Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006488.1 Hibiscus syriacus cultivar Beakdansim tig00015780_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: 55670
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:980 original size:18 final size:17
Alignment explanation
Indices: 957--990 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
947 AACGTAGGAA
957 AAATTCCTCAACTCTCTG
1 AAATT-CTCAACTCTCTG
*
975 AAATTCTTAACTCTCT
1 AAATTCTCAACTCTCT
991 TGGCTGACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.29, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATTCTCAACTCTCTG
Found at i:3801 original size:8 final size:8
Alignment explanation
Indices: 3786--3816 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
3776 TTGTTCTCTT
3786 TCATTTCG
1 TCATTTCG
*
3794 TTATTTCG
1 TCATTTCG
3802 TCATTTCG
1 TCATTTCG
3810 TCATTTC
1 TCATTTC
3817 TTATCCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.13, C:0.23, G:0.10, T:0.55
Consensus pattern (8 bp):
TCATTTCG
Found at i:8468 original size:2 final size:2
Alignment explanation
Indices: 8461--8485 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8451 CTCTTAAAAT
8461 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
8486 CAAATTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10800 original size:2 final size:2
Alignment explanation
Indices: 10793--10853 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
10783 TAAAAACAAC
10793 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
10835 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
10854 GTGGTTCTAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11488 original size:20 final size:20
Alignment explanation
Indices: 11463--11500 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11453 ACCAATATTA
* *
11463 AATTTTGATTATGATTAAAT
1 AATTTTAATTATAATTAAAT
11483 AATTTTAATTATAATTAA
1 AATTTTAATTATAATTAA
11501 TAAAGTCCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
AATTTTAATTATAATTAAAT
Found at i:13292 original size:39 final size:39
Alignment explanation
Indices: 13234--13309 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
13224 GGATTCAAAT
** *
13234 AAGATTATGGTCGTGTTTGTCAAGATTACGAACATAAAC
1 AAGATTATGGTCGCATTTGTCAAGATTACAAACATAAAC
*
13273 AAGATTGTGGTCGCATTTGTCAAGATTACAAACATAA
1 AAGATTATGGTCGCATTTGTCAAGATTACAAACATAA
13310 CGGATGTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (39 bp):
AAGATTATGGTCGCATTTGTCAAGATTACAAACATAAAC
Found at i:16388 original size:61 final size:60
Alignment explanation
Indices: 16323--16445 Score: 133
Period size: 60 Copynumber: 2.0 Consensus size: 60
16313 AGTACGCAAT
** * * *
16323 TGGTCCTCC-GACAATAGGATGTTGTTTTTATTGAGTCCCTTGACTATTA-AAAGTTATAAAA
1 TGGTCC-CCTGACAATAGGACATTG-CTTTATTGAGTCCCTAGACTATTAGAAA-TTACAAAA
* * *
16384 TGGTCCCCTGACTATAGGACATTGCTTTGTTGAGTCTCTAGACTATTAGAAATTACAAAA
1 TGGTCCCCTGACAATAGGACATTGCTTTATTGAGTCCCTAGACTATTAGAAATTACAAAA
16444 TG
1 TG
16446 ACCACTCAAC
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
60 31 0.60
61 21 0.40
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (60 bp):
TGGTCCCCTGACAATAGGACATTGCTTTATTGAGTCCCTAGACTATTAGAAATTACAAAA
Found at i:19858 original size:32 final size:32
Alignment explanation
Indices: 19810--20006 Score: 168
Period size: 32 Copynumber: 6.3 Consensus size: 32
19800 TATAGAATAG
* *
19810 ACACATCGTTCAAACATATCGCGATCATATGC
1 ACACATCATTCAAACATATCACGATCATATGC
* * * *
19842 ACACATCATTCGAACATATCATGATCGTATGA
1 ACACATCATTCAAACATATCACGATCATATGC
* * *
19874 AAACATCGTTCAAACATGTCACGATC--ATGC
1 ACACATCATTCAAACATATCACGATCATATGC
* * *
19904 ATACATCATTCAAACATACCATGATCATATGC
1 ACACATCATTCAAACATATCACGATCATATGC
