Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001037.1 Hibiscus syriacus cultivar Beakdansim tig00002061_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: 99515
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1461 original size:13 final size:12
Alignment explanation
Indices: 1424--1461 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
1414 GCAAAGATAG
1424 AGAAAAAAACAA
1 AGAAAAAAACAA
*
1436 AGAAAAAATCAA
1 AGAAAAAAACAA
1448 AGAAAAAGAACAA
1 AGAAAAA-AACAA
1461 A
1 A
1462 AAGAAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.79, C:0.08, G:0.11, T:0.03
Consensus pattern (12 bp):
AGAAAAAAACAA
Found at i:2829 original size:30 final size:30
Alignment explanation
Indices: 2784--3026 Score: 138
Period size: 30 Copynumber: 7.9 Consensus size: 30
2774 ATATAAATCA
2784 TCTTTGAGT-TGTTTCTCTTGAAACAAAAG
1 TCTTTGAGTCTGTTTCTCTTGAAACAAAAG
* * ***
2813 TCTTAGAGTCTGTTTCTTTTGAAACAAGTT
1 TCTTTGAGTCTGTTTCTCTTGAAACAAAAG
* ** * *
2843 TCTCTTGAGACAATTTCTTTTGAAA-AAAAA
1 TCT-TTGAGTCTGTTTCTCTTGAAACAAAAG
* * *
2873 TCTTTGAATCTGCTTCT-TTGGAAACAAAGTTTTG
1 TCTTTGAGTCTGTTTCTCTT-GAAACAAA----AG
* * * **
2907 TCTCTCTTGAGACAGTTTCTATTGAAGGAAAA-
1 --TCT-TTGAGTCTGTTTCTCTTGAAACAAAAG
* *
2939 TCTTTAAGTCTGTTTCTCTTGAAACAAATG
1 TCTTTGAGTCTGTTTCTCTTGAAACAAAAG
2969 TCTTTGAGTCTGTTTCTCTTGAAACAAACA-
1 TCTTTGAGTCTGTTTCTCTTGAAACAAA-AG
* * *
2999 TCTTTAAGATC-GTTTCCCTTAAAACAAA
1 TCTTTGAG-TCTGTTTCTCTTGAAACAAA
3027 TTTTGTCTCT
Statistics
Matches: 161, Mismatches: 38, Indels: 29
0.71 0.17 0.13
Matches are distributed among these distances:
28 2 0.01
29 40 0.25
30 79 0.49
31 19 0.12
36 3 0.02
37 16 0.10
38 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.40
Consensus pattern (30 bp):
TCTTTGAGTCTGTTTCTCTTGAAACAAAAG
Found at i:2865 original size:15 final size:16
Alignment explanation
Indices: 2824--2867 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
2814 CTTAGAGTCT
2824 GTTTCTTTTGAAACAA
1 GTTTCTTTTGAAACAA
* *
2840 GTTTCTCTTGAGACAA
1 GTTTCTTTTGAAACAA
2856 -TTTCTTTTGAAA
1 GTTTCTTTTGAAA
2868 AAAAATCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (16 bp):
GTTTCTTTTGAAACAA
Found at i:2891 original size:60 final size:63
Alignment explanation
Indices: 2795--2965 Score: 170
Period size: 66 Copynumber: 2.7 Consensus size: 63
2785 CTTTGAGTTG
* * * *
2795 TTTCTCTTGAAACAAAAGTCTTAGAGTCTGTTTCTTTTGAAACAAG-T-T-TCTCTTGAGACAA
1 TTTCTATTGAAA-AAAAATCTTTGAATCTGTTTCTTTTGAAACAAGTTGTCTCTCTTGAGACAA
* * *
2856 TTTCTTTTGAAAAAAAATCTTTGAATCTGCTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACA
1 TTTCTATTGAAAAAAAATCTTTGAATCTGTTTCTTTTGAAAC-AAG--TTGTCTCTCTTGAGACA
*
2921 G
63 A
** *
2922 TTTCTATTGAAGGAAAATCTTT-AAGTCTGTTTCTCTTGAAACAA
1 TTTCTATTGAAAAAAAATCTTTGAA-TCTGTTTCTTTTGAAACAA
2966 ATGTCTTTGA
Statistics
Matches: 90, Mismatches: 13, Indels: 10
0.80 0.12 0.09
Matches are distributed among these distances:
60 25 0.28
61 14 0.16
64 1 0.01
65 5 0.06
66 45 0.50
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (63 bp):
TTTCTATTGAAAAAAAATCTTTGAATCTGTTTCTTTTGAAACAAGTTGTCTCTCTTGAGACAA
Found at i:2926 original size:66 final size:66
Alignment explanation
Indices: 2843--2966 Score: 171
Period size: 66 Copynumber: 1.9 Consensus size: 66
2833 GAAACAAGTT
*
2843 TCTCTTGAGACAATTTCTTTTGAAAAAAAATCTTTGAA-TCTGCTTCT-TTGGAAACAAAGTTTT
1 TCTCTTGAGACAATTTCTATTGAAAAAAAATCTTT-AAGTCTGCTTCTCTT-GAAACAAAGTTTT
2906 GTC
64 GTC
* ** *
2909 TCTCTTGAGACAGTTTCTATTGAAGGAAAATCTTTAAGTCTGTTTCTCTTGAAACAAA
1 TCTCTTGAGACAATTTCTATTGAAAAAAAATCTTTAAGTCTGCTTCTCTTGAAACAAA
2967 TGTCTTTGAG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
65 2 0.04
66 47 0.92
67 2 0.04
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (66 bp):
TCTCTTGAGACAATTTCTATTGAAAAAAAATCTTTAAGTCTGCTTCTCTTGAAACAAAGTTTTGT
C
Found at i:12306 original size:40 final size:40
Alignment explanation
Indices: 12262--12366 Score: 147
Period size: 40 Copynumber: 2.6 Consensus size: 40
12252 ACTCAACATG
* * * *
12262 TCTTCATCGCGTAGGAACCGTGTCATTCTCCGACCAGATC
1 TCTTCATCACGTAGGAACCGTGTCATCCACCGACCAGACC
*
12302 TCTTCATCACGTAGGAACTGTGTCATCCACCGACCAGACC
1 TCTTCATCACGTAGGAACCGTGTCATCCACCGACCAGACC
* *
12342 TTTTCATCACGTAGGAGCCGTGTCA
1 TCTTCATCACGTAGGAACCGTGTCA
12367 CCCCTAGATA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (40 bp):
TCTTCATCACGTAGGAACCGTGTCATCCACCGACCAGACC
Found at i:12397 original size:43 final size:43
Alignment explanation
Indices: 12345--12450 Score: 149
Period size: 43 Copynumber: 2.5 Consensus size: 43
12335 CCAGACCTTT
* *
12345 TCATCACGTAGGAGCCGTGTCACCCCTAGATAACTAGTCGTCC
1 TCATCACGTAGGAGCCGTGTCAACCCTAGATAACCAGTCGTCC
* * *
12388 TCATCACGTAGGAGCCATGCCAACCTTAGATAACCAGTCGTCC
1 TCATCACGTAGGAGCCGTGTCAACCCTAGATAACCAGTCGTCC
* *
12431 TCATCGCGTAGGAACCGTGT
1 TCATCACGTAGGAGCCGTGT
12451 TATCACCCTT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.23
Consensus pattern (43 bp):
TCATCACGTAGGAGCCGTGTCAACCCTAGATAACCAGTCGTCC
Found at i:12751 original size:3 final size:3
Alignment explanation
Indices: 12743--12803 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
12733 TCAAAAAATA
12743 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12791 TAT TA- TAT TAT TA
1 TAT TAT TAT TAT TA
12804 CATGTTTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:13315 original size:18 final size:18
Alignment explanation
Indices: 13292--13330 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
13282 AACCACAAAT
13292 CCACCATCAATCACCAAG
1 CCACCATCAATCACCAAG
13310 CCACCATCAATCACCAAG
1 CCACCATCAATCACCAAG
13328 CCA
1 CCA
13331 TTAGAGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.46, G:0.05, T:0.10
Consensus pattern (18 bp):
CCACCATCAATCACCAAG
Found at i:14329 original size:30 final size:30
Alignment explanation
Indices: 14295--14490 Score: 189
Period size: 30 Copynumber: 6.6 Consensus size: 30
14285 GTAATTAATG
* **
14295 TTTAGCCCTTTTAGTTTCTGTTAATACCAT
1 TTTAGCCCTTTAAGTTTCTGTTTTTACCAT
* * *
14325 TTTAGCCCCTTAAGTTTATGTTTTTACTAT
1 TTTAGCCCTTTAAGTTTCTGTTTTTACCAT
* * *
14355 TTTGGCCCTTTAAATTTCTG-TTTTGCCAT
1 TTTAGCCCTTTAAGTTTCTGTTTTTACCAT
** * * **
14384 TTTAATCCTTTAAATTTCAGTTTTTATTAT
1 TTTAGCCCTTTAAGTTTCTGTTTTTACCAT
*
14414 TTTAGCCCTTTAAGTTTCT-TTTTTTCCAT
1 TTTAGCCCTTTAAGTTTCTGTTTTTACCAT
** * *
14443 TTTATTCCTTTAAGTTTTTGTTTATACCAT
1 TTTAGCCCTTTAAGTTTCTGTTTTTACCAT
*
14473 TTTAGTCCTTTAAGTTTC
1 TTTAGCCCTTTAAGTTTC
14491 ATTTTTTTTG
Statistics
Matches: 131, Mismatches: 33, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
29 46 0.35
30 85 0.65
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.56
Consensus pattern (30 bp):
TTTAGCCCTTTAAGTTTCTGTTTTTACCAT
Found at i:14496 original size:59 final size:58
Alignment explanation
Indices: 14295--14497 Score: 201
Period size: 59 Copynumber: 3.4 Consensus size: 58
14285 GTAATTAATG
* * * ** *
14295 TTTAGCCCTTTTAGTTTCTGTTAATACCATTTTAGCCCCTTAAGTTTATGTTTTTACTAT
1 TTTAGCCCTTTAAGTTTCT-TT-TTTCCATTTTAATCCTTTAAGTTTATGTTTTTACTAT
* * * * *
14355 TTTGGCCCTTTAAATTTCTGTTTTGCCATTTTAATCCTTTAAATTTCA-GTTTTTATTAT
1 TTTAGCCCTTTAAGTTTCT-TTTTTCCATTTTAATCCTTTAAGTTT-ATGTTTTTACTAT
* * * *
14414 TTTAGCCCTTTAAGTTTCTTTTTTTCCATTTTATTCCTTTAAGTTTTTGTTTATACCAT
1 TTTAGCCCTTTAAGTTTC-TTTTTTCCATTTTAATCCTTTAAGTTTATGTTTTTACTAT
*
14473 TTTAGTCCTTTAAGTTTCATTTTTT
1 TTTAGCCCTTTAAGTTTC-TTTTTT
14498 TTGCTATTTT
Statistics
Matches: 119, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
59 98 0.82
60 21 0.18
ACGTcount: A:0.19, C:0.16, G:0.08, T:0.57
Consensus pattern (58 bp):
TTTAGCCCTTTAAGTTTCTTTTTTCCATTTTAATCCTTTAAGTTTATGTTTTTACTAT
Found at i:20094 original size:24 final size:20
Alignment explanation
Indices: 20067--20124 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
20057 GCATGGGTAG
20067 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
20091 TGCATCCATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
20111 TGTATCGATGCACT
1 TGCATCGATGCACT
20125 TTAAGTGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:20625 original size:21 final size:22
Alignment explanation
Indices: 20601--20645 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
20591 GTCTATGAAG
20601 AGTCATAGGAGAAT-AAATATA
1 AGTCATAGGAGAATGAAATATA
* *
20622 AGTCATATGATAATGAAATATA
1 AGTCATAGGAGAATGAAATATA
20644 AG
1 AG
20646 ACTATGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.27
Consensus pattern (22 bp):
AGTCATAGGAGAATGAAATATA
Found at i:24620 original size:2 final size:2
Alignment explanation
Indices: 24574--24607 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
24564 ATGTTGTTAA
24574 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
24608 TGCAATGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24731 original size:54 final size:54
Alignment explanation
Indices: 24642--24978 Score: 423
Period size: 54 Copynumber: 6.2 Consensus size: 54
24632 GTACTACAGA
** **
24642 CACTATGTGTGCAAATC-CATGGGATTCATCATGAGTTGATGAATAATTGTACAAG
1 CACTATGTGTGCAACCCACAT--GATTCATCATGAGTTGATGAATAACCGTACAAG
* * *
24697 CACTATGTGTGCAACCCACATGATTCATCATGAGTTGATAAATAATCGTACAGG
1 CACTATGTGTGCAACCCACATGATTCATCATGAGTTGATGAATAACCGTACAAG
* * *
24751 CTCTATGTGTGCAACCCACAGGATTCATCATGAGTTGATGAATAACCGTACATG
1 CACTATGTGTGCAACCCACATGATTCATCATGAGTTGATGAATAACCGTACAAG
*
24805 CACTATGTGTGCAACCCAC-TGGTTCATCATGAGTTGATGAATAACCGTACATA-
1 CACTATGTGTGCAACCCACATGATTCATCATGAGTTGATGAATAACCGTACA-AG
* * *
24858 CACTATGTGTACAACCTACGA-GATTCATCATGAGTTGATGAATAACCGTATAAG
1 CACTATGTGTGCAACCCAC-ATGATTCATCATGAGTTGATGAATAACCGTACAAG
* * * *
24912 CAATATGTGTGCAACCCACGA-GATTCATCATGAGTTGATGAATTACCGTATAGG
1 CACTATGTGTGCAACCCAC-ATGATTCATCATGAGTTGATGAATAACCGTACAAG
*
24966 CACAATGTGTGCA
1 CACTATGTGTGCA
24979 TCTTAATTAA
Statistics
Matches: 252, Mismatches: 25, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
53 48 0.19
54 186 0.74
55 15 0.06
56 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (54 bp):
CACTATGTGTGCAACCCACATGATTCATCATGAGTTGATGAATAACCGTACAAG
Found at i:24888 original size:107 final size:107
Alignment explanation
Indices: 24636--24975 Score: 432
Period size: 107 Copynumber: 3.1 Consensus size: 107
24626 CTATGTGTAC
* * ** **
24636 TACAGACACTATGTGTGCAAATCCATGGGATTCATCATGAGTTGATGAATAATTGTACAAGCACT
1 TACAGACACTATGTGTAC-AACCCACAGGATTCATCATGAGTTGATGAATAACCGTACAAGCACT
* * *
24701 ATGTGTGCAACCCACATGATTCATCATGAGTTGATAAATAATCG
65 ATGTGTGCAACCCAC-TGGTTCATCATGAGTTGATGAATAACCG
* * * *
24745 TACAGGCTCTATGTGTGCAACCCACAGGATTCATCATGAGTTGATGAATAACCGTACATGCACTA
1 TACAGACACTATGTGTACAACCCACAGGATTCATCATGAGTTGATGAATAACCGTACAAGCACTA
24810 TGTGTGCAACCCACTGGTTCATCATGAGTTGATGAATAACCG
66 TGTGTGCAACCCACTGGTTCATCATGAGTTGATGAATAACCG
* * * *
24852 TACATACACTATGTGTACAACCTAC-GAGATTCATCATGAGTTGATGAATAACCGTATAAGCAAT
1 TACAGACACTATGTGTACAACCCACAG-GATTCATCATGAGTTGATGAATAACCGTACAAGCACT
*
24916 ATGTGTGCAACCCAC-GAGATTCATCATGAGTTGATGAATTACCG
65 ATGTGTGCAACCCACTG-G-TTCATCATGAGTTGATGAATAACCG
* * *
24960 TATAGGCACAATGTGT
1 TACAGACACTATGTGT
24976 GCATCTTAAT
Statistics
Matches: 204, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
106 2 0.01
107 95 0.47
108 91 0.45
109 16 0.08
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (107 bp):
TACAGACACTATGTGTACAACCCACAGGATTCATCATGAGTTGATGAATAACCGTACAAGCACTA
TGTGTGCAACCCACTGGTTCATCATGAGTTGATGAATAACCG
Found at i:24939 original size:161 final size:162
Alignment explanation
Indices: 24636--24978 Score: 462
Period size: 161 Copynumber: 2.1 Consensus size: 162
24626 CTATGTGTAC
* * **
24636 TACAGACACTATGTGTGCAAATCCATGGGATTCATCATGAGTTGATGAATAATTGTACAAGCACT
1 TACAGGCACTATGTGTGC-AACCCATGGGATTCATCATGAGTTGATGAATAACCGTACAAGCACT
* * * **
24701 ATGTGTGCAACCCACATGATTCATCATGAGTTGATAAATAATCGTACAGGCTCTATGTGTGCAAC
65 ATGTGTACAACCCACATGATTCATCATGAGTTGATAAATAACCGTACAAGCAATATGTGTGCAAC
24766 CCACAGGATTCATCATGAGTTGATGAATAACCG
130 CCACAGGATTCATCATGAGTTGATGAATAACCG
*
24799 TACATGCACTATGTGTGCAACCCACT-GG-TTCATCATGAGTTGATGAATAACCGTACATA-CAC
1 TACAGGCACTATGTGTGCAACCCA-TGGGATTCATCATGAGTTGATGAATAACCGTACA-AGCAC
* * *
24861 TATGTGTACAACCTACGA-GATTCATCATGAGTTGATGAATAACCGTATAAGCAATATGTGTGCA
64 TATGTGTACAACCCAC-ATGATTCATCATGAGTTGATAAATAACCGTACAAGCAATATGTGTGCA
*
24925 ACCCAC-GAGATTCATCATGAGTTGATGAATTACCG
128 ACCCACAG-GATTCATCATGAGTTGATGAATAACCG
* *
24960 TATAGGCACAATGTGTGCA
1 TACAGGCACTATGTGTGCA
24979 TCTTAATTAA
Statistics
Matches: 159, Mismatches: 17, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
160 1 0.01
161 132 0.83
162 9 0.06
163 17 0.11
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (162 bp):
TACAGGCACTATGTGTGCAACCCATGGGATTCATCATGAGTTGATGAATAACCGTACAAGCACTA
TGTGTACAACCCACATGATTCATCATGAGTTGATAAATAACCGTACAAGCAATATGTGTGCAACC
CACAGGATTCATCATGAGTTGATGAATAACCG
Found at i:26556 original size:54 final size:54
Alignment explanation
Indices: 26466--26807 Score: 515
Period size: 54 Copynumber: 6.3 Consensus size: 54
26456 GTATGTGTAC
*
26466 TACAGACACTATGTGTGCAAACCCACGAGATTCATCATGAGTTGATGAATAACCG
1 TACAGGCACTATGTGTGC-AACCCACGAGATTCATCATGAGTTGATGAATAACCG
* *
26521 TATAGGAACTATGTGTGCAACCCACGAGATTCATCATGAGTTGATGAATAACCG
1 TACAGGCACTATGTGTGCAACCCACGAGATTCATCATGAGTTGATGAATAACCG
* *
26575 TACAGGCACTATGTGTGCAACCCACGGGATTCATAATGAGTTGATGAATAACCG
1 TACAGGCACTATGTGTGCAACCCACGAGATTCATCATGAGTTGATGAATAACCG
* * *
26629 TACATGCACTATGTGTGCAACCCACGGGATTCATCATGAGTTGATGAATAACCA
1 TACAGGCACTATGTGTGCAACCCACGAGATTCATCATGAGTTGATGAATAACCG
* * *
26683 TACAAGCACTATGTATGTAACCCAC-ATGATTCATCATGAGTTGATGAATAACCG
1 TACAGGCACTATGTGTGCAACCCACGA-GATTCATCATGAGTTGATGAATAACCG
* * * *
26737 TACAGGCACTATGTGTACAACCCACGGGATTCATCATGAGTTGATGAATTACCT
1 TACAGGCACTATGTGTGCAACCCACGAGATTCATCATGAGTTGATGAATAACCG
*
26791 TATAGGCACTATGTGTG
1 TACAGGCACTATGTGTG
26808 TATCCTAATG
Statistics
Matches: 261, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
54 246 0.94
55 15 0.06
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (54 bp):
TACAGGCACTATGTGTGCAACCCACGAGATTCATCATGAGTTGATGAATAACCG
Found at i:35417 original size:42 final size:43
Alignment explanation
Indices: 35358--35446 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
35348 TATTTTGTTT
*
35358 GGGTCGGGTTGGG-TTTTTTAAGTGTGATATTCGGGTCGAGTC
1 GGGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAGTC
* *
35400 GGGTCGGGTCGGGTTTTTTTAAGTGTGATATTTGGGTCGGGTC
1 GGGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAGTC
35443 GGGT
1 GGGT
35447 TTAGGGTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
42 12 0.28
43 31 0.72
ACGTcount: A:0.10, C:0.09, G:0.43, T:0.38
Consensus pattern (43 bp):
GGGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAGTC
Found at i:36142 original size:16 final size:18
Alignment explanation
Indices: 36117--36162 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
36107 TATGGAATTG
36117 GATTCAAATTCC-T-ACA
1 GATTCAAATTCCTTCACA
*
36133 GATTCCAATTCCTTCACA
1 GATTCAAATTCCTTCACA
*
36151 GATTCTAATTCC
1 GATTCAAATTCC
36163 CTTATAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 11 0.42
17 1 0.04
18 14 0.54
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (18 bp):
GATTCAAATTCCTTCACA
Found at i:37383 original size:23 final size:23
Alignment explanation
Indices: 37365--37423 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
37355 CTCGTATAAA
37365 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
37388 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
37411 TACACCGAAGTGC
1 TGCACCGAAGTGC
37424 TATATAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:39010 original size:20 final size:20
Alignment explanation
Indices: 38985--39022 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38975 TCTCCTTTGA
38985 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
39005 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
39023 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:39250 original size:25 final size:25
Alignment explanation
Indices: 39216--39265 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
39206 CATCAACTTT
39216 TCACTCAATACTTCTATTTTAAGCC
1 TCACTCAATACTTCTATTTTAAGCC
39241 TCACTCAATACTTCTATTTTAAGCC
1 TCACTCAATACTTCTATTTTAAGCC
39266 CCTATCATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (25 bp):
TCACTCAATACTTCTATTTTAAGCC
Found at i:40670 original size:19 final size:19
Alignment explanation
Indices: 40646--40690 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
40636 CTCAAATATA
40646 CAAATCCTTAACTTGTATC
1 CAAATCCTTAACTTGTATC
*
40665 CAAATCTTTAACTTGTATC
1 CAAATCCTTAACTTGTATC
*
40684 CAGATCC
1 CAAATCC
40691 ACTTCATATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.36
Consensus pattern (19 bp):
CAAATCCTTAACTTGTATC
Found at i:42127 original size:23 final size:23
Alignment explanation
Indices: 42109--42169 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
42099 CTCGTATAAA
*
42109 TGCACCGAAATGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
42132 TGCACCGAAGTGCCTCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
42155 TGCACTGAAGTGCCA
1 TGCACCGAAGTGCCA
42170 TATAAAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:43778 original size:24 final size:20
Alignment explanation
Indices: 43722--43779 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
43712 TCCCCTTTGA
*
43722 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
43742 AGTTCATCGATGCATTCTGTAAC
1 AGTGCATCGATGCATTC--T-AC
43765 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
43780 CTACCCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:47446 original size:638 final size:642
Alignment explanation
Indices: 46229--47512 Score: 2355
Period size: 638 Copynumber: 2.0 Consensus size: 642
46219 ACAAATTAGT
46229 GAATTTGTTCGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGGTTGAGAAAG
1 GAATTTGTTCGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGGTTGAGAAAG
*
46294 TCGAACCACTCTAAATCATTGTGCAAATATTTTCAATTTTCTGCAAAAGCTTCCACCAAAATTTT
66 TCGAACCACTCTAAATCATTGTGCAAATATTTTCAATTTTCTGCAAAAACTTCCACCAAAATTTT
* *
46359 TATTGTCAATTCACCCCCTCTTGGCTATTTCGTCGATCGATTAACTCAACAAATTTTAATTTTAA
131 TATTGTCAATTCACCCCCTCTTGGCTATTTCGTCGATCGATTAACT-AACAAATATTAACTTTAA
**
46424 TATTAATCATTAACTTTTTTTGATAACTTGATATTTATTTTTATCATTGCTTTTTATTTAATATT
195 TATTAATCATT-ACTTAATTT-ATAACTTGATATTTATTTTTATCATTGCTTTTTATTTAATATT
*
46489 ACTTTTGATTCGTAGATTTGACTTGCTATTAATATTGATCATTCATATCGATTTAATAAATTTGA
258 ACTTTTGATTCATAGATTTGACTTGCTATTAATATTGATCATTCATATCGATTTAATAAATTTGA
46554 ACTTTTATTTATTGTTTTGTGGGTTTATTCGTAGATTTGAATACATCTCTAAGTTATAATTGTTA
323 ACTTTTATTTATTGTTTTGTGGGTTTATTCGTAGATTTGAATACATCTCTAAGTTATAATTGTTA
46619 CATATTTTATTTAATTTATTTAATTTTTTTAAATTAAAGGTTCAACTCGGACGAGTACTTGTACA
388 CATATTTTATTTAATTTATTTAATTTTTTTAAATTAAAGGTTCAACTCGGACGAGTACTTGTACA
46684 TTGATGTTATGACATTTCTATTTAAACAATAAGAAACGAAGCATATGATTTAGAATAATTCGAAT
453 TTGATGTTATGACATTTCTATTTAAACAATAAGAAACGAAGCATATGATTTAGAATAATTCGAAT
46749 TATCCCAAAGTAGTTCACCACACAGTCGTAGAATAATTCGAATTAGCAAGTTAGTGAGGTTTCTT
518 TATCCCAAAGTAGTTCACCACACAGTCGTAGAATAATTCGAATTAGCAAGTTAGTGAGGTTTCTT
* *
46814 CTGTAAGTTTGCGAAATTTATGTATTTCTGTTTGAGAGAGAGTGTGTTATCAAGAATTTG
583 CTGTAAGTTTGCGAAATTTATGTATTTCTGTTTGAAAGAGAGAGTGTTATCAAGAATTTG
46874 GAATTTGTTCGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGGTTGAGAAAG
1 GAATTTGTTCGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGGTTGAGAAAG
*
46939 TCGAACCACTCTAAATCGTTGTGCAAATATTTTCAATTTTCTGCAAAAACTTCCACCAAAATTTT
66 TCGAACCACTCTAAATCATTGTGCAAATATTTTCAATTTTCTGCAAAAACTTCCACCAAAATTTT
***
47004 TATTGTCAATTCACCCCCTCTTGGCTATTTCGTCGATCGATTTAA-T-ATTGATCATTAACTTTA
131 TATTGTCAATTCACCCCCTCTTGGCTATTTCGTