACAGTAGAATGAATCAATGTTTCTC-GATCT
1 AACAAGTCAACCTCGATTCAATCTTCCATAAAGAACAGTAGAATGAATCAACG-TCCCCAGATCT
*
156746 GATCTACCCTGAAGAAA
65 GATCTACCCTCAAGAAA
156763 TAGTGGAGCA
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
87 64 0.96
88 3 0.04
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (87 bp):
AACAAGTCAACCTCGATTCAATCTTCCATAAAGAACAGTAGAATGAATCAACGTCCCCAGATCTG
ATCTACCCTCAAGAAAAAGCAT
Found at i:156914 original size:3 final size:3
Alignment explanation
Indices: 156906--156949 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
156896 CGAAGACCCT
156906 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
156950 TTACATTTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:157253 original size:20 final size:21
Alignment explanation
Indices: 157228--157268 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
157218 ATTGTCGATG
*
157228 AGCCGAGTCACCCCC-ATTTC
1 AGCCGAATCACCCCCTATTTC
157248 AGCCGAATCACCCCCTATTTC
1 AGCCGAATCACCCCCTATTTC
157269 TAATCATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.22, C:0.44, G:0.12, T:0.22
Consensus pattern (21 bp):
AGCCGAATCACCCCCTATTTC
Found at i:157580 original size:18 final size:18
Alignment explanation
Indices: 157530--157584 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
157520 AGAGGATTGA
157530 AACAAAATAGAAAAAAATG
1 AACAAAATAGAAAAAAA-G
*
157549 AACAAGATTA-AAAAAAAG
1 AACAA-AATAGAAAAAAAG
*
157567 AACAAAAAAGAAAAAAAG
1 AACAAAATAGAAAAAAAG
157585 GGAAGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 2 0.06
18 14 0.45
19 12 0.39
20 3 0.10
ACGTcount: A:0.76, C:0.05, G:0.11, T:0.07
Consensus pattern (18 bp):
AACAAAATAGAAAAAAAG
Found at i:165422 original size:3 final size:3
Alignment explanation
Indices: 165416--165591 Score: 58
Period size: 3 Copynumber: 55.3 Consensus size: 3
165406 GTTATTATCC
* * *
165416 TAT TAT TACT TAAT TAT TATT TAA TAT TAT TAT CAT AAT TAT T-T TAT
1 TAT TAT TA-T T-AT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
165463 ATAT TA- TAGT TAT TCT AAT ATATT TAGT TAT TAT TAT ATAT TAG T-T
1 -TAT TAT TA-T TAT TAT TAT -TA-T TA-T TAT TAT TAT -TAT TAT TAT
* * * *
165509 TA- TAT TAT TGT TAT ATATT TACT GAA TAT CAT TAT TAT TAT TAGT TAT
1 TAT TAT TAT TAT TAT -TA-T TA-T TAT TAT TAT TAT TAT TAT TA-T TAT
* *
165557 TAT TACA TAT TAA TAT T-T ATAGT TAT TA- TAT TAT T
1 TAT TA-T TAT TAT TAT TAT -TA-T TAT TAT TAT TAT T
165592 TACTATAGTA
Statistics
Matches: 128, Mismatches: 25, Indels: 40
0.66 0.13 0.21
Matches are distributed among these distances:
2 10 0.08
3 80 0.62
4 34 0.27
5 4 0.03
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:165558 original size:10 final size:9
Alignment explanation
Indices: 165416--165591 Score: 58
Period size: 10 Copynumber: 18.4 Consensus size: 9
165406 GTTATTATCC
165416 TATTATTACT
1 TATTATTA-T
165426 TAATTATTATT
1 T-ATTATTA-T
*
165437 TAATATTAT
1 TATTATTAT
* *
165446 TATCATAAT
1 TATTATTAT
165455 TATT-TTAT
1 TATTATTAT
165463 ATATTA-TAGT
1 -TATTATTA-T
* *
165473 TATTCTAAT
1 TATTATTAT
165482 ATATTTAGTTAT
1 -TA-TTA-TTAT
165494 TATTATATAT
1 TATTAT-TAT
*
165504 TAGT-TTA-
1 TATTATTAT
*
165511 TATTATTGT
1 TATTATTAT
165520 TATATATTTACT
1 TAT-TA-TTA-T
* * *
165532 GAATATCAT
1 TATTATTAT
165541 TATTATTAT
1 TATTATTAT
165550 TAGTTATTAT
1 TA-TTATTAT
* *
165560 TACATATTAA
1 TA-TTATTAT
165570 TATT-TATAGT
1 TATTAT-TA-T
165580 TATTA-TAT
1 TATTATTAT
165588 TATT
1 TATT
165592 TACTATAGTA
Statistics
Matches: 122, Mismatches: 26, Indels: 38
0.66 0.14 0.20
Matches are distributed among these distances:
7 3 0.02
8 13 0.11
9 40 0.33
10 44 0.36
11 17 0.14
12 5 0.04
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.57
Consensus pattern (9 bp):
TATTATTAT
Found at i:169605 original size:31 final size:31
Alignment explanation
Indices: 169570--169631 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
169560 GACCAAATAC
* *
169570 TAGTCAGGGTGCATTCAGATTATGCATAGTA
1 TAGTCAGGGTGCATTCAGATAATGCACAGTA
* *
169601 TAGTCAGGTTGCATTTAGATAATGCACAGTA
1 TAGTCAGGGTGCATTCAGATAATGCACAGTA
169632 CAATCAGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (31 bp):
TAGTCAGGGTGCATTCAGATAATGCACAGTA
Found at i:169639 original size:31 final size:31
Alignment explanation
Indices: 169573--169641 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
169563 CAAATACTAG
* * * * *
169573 TCAGGGTGCATTCAGATTATGCATAGTATAG
1 TCAGGTTGCATTCAGATAATGCACAGTACAA
*
169604 TCAGGTTGCATTTAGATAATGCACAGTACAA
1 TCAGGTTGCATTCAGATAATGCACAGTACAA
169635 TCAGGTT
1 TCAGGTT
169642 TAAAGCGACA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.32
Consensus pattern (31 bp):
TCAGGTTGCATTCAGATAATGCACAGTACAA
Found at i:170563 original size:75 final size:76
Alignment explanation
Indices: 170451--170646 Score: 290
Period size: 75 Copynumber: 2.6 Consensus size: 76
170441 GTTGTACAAG
* * *
170451 GGGGGAATCGGTACCCCCT-TGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG-C
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCC
**
170513 AAAACTGTTTA
66 AAAACCATTTA
* *
170524 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCC
170589 AAAACCATTTA
66 AAAACCATTTA
*
170600 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCA
170647 ATCTGTAATT
Statistics
Matches: 111, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
73 17 0.15
74 7 0.06
75 32 0.29
76 31 0.28
77 24 0.22
ACGTcount: A:0.19, C:0.24, G:0.33, T:0.23
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCC
AAAACCATTTA
Found at i:171276 original size:17 final size:17
Alignment explanation
Indices: 171254--171297 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
171244 GTTCATAAAT
*
171254 CAAAATCCAACAATCCA
1 CAAAATCAAACAATCCA
171271 CAAAATCAAACAATCCA
1 CAAAATCAAACAATCCA
171288 -AAATATCAAA
1 CAAA-ATCAAA
171298 AATGTTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCAAACAATCCA
Found at i:177155 original size:22 final size:21
Alignment explanation
Indices: 177113--177152 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
177103 GAGTTTGTTT
*
177113 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
177134 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
177153 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:179182 original size:75 final size:77
Alignment explanation
Indices: 179073--179271 Score: 298
Period size: 77 Copynumber: 2.6 Consensus size: 77
179063 CCGTTGTACA
* * * *
179073 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTC-GGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCAGG-
*
179136 G-CAAAACTATTT
65 GCCAAAACCATTT
*
179148 A-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCAGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCAGGG
179212 CCAAAACCATTT
66 CCAAAACCATTT
*
179224 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCA
179272 ATCTGTAATT
Statistics
Matches: 113, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
74 17 0.15
75 38 0.34
76 13 0.12
77 45 0.40
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.23
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCAGGG
CCAAAACCATTT
Found at i:184052 original size:58 final size:58
Alignment explanation
Indices: 183984--184184 Score: 203
Period size: 58 Copynumber: 3.5 Consensus size: 58
183974 GGATTATATC
** * *
183984 CCCT-TCCTGACTCTATATAGGATTATATCTCCATCTTGACTCTACATGAAATTGTAT
1 CCCTGTCCTGACTCTGCATGGGATTATATCTCCATCTTGACTCTACATGGAATTGTAT
* *
184041 CCCTGTCCTGACTCTGCATGGGATTATATCT-CAGTATTGACTCTACATGGTATTGTAT
1 CCCTGTCCTGACTCTGCATGGGATTATATCTCCA-TCTTGACTCTACATGGAATTGTAT
* * * * * * * * * *
184099 ACATGTCCCGACTCTGCATGTGATTATATCCCCGTCCTGATTCTACATGGGATTATAT
1 CCCTGTCCTGACTCTGCATGGGATTATATCTCCATCTTGACTCTACATGGAATTGTAT
*
184157 CACC-GTCCT-ACTCTGTATGGGATTATAT
1 C-CCTGTCCTGACTCTGCATGGGATTATAT
184185 TCCCGTCCTG
Statistics
Matches: 118, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
57 23 0.19
58 93 0.79
59 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (58 bp):
CCCTGTCCTGACTCTGCATGGGATTATATCTCCATCTTGACTCTACATGGAATTGTAT
Found at i:184190 original size:28 final size:29
Alignment explanation
Indices: 183961--184194 Score: 145
Period size: 29 Copynumber: 8.1 Consensus size: 29
183951 TGATGCATTT
* * * *
183961 CTGATTCTGTATGGGATTATATCCCCTTC
1 CTGACTCTGCATGGGATTATATTCCCGTC
** * *
183990 CTGACTCTATATAGGATTATA-TCTCCATC
1 CTGACTCTGCATGGGATTATATTC-CCGTC
* * ** *
184019 TTGACTCTACATGAAATTGTA-TCCCTGTC
1 CTGACTCTGCATGGGATTATATTCCC-GTC
* *
184048 CTGACTCTGCATGGGATTATA-TCTCAGTA
1 CTGACTCTGCATGGGATTATATTC-CCGTC
* * * * * **
184077 TTGACTCTACATGGTATTGTATACATGTC
1 CTGACTCTGCATGGGATTATATTCCCGTC
* * *
184106 CCGACTCTGCATGTGATTATATCCCCGTC
1 CTGACTCTGCATGGGATTATATTCCCGTC
* *
184135 CTGATTCTACATGGGATTATA-TCACCGTC
1 CTGACTCTGCATGGGATTATATTC-CCGTC
*
184164 CT-ACTCTGTATGGGATTATATTCCCGTC
1 CTGACTCTGCATGGGATTATATTCCCGTC
184192 CTG
1 CTG
184195 TTTCCGTTTG
Statistics
Matches: 154, Mismatches: 44, Indels: 14
0.73 0.21 0.07
Matches are distributed among these distances:
28 26 0.17
29 126 0.82
30 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (29 bp):
CTGACTCTGCATGGGATTATATTCCCGTC
Found at i:187054 original size:26 final size:27
Alignment explanation
Indices: 187021--187077 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
187011 GGACTTAAAA
**
187021 ATTATTATAAATATTAATTATA-TATT
1 ATTATTATAAATACAAATTATATTATT
*
187047 ATTATTATTAATACAAATTATATTATT
1 ATTATTATAAATACAAATTATATTATT
187074 -TTAT
1 ATTAT
187078 GTAGGCCTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTATTATAAATACAAATTATATTATT
Found at i:189693 original size:35 final size:36
Alignment explanation
Indices: 189633--189706 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 36
189623 TAAATAATCG
189633 AATATTCTTTATCTTTTCTAATGATTTGATAGTTTT
1 AATATTCTTTATCTTTTCTAATGATTTGATAGTTTT
*
189669 AATATTTTTTATC-TTTCTAATGATTTGATAGTTTT
1 AATATTCTTTATCTTTTCTAATGATTTGATAGTTTT
189704 AAT
1 AAT
189707 TAAATCTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 25 0.68
36 12 0.32
ACGTcount: A:0.27, C:0.07, G:0.08, T:0.58
Consensus pattern (36 bp):
AATATTCTTTATCTTTTCTAATGATTTGATAGTTTT
Found at i:195159 original size:29 final size:29
Alignment explanation
Indices: 195054--195151 Score: 117
Period size: 29 Copynumber: 3.3 Consensus size: 29
195044 TGAAAAAATT
*
195054 AAATATTTTATGTACTTATTTTAACAAAA
1 AAATATTTTATGTACTTATTTTGACAAAA
* *
195083 AAATATTTTACGTACTCATTTTGACCAAAA
1 AAATATTTTATGTACTTATTTTGA-CAAAA
* **
195113 AAGTAATTTT-TGTACTTATTTTGATTAAA
1 AAAT-ATTTTATGTACTTATTTTGACAAAA
195142 AAATATTTTA
1 AAATATTTTA
195152 AATACTTAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
28 5 0.09
29 27 0.47
30 20 0.35
31 5 0.09
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (29 bp):
AAATATTTTATGTACTTATTTTGACAAAA
Found at i:198890 original size:18 final size:18
Alignment explanation
Indices: 198867--198909 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
198857 TCGTTGTTAT
198867 TGCATTTTTAGATTTTGC
1 TGCATTTTTAGATTTTGC
198885 TGCATTTTTAGATTTTGC
1 TGCATTTTTAGATTTTGC
*
198903 TACATTT
1 TGCATTT
198910 ATGTTATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.56
Consensus pattern (18 bp):
TGCATTTTTAGATTTTGC
Found at i:198965 original size:20 final size:20
Alignment explanation
Indices: 198940--198980 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
198930 GTTTATTTGG
198940 TATTTGG-TACTTGAATGTTT
1 TATTTGGTTACTTGAAT-TTT
*
198960 TATTTGGTTATTTGAATTTT
1 TATTTGGTTACTTGAATTTT
198980 T
1 T
198981 GTTATTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.20, C:0.02, G:0.17, T:0.61
Consensus pattern (20 bp):
TATTTGGTTACTTGAATTTT
Found at i:199551 original size:20 final size:20
Alignment explanation
Indices: 199522--199594 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
199512 TTTTTGGCTC
199522 AAAGGATCGATCCCCTAGCA
1 AAAGGATCGATCCCCTAGCA
*
199542 AAAGGTTCGATCCCCTAGC-
1 AAAGGATCGATCCCCTAGCA
* * * *
199561 AAATGATCGATCCCTTATACC
1 AAAGGATCGATCCCCTA-GCA
199582 AAAGGATCGATCC
1 AAAGGATCGATCC
199595 TTGGATAACA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.31
20 19 0.42
21 12 0.27
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.21
Consensus pattern (20 bp):
AAAGGATCGATCCCCTAGCA
Found at i:199589 original size:21 final size:20
Alignment explanation
Indices: 199521--199594 Score: 62
Period size: 19 Copynumber: 3.7 Consensus size: 20
199511 ATTTTTGGCT
*
199521 CAAAGGATCGATCCCCTA-GC
1 CAAAGGATCGAT-CCCTATAC
* * * *
199541 AAAAGGTTCGATCCC-CTAG
1 CAAAGGATCGATCCCTATAC
*
199560 CAAATGATCGATCCCTTATAC
1 CAAAGGATCGATCCC-TATAC
199581 CAAAGGATCGATCC
1 CAAAGGATCGATCC
199595 TTGGATAACA
Statistics
Matches: 40, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
19 15 0.38
20 10 0.25
21 15 0.38
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAGGATCGATCCCTATAC
Found at i:201235 original size:20 final size:20
Alignment explanation
Indices: 201212--201271 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
201202 ATTTACATAA
*
201212 AAATTAAATATTTTATAATT
1 AAATTAAATAATTTATAATT
* *
201232 AAA-TAAACAGTTTATAATT
1 AAATTAAATAATTTATAATT
* *
201251 AATTTAAATAATATATAATT
1 AAATTAAATAATTTATAATT
201271 A
1 A
201272 TAAAATATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
AAATTAAATAATTTATAATT
Found at i:201237 original size:26 final size:26
Alignment explanation
Indices: 201189--201238 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
201179 CCGAAATTTT
* *
201189 TTAAAATTTTCTAATTTACATAAAAA
1 TTAAAATTTTATAATTTAAATAAAAA
201215 TTAAATATTTTATAA-TTAAATAAA
1 TTAAA-ATTTTATAATTTAAATAAA
201239 CAGTTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
TTAAAATTTTATAATTTAAATAAAAA
Found at i:201238 original size:19 final size:20
Alignment explanation
Indices: 201216--201271 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
201206 ACATAAAAAT
*
201216 TAAATATTTTATAATTAA-A
1 TAAATAATTTATAATTAATA
* * *
201235 TAAACAGTTTATAATTAATT
1 TAAATAATTTATAATTAATA
*
201255 TAAATAATATATAATTA
1 TAAATAATTTATAATTA
201272 TAAAATATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
TAAATAATTTATAATTAATA
Found at i:201569 original size:184 final size:185
Alignment explanation
Indices: 201218--201593 Score: 587
Period size: 184 Copynumber: 2.0 Consensus size: 185
201208 ATAAAAATTA
* * *
201218 AATATTTTATAATTAAATAAACAGTTTATAATTAATTTAAATAATATATAATTATAAAATATAAA
1 AATATTTTATAATTAAATAAACAATTTACAATTAATTTAAATAATATATAATTATAAAATAAAAA
* *
201283 TTTTATATAAATTTTTTAATTAATTAATATCGATTTAGGTTTAAAAGTTATTGGAACTTAATTTA
66 TTTTATATAAACTTTTTAATTAATTAATATCGATTTAGGTTTAAAAGTTATTGGAACTTAAATTA
* * *
201348 TTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATATTATATTT
131 TTAATTAGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATAAAATATATTT
*
201403 AATATTTTTTAATTCAGAA-AAACAATTTACAATTAATTT-AA-AATATATAATTATAAAATAAA
1 AATATTTTATAATT-A-AATAAACAATTTACAATTAATTTAAATAATATATAATTATAAAATAAA
* *
201465 AATTTTATATAAACTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGACCTTAAAT
64 AATTTTATATAAACTTTTTAATTAATTAATATCGATTTAGGTTTAAAAGTTATTGGAACTTAAAT
* *
201530 TATTAATTATGTTTTAAATGGTTTGGGTTGAGCCCATATGTTATATAAAATATATTT
129 TATTAATTAGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATAAAATATATTT
*
201587 AAAATTT
1 AATATTT
201594 AAAATTTTAT
Statistics
Matches: 175, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
184 139 0.79
185 15 0.09
186 19 0.11
187 2 0.01
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.45
Consensus pattern (185 bp):
AATATTTTATAATTAAATAAACAATTTACAATTAATTTAAATAATATATAATTATAAAATAAAAA
TTTTATATAAACTTTTTAATTAATTAATATCGATTTAGGTTTAAAAGTTATTGGAACTTAAATTA
TTAATTAGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATAAAATATATTT
Done.