** * * * *
19936 ACACATCATTTGAACGTATCATGATCGTATGA
1 ACACATCATTCAAACATATCACGATCATATGC
* ** *
19968 AAACATTGTTCAAACTTATCACGATC--ATGC
1 ACACATCATTCAAACATATCACGATCATATGC
19998 ACACATCAT
1 ACACATCAT
20007 ACACCAATTT
Statistics
Matches: 128, Mismatches: 35, Indels: 6
0.76 0.21 0.04
Matches are distributed among these distances:
30 33 0.26
32 95 0.74
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.27
Consensus pattern (32 bp):
ACACATCATTCAAACATATCACGATCATATGC
Found at i:19942 original size:62 final size:63
Alignment explanation
Indices: 19810--19942 Score: 178
Period size: 62 Copynumber: 2.1 Consensus size: 63
19800 TATAGAATAG
* * * *
19810 ACACATCGTTCAAACATATCGCGATCATATGCACACATCATTCGAACATATCATGATCGTATGA
1 ACACATCGTTCAAACATATCACGATCA-ATGCACACATCATTCAAACATACCATGATCATATGA
* * * *
19874 AAACATCGTTCAAACATGTCACGATC-ATGCATACATCATTCAAACATACCATGATCATATGC
1 ACACATCGTTCAAACATATCACGATCAATGCACACATCATTCAAACATACCATGATCATATGA
19936 ACACATC
1 ACACATC
19943 ATTTGAACGT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
62 37 0.62
64 23 0.38
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.26
Consensus pattern (63 bp):
ACACATCGTTCAAACATATCACGATCAATGCACACATCATTCAAACATACCATGATCATATGA
Found at i:19973 original size:94 final size:94
Alignment explanation
Indices: 19810--20006 Score: 304
Period size: 94 Copynumber: 2.1 Consensus size: 94
19800 TATAGAATAG
* * *
19810 ACACATCGTTCAAACATATCGCGATCATATGCACACATCATTCGAACATATCATGATCGTATGAA
1 ACACATCATTCAAACATACCACGATCATATGCACACATCATTCGAACATATCATGATCGTATGAA
*
19875 AACATCGTTCAAACATGTCACGATCATGC
66 AACATCGTTCAAACATATCACGATCATGC
* * * *
19904 ATACATCATTCAAACATACCATGATCATATGCACACATCATTTGAACGTATCATGATCGTATGAA
1 ACACATCATTCAAACATACCACGATCATATGCACACATCATTCGAACATATCATGATCGTATGAA
* *
19969 AACATTGTTCAAACTTATCACGATCATGC
66 AACATCGTTCAAACATATCACGATCATGC
19998 ACACATCAT
1 ACACATCAT
20007 ACACCAATTT
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.27
Consensus pattern (94 bp):
ACACATCATTCAAACATACCACGATCATATGCACACATCATTCGAACATATCATGATCGTATGAA
AACATCGTTCAAACATATCACGATCATGC
Found at i:20702 original size:24 final size:24
Alignment explanation
Indices: 20670--20715 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
20660 TTCATTTGAA
20670 GGTATTTATAAGAGAGATTAGGGC
1 GGTATTTATAAGAGAGATTAGGGC
*
20694 GGTATTTATAAGAGAGGTTAGG
1 GGTATTTATAAGAGAGATTAGG
20716 TGGGCGTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.30
Consensus pattern (24 bp):
GGTATTTATAAGAGAGATTAGGGC
Found at i:21412 original size:3 final size:3
Alignment explanation
Indices: 21404--21447 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
21394 AATTTTAATT
21404 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA T
21448 GTTTATTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:21454 original size:22 final size:22
Alignment explanation
Indices: 21404--21447 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
21394 AATTTTAATT
21404 TTATTA-TTATTATTATTATTA
1 TTATTATTTATTATTATTATTA
21425 TTATTATTTATTATTATTATTA
1 TTATTATTTATTATTATTATTA
21447 T
1 T
21448 GTTTATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATTATTTATTATTATTATTA
Found at i:23529 original size:17 final size:18
Alignment explanation
Indices: 23507--23540 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
23497 AAGTCGATTA
*
23507 TATTTTACTAAT-TAATT
1 TATTTTAATAATGTAATT
23524 TATTTTAATAATGTAAT
1 TATTTTAATAATGTAAT
23541 GTGTGTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TATTTTAATAATGTAATT
Found at i:27504 original size:26 final size:25
Alignment explanation
Indices: 27475--27552 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 25
27465 AATTTTTGAC
27475 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
27501 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
* *
27521 GTTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
27547 ATTCTT
1 ATTCTT
27553 TCCACCTTGA
Statistics
Matches: 38, Mismatches: 8, Indels: 13
0.64 0.14 0.22
Matches are distributed among these distances:
20 10 0.26
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.13
26 13 0.34
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:28198 original size:24 final size:24
Alignment explanation
Indices: 28171--28217 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
28161 AGCGAAGAGA
28171 AAAG-AAAAACAAAGAGAA-AGAAAC
1 AAAGTAAAAA-AAA-AGAAGAGAAAC
28195 AAAGTAAAAAAAAAGAAGAGAAA
1 AAAGTAAAAAAAAAGAAGAGAAA
28218 GAGGACAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 12 0.57
25 5 0.24
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (24 bp):
AAAGTAAAAAAAAAGAAGAGAAAC
Found at i:29407 original size:4 final size:4
Alignment explanation
Indices: 29398--29763 Score: 700
Period size: 4 Copynumber: 92.0 Consensus size: 4
29388 TAGATCGAGA
29398 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
29446 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ATAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
29494 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
29542 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
29590 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
29638 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
29686 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ATAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
29734 ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
29764 GATACATAAA
Statistics
Matches: 356, Mismatches: 4, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
2 2 0.01
4 354 0.99
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:30096 original size:2 final size:2
Alignment explanation
Indices: 30089--30133 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
30079 ATTTTCTTAA
30089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30131 AT A
1 AT A
30134 ATAAATAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30478 original size:35 final size:36
Alignment explanation
Indices: 30439--30534 Score: 108
Period size: 36 Copynumber: 2.7 Consensus size: 36
30429 GTTTCACATT
*
30439 AAACAAA-GTTGATCTCACTTGAGATC-GTTTCTC-AA
1 AAACAAACGTTG-TCTCACTTGAGA-CAATTTCTCTAA
*
30474 AAACAAACGTTGTCTCGCTTGAGACAATTTCTCTAA
1 AAACAAACGTTGTCTCACTTGAGACAATTTCTCTAA
** *
30510 AAACAAATTTTGTCTCATTTGAGAC
1 AAACAAACGTTGTCTCACTTGAGAC
30535 TATATCTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
34 1 0.02
35 24 0.46
36 27 0.52
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (36 bp):
AAACAAACGTTGTCTCACTTGAGACAATTTCTCTAA
Found at i:30523 original size:36 final size:36
Alignment explanation
Indices: 30466--30569 Score: 115
Period size: 36 Copynumber: 3.0 Consensus size: 36
30456 CTTGAGATCG
**
30466 TTTCTC-AAAAACAAACGTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
** *
30501 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* * *
30537 TATCT-T-AAAGCAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
30570 TCATTTTCTC
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
34 22 0.39
35 7 0.12
36 28 0.49
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:30858 original size:29 final size:28
Alignment explanation
Indices: 30820--31064 Score: 171
Period size: 29 Copynumber: 8.5 Consensus size: 28
30810 GTTTCTCTTG
30820 AAAAAATCTTTGAGTTTGTTCCTTTTGA
1 AAAAAATCTTTGAGTTTGTTCCTTTTGA
*
30848 ATAAAAATCTTGGAGTTTGTTCCTTTTGA
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
* *
30877 ATAAATATCTTTGAG-TTGTTTCTTTTG-
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
* * **
30904 -AAAAATCTTTGAGTCTATTTATTTTGA
1 AAAAAATCTTTGAGTTTGTTCCTTTTGA
* *** * *
30931 AACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG-
1 AA-AAA-------ATCT-TTGAGTTTGTTCCTTTTGA
*
30967 AAAAAATCTTTGAGTTTGTTCATTTTGA
1 AAAAAATCTTTGAGTTTGTTCCTTTTGA
*
30995 ATAAAAATCTTGGAGTTTGTTCCTTTTGA
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
* *
31024 ATAAATATCTTTGAG-TTGTTTCTTTTG-
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
31051 -AAAAATCTTTGAGT
1 AAAAAATCTTTGAGT
31065 CTATTTATTT
Statistics
Matches: 174, Mismatches: 27, Indels: 34
0.74 0.11 0.14
Matches are distributed among these distances:
25 24 0.14
26 9 0.05
27 12 0.07
28 28 0.16
29 80 0.46
35 3 0.02
36 5 0.03
37 13 0.07
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (28 bp):
AAAAAATCTTTGAGTTTGTTCCTTTTGA
Found at i:30929 original size:54 final size:54
Alignment explanation
Indices: 30817--31064 Score: 137
Period size: 54 Copynumber: 4.3 Consensus size: 54
30807 ACAGTTTCTC
* * *
30817 TTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTGAAAAAATCTTTGAGTTTGTTCCTTTTG-A-AAAAATCTTGGAGTCTATTCATT
* * *
30873 TTGAATAAATATCTTTGAG-TTGTTTCTTTTG-AAAAATCTTTGAGTCTATTTATT
1 TTGAA-AAA-ATCTTTGAGTTTGTTCCTTTTGAAAAAATCTTGGAGTCTATTCATT
*** * * * * *
30927 TTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCATT
1 TTGAAA-AAA--------TCT-TTGAGTTTGTTCCTTTTGAAAAAATCTTGGAGTCTATTCATT
* * *
30991 TTGAATAAAAATCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGT-TGTTTC-TT
1 TTG-A-AAAAATCTTTGAGTTTGTTCCTTTTGAA-AAA-ATCTTGGAGTCT-ATTCATT
31048 TTG-AAAAATCTTTGAGT
1 TTGAAAAAATCTTTGAGT
31065 CTATTTATTT
Statistics
Matches: 153, Mismatches: 20, Indels: 40
0.72 0.09 0.19
Matches are distributed among these distances:
53 2 0.01
54 38 0.25
56 19 0.12
57 26 0.17
58 22 0.14
61 3 0.02
62 5 0.03
63 9 0.06
64 23 0.15
65 4 0.03
66 2 0.01
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.47
Consensus pattern (54 bp):
TTGAAAAAATCTTTGAGTTTGTTCCTTTTGAAAAAATCTTGGAGTCTATTCATT
Found at i:30965 original size:147 final size:147
Alignment explanation
Indices: 30791--31125 Score: 613
Period size: 147 Copynumber: 2.3 Consensus size: 147
30781 AAAATGATTT
* *
30791 TTTTGTCTCTCCTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAAT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCATTTTGAATAAAAAT
30856 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
66 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
30921 TTTATTTTGAAACAAAG
131 TTTATTTTGAAACAAAG
30938 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCATTTTGAATAAAAAT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCATTTTGAATAAAAAT
31003 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
66 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
31068 TTTATTTTGAAACAAAG
131 TTTATTTTGAAACAAAG
* *
31085 TTTTGTCTCTCTTGAGACA-ATT-TCGTG-AAAAATCTTTGAGT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGT
31126 CTGAAACAAA
Statistics
Matches: 184, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
144 14 0.08
145 4 0.02
146 2 0.01
147 164 0.89
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (147 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCATTTTGAATAAAAAT
CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
TTTATTTTGAAACAAAG
Found at i:31153 original size:52 final size:53
Alignment explanation
Indices: 31075--31178 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
31065 CTATTTATTT
31075 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
31127 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAATCTTTGAG
31179 ATTGTTTCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 36 0.73
54 13 0.27
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:31220 original size:29 final size:30
Alignment explanation
Indices: 31164--31296 Score: 113
Period size: 30 Copynumber: 4.2 Consensus size: 30
31154 CAATTTTGTG
31164 AAAAAAATCTTTGAGATTGTTTCTTTTGAA
1 AAAAAAATCTTTGAGATTGTTTCTTTTGAA
* *
31194 AAAAAAATCTTTGAGTTTGTTTCTTTGGAA
1 AAAAAAATCTTTGAGATTGTTTCTTTTGAA
** * *
31224 ACAAAATTTTGTCTCTCTTAAGATAGTTTCTTTTGAA
1 A-AAAA-----AATCT-TTGAGATTGTTTCTTTTGAA
* * *
31261 ACAAAAATCTTTGAGTTTGTTTCTTTGGAA
1 AAAAAAATCTTTGAGATTGTTTCTTTTGAA
*
31291 ACAAAA
1 AAAAAA
31297 TTTTTTCTCT
Statistics
Matches: 81, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
30 51 0.63
31 7 0.09
36 6 0.07
37 17 0.21
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.42
Consensus pattern (30 bp):
AAAAAAATCTTTGAGATTGTTTCTTTTGAA
Found at i:31253 original size:67 final size:67
Alignment explanation
Indices: 31177--31349 Score: 269
Period size: 67 Copynumber: 2.6 Consensus size: 67
31167 AAAATCTTTG
*
31177 AGATTGTTTCTTTTGAAAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1 AGATAGTTTCTTTTGAAAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
31242 TA
66 TA
* *
31244 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTTTCTCTCT
1 AGATAGTTTCTTTTGAAAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
31309 TA
66 TA
* * * *
31311 AAATAATTTCTTTTG--AAAAAAATCTTTGAATCTGTTTCT
1 AGATAGTTTCTTTTGAAAAAAAAATCTTTGAGTTTGTTTCT
31350 CTTAAAATGA
Statistics
Matches: 98, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
65 21 0.21
67 77 0.79
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (67 bp):
AGATAGTTTCTTTTGAAAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
TA
Found at i:31262 original size:37 final size:37
Alignment explanation
Indices: 31212--31338 Score: 108
Period size: 37 Copynumber: 3.6 Consensus size: 37
31202 CTTTGAGTTT
31212 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* * * * *
31249 GTTTCTTTTGAAACAAAA------ATCT-TTGAGTTT
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* *
31279 GTTTCTTTGGAAACAAAATTTTTTCTCTCTTAAAATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* *
31316 ATTTCTTTTGAAA-AAAATCTTTG
1 GTTTCTTTGGAAACAAAAT-TTTG
31339 AATCTGTTTC
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
30 22 0.32
31 3 0.04
36 8 0.12
37 35 0.51
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (37 bp):
GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
Found at i:31599 original size:120 final size:119
Alignment explanation
Indices: 31449--31673 Score: 269
Period size: 120 Copynumber: 1.9 Consensus size: 119
31439 CTTAACAAAA
* * * *
31449 TCATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTCTCTCTT-GAGACAGTTTCTAATGAAA
1 TCATCTTTGAGTATATTTCTTTAAAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTAATGAAA
31512 AACTAA-CTTTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGATATGAT
64 AA--AATC-TTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATATGAT
* ** **
31569 TCATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAA
1 TCATCTTTGAGTATATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAA
* * *
31634 AATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
66 AATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTC
31674 TCGAGACAAC
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
118 23 0.26
119 19 0.21
120 43 0.48
121 4 0.04
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (119 bp):
TCATCTTTGAGTATATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAA
AATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATATGAT
Found at i:31650 original size:64 final size:63
Alignment explanation
Indices: 31571--31695 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 63
31561 GATATGATTC
* *
31571 ATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAAAAA
* * **
31635 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
31696 CACCAACCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 19 0.35
64 36 0.65
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAA
Found at i:31882 original size:15 final size:15
Alignment explanation
Indices: 31862--31896 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
31852 GTTTCACTTG
31862 AAACATTGTCTCTTA
1 AAACATTGTCTCTTA
*
31877 AAACATTTTCTCTTA
1 AAACATTGTCTCTTA
31892 AAACA
1 AAACA
31897 AGATCATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (15 bp):
AAACATTGTCTCTTA
Found at i:32633 original size:40 final size:40
Alignment explanation
Indices: 32577--32951 Score: 202
Period size: 40 Copynumber: 8.6 Consensus size: 40
32567 ATGGCCAATA
* *
32577 GTCCTCATCTCATAGGAACCGTGTCATCCCCAGACCAGACC
1 GTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAG-CC
* * ** *
32618 -TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCA
1 GTCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAGCC
* *
32660 GTCCTCATCACGTAGGAACCAAGTTATCACCACTCCTAAAGATGGCCAGCC
1 GTCCTCATCACGTAGGAACC--G-TGTCATC-C-CC---AGA---CCAGCC
*
32711 GTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACC
1 GTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAG-CC
* * * **
32752 -TCCTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCC
1 GTCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAGCC
* * *
32794 GTCCTCATCACGTAGGAACTAAGTTATCACCACTCCTAAAGATGACCAGCC
1 GTCCTCATCACGTAGGAAC--CG-TGTCATC-C-CC-----A-GACCAGCC
32845 GTCCTCATCACGTAGGAACCGTGTCATCCCTC-GACCAGACC
1 GTCCTCATCACGTAGGAACCGTGTCATCCC-CAGACCAG-CC
* *
32886 -TCCTCATCACGTAGGAGCCGTGTCA-CCCTTAGATAACCAGCC
1 GTCCTCATCACGTAGGAACCGTGTCATCCC-CAG---ACCAGCC
*
32928 GTCCTCATCATGTAGGAACCGTGT
1 GTCCTCATCACGTAGGAACCGTGT
32952 TATCACCTTT
Statistics
Matches: 260, Mismatches: 36, Indels: 74
0.70 0.10 0.20
Matches are distributed among these distances:
39 4 0.02
40 87 0.33
41 4 0.02
42 5 0.02
43 72 0.28
45 2 0.01
46 13 0.05
47 5 0.02
48 11 0.04
49 2 0.01
51 53 0.20
53 1 0.00
54 1 0.00
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.21
Consensus pattern (40 bp):
GTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGCC
Found at i:32730 original size:51 final size:47
Alignment explanation
Indices: 32609--32949 Score: 182
Period size: 43 Copynumber: 7.6 Consensus size: 47
32599 GTCATCCCCA
* * *
32609 GACCAGACC-TCCTCATCACGTAGGAGCCGTGTCA--A-CC-ATAGAT
1 GACCAG-CCGTCCTCATCACGTAGGAACCGTATCACCACCCTAAAGAT
* *
32652 AACCAGCAGTCCTCATCACGTAGGAACCAAGTTATCACCACTCCTAAAGAT
1 GACCAGCCGTCCTCATCACGTAGGAACC--G-TATCACCAC-CCTAAAGAT
* * *
32703 GGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATC-CCC------T
1 GACCAGCCGTCCTCATCACGTAGGAACCGTATCACCACCCTAAAGAT
* * * *
32743 GACCAGACC-TCCTCATCACGTAAGAGCCGTGTCA--A-CC-ATAGAT
1 GACCAG-CCGTCCTCATCACGTAGGAACCGTATCACCACCCTAAAGAT
* *
32786 AACCAGCCGTCCTCATCACGTAGGAACTAAGTTATCACCACTCCTAAAGAT
1 GACCAGCCGTCCTCATCACGTAGGAAC--CG-TATCACCAC-CCTAAAGAT
* * *
32837 GACCAGCCGTCCTCATCACGTAGGAACCGTGTCA--TCCCT-----C
1 GACCAGCCGTCCTCATCACGTAGGAACCGTATCACCACCCTAAAGAT
* * *
32877 GACCAGACC-TCCTCATCACGTAGGAGCCGTGT---CACCCT-TAGAT
1 GACCAG-CCGTCCTCATCACGTAGGAACCGTATCACCACCCTAAAGAT
* *
32920 AACCAGCCGTCCTCATCATGTAGGAACCGT
1 GACCAGCCGTCCTCATCACGTAGGAACCGT
32950 GTTATCACCT
Statistics
Matches: 236, Mismatches: 30, Indels: 64
0.72 0.09 0.19
Matches are distributed among these distances:
38 2 0.01
39 4 0.02
40 57 0.24
41 4 0.02
42 5 0.02
43 69 0.29
45 5 0.02
46 11 0.05
47 1 0.00
48 11 0.05
49 2 0.01
50 4 0.02
51 61 0.26
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.20
Consensus pattern (47 bp):
GACCAGCCGTCCTCATCACGTAGGAACCGTATCACCACCCTAAAGAT
Found at i:32805 original size:134 final size:134
Alignment explanation
Indices: 32577--32958 Score: 640
Period size: 134 Copynumber: 2.9 Consensus size: 134
32567 ATGGCCAATA
* * *
32577 GTCCTCATCTCATAGGAACCGTGTCATCCCCAGACCAGACCTCCTCATCACGTAGGAGCCGTGTC
1 GTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTC
* *
32642 AACCATAGATAACCAGCAGTCCTCATCACGTAGGAACCAAGTTATCACCACTCCTAAAGATGGCC
66 AACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCAAGTTATCACCACTCCTAAAGATGACC
32707 AGCC
131 AGCC
*
32711 GTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGTAAGAGCCGTGTC
1 GTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTC
*
32776 AACCATAGATAACCAGCCGTCCTCATCACGTAGGAACTAAGTTATCACCACTCCTAAAGATGACC
66 AACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCAAGTTATCACCACTCCTAAAGATGACC
32841 AGCC
131 AGCC
32845 GTCCTCATCACGTAGGAACCGTGTCAT-CCCTCGACCAGACCTCCTCATCACGTAGGAGCCGTGT
1 GTCCTCATCACGTAGGAACCGTGTCATCCCCT-GACCAGACCTCCTCATCACGTAGGAGCCGTGT
* * * **
32909 CACCCTTAGATAACCAGCCGTCCTCATCATGTAGGAACCGTGTTATCACC
65 CAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCAAGTTATCACC
32959 TTTAGATGGC
Statistics
Matches: 233, Mismatches: 14, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
133 4 0.02
134 229 0.98
ACGTcount: A:0.27, C:0.35, G:0.18, T:0.21
Consensus pattern (134 bp):
GTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTC
AACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCAAGTTATCACCACTCCTAAAGATGACC
AGCC
Found at i:33181 original size:3 final size:3
Alignment explanation
Indices: 33173--33216 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
33163 AATTTTAATT
33173 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA T
33217 GTTTATTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:33223 original size:22 final size:22
Alignment explanation
Indices: 33173--33216 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
33163 AATTTTAATT
33173 TTATTA-TTATTATTATTATTA
1 TTATTATTTATTATTATTATTA
33194 TTATTATTTATTATTATTATTA
1 TTATTATTTATTATTATTATTA
33216 T
1 T
33217 GTTTATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATTATTTATTATTATTATTA
Found at i:35286 original size:24 final size:24
Alignment explanation
Indices: 35254--35299 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
35244 TTCATTTGAA
35254 GGTATTTATAAGAGAGATTAGGGC
1 GGTATTTATAAGAGAGATTAGGGC
*
35278 GGTATTTATAAGAGAGGTTAGG
1 GGTATTTATAAGAGAGATTAGG
35300 TGGGCGTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.30
Consensus pattern (24 bp):
GGTATTTATAAGAGAGATTAGGGC
Found at i:46786 original size:15 final size:14
Alignment explanation
Indices: 46759--46787 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
46749 CACTAAACAC
46759 CTAAGGGGGAAAAA
1 CTAAGGGGGAAAAA
46773 CTAAGGGGGAAAAA
1 CTAAGGGGGAAAAA
46787 C
1 C
46788 AGAAATTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.10, G:0.34, T:0.07
Consensus pattern (14 bp):
CTAAGGGGGAAAAA
Found at i:50830 original size:13 final size:13
Alignment explanation
Indices: 50812--50837 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50802 TAGCCCTTAA
50812 ATTCTAGCCTCTG
1 ATTCTAGCCTCTG
50825 ATTCTAGCCTCTG
1 ATTCTAGCCTCTG
50838 TTCATCGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.15, T:0.38
Consensus pattern (13 bp):
ATTCTAGCCTCTG
Found at i:54187 original size:112 final size:109
Alignment explanation
Indices: 53835--54258 Score: 540
Period size: 112 Copynumber: 3.8 Consensus size: 109
53825 CATGGTATAA
* * * *
53835 TTCGTCTAAATCAAAAGAGATAAACATCACAATCATTAATTTTCCGTCTAAATCATAAAGATAAA
1 TTCGTCTAAATCATAAGAGATAAACATCACAATCATCAATTCTCCATCTAAATCAT-AAGATAAA
53900 CCCAACAA-CATCAATTCTCAATCGTCGTCTTATCACGATTATAATTC
65 -CCAACAATCATCAATTCTCAATCGTCGTCTTATCACGATTA-AA-TC
* * *
53947 TTCGTCTAAATTAGAAGAGATAAACATTAACAATCATC-ATTCTCCATCTAAATCATAAGAATAA
1 TTCGTCTAAATCATAAGAGATAAACA-TCACAATCATCAATTCTCCATCTAAATCATAAG-ATAA
54011 CCACCAACAATCATCAATTCTCAATCGTCGTCTTATCACGATT-AATC
64 --ACCAACAATCATCAATTCTCAATCGTCGTCTTATCACGATTAAATC
54058 TTCGTCTAAATCATAAGAGATAAACCATCAACAATCATCAATTCTCCATCTAAATCATAAGTGAT
1 TTCGTCTAAATCATAAGAGATAAA-CATC-ACAATCATCAATTCTCCATCTAAATCATAA--GAT
*
54123 AAACCACCAA-CATC-ATTCTCAATCGTCGTCTTATCACGATTAGACATC
62 AAACCAACAATCATCAATTCTCAATCGTCGTCTTATCACGATTA-A-ATC
*
54171 -TCGTCTAAATCATAAGAGATAAATCCATCA-AATCATCAATTCTCCGTCTAAATCATAAGATAA
1 TTCGTCTAAATCATAAGAGATAAA--CATCACAATCATCAATTCTCCATCTAAATCATAAGATAA
54234 ACCATCAACAATCATC-ATTCTCAAT
64 A-C--CAACAATCATCAATTCTCAAT
54259 TGAATCTGGT
Statistics
Matches: 282, Mismatches: 12, Indels: 35
0.86 0.04 0.11
Matches are distributed among these distances:
109 6 0.02
110 28 0.10
111 59 0.21
112 94 0.33
113 57 0.20
114 37 0.13
115 1 0.00
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (109 bp):
TTCGTCTAAATCATAAGAGATAAACATCACAATCATCAATTCTCCATCTAAATCATAAGATAAAC
CAACAATCATCAATTCTCAATCGTCGTCTTATCACGATTAAATC
Found at i:54245 original size:224 final size:222
Alignment explanation
Indices: 53835--54258 Score: 610
Period size: 224 Copynumber: 1.9 Consensus size: 222
53825 CATGGTATAA
* * *
53835 TTCGTCTAAATCAAAAGAGATAAACATCACAATCATTAATTTTCCGTCTAAATCATAAAGATAAA
1 TTCGTCTAAATCAAAAGAGATAAACATCACAATCATCAATTCTCCATCTAAATCATAAAGATAAA
* *
53900 CCCAACAACATCAATTCTCAATCGTCGTCTTATCACGATTATAATTCTTCGTCTAAATTAGAAGA
66 CCCAACAACATCAATTCTCAATCGTCGTCTTATCACGATTAGAATTCTTCGTCTAAATCAGAAGA
53965 GATAAACATTAACAATCATCATTCTCCATCTAAATCATAAGAATAACCACCAACAATCATCAATT
131 GATAAACATTAACAATCATCATTCTCCATCTAAATCATAAGAATAACCACCAACAATCATC-ATT
54030 CTCAATCGTCGTCTTATCACGATTAATC
195 CTCAATCGTCGTCTTATCACGATTAATC
* *
54058 TTCGTCTAAATCATAAGAGATAAACCATCAACAATCATCAATTCTCCATCTAAATCATAAGTGAT
1 TTCGTCTAAATCAAAAGAGATAAA-CATC-ACAATCATCAATTCTCCATCTAAATCATAA-AGAT
* *
54123 AAA-CCACCAACATC-ATTCTCAATCGTCGTCTTATCACGATTAGACA-TC-TCGTCTAAATCAT
63 AAACCCAACAACATCAATTCTCAATCGTCGTCTTATCACGATTAGA-ATTCTTCGTCTAAATCAG
* * *
54184 AAGAGATAAATCCA-TCA-AATCATCAATTCTCCGTCTAAATCATAAG-ATAAACCATCAACAAT
127 AAGAGATAAA--CATTAACAATCATC-ATTCTCCATCTAAATCATAAGAAT-AACCACCAACAAT
54246 CATCATTCTCAAT
188 CATCATTCTCAAT
54259 TGAATCTGGT
Statistics
Matches: 181, Mismatches: 12, Indels: 16
0.87 0.06 0.08
Matches are distributed among these distances:
223 62 0.34
224 73 0.40
225 40 0.22
226 6 0.03
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (222 bp):
TTCGTCTAAATCAAAAGAGATAAACATCACAATCATCAATTCTCCATCTAAATCATAAAGATAAA
CCCAACAACATCAATTCTCAATCGTCGTCTTATCACGATTAGAATTCTTCGTCTAAATCAGAAGA
GATAAACATTAACAATCATCATTCTCCATCTAAATCATAAGAATAACCACCAACAATCATCATTC
TCAATCGTCGTCTTATCACGATTAATC
Found at i:54254 original size:41 final size:43
Alignment explanation
Indices: 54172--54255 Score: 122
Period size: 41 Copynumber: 2.0 Consensus size: 43
54162 TTAGACATCT
54172 CGTCTAAATCATAAGAGATAAATCCATCAAATCATCAATTCTC
1 CGTCTAAATCATAAGAGATAAATCCATCAAATCATCAATTCTC
54215 CGTCTAAATCAT-A-AGATAAA-CCATCAACAATCATC-ATTCTC
1 CGTCTAAATCATAAGAGATAAATCCATC-A-AATCATCAATTCTC
54256 AATTGAATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
40 5 0.13
41 14 0.36
42 8 0.21
43 12 0.31
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (43 bp):
CGTCTAAATCATAAGAGATAAATCCATCAAATCATCAATTCTC
Done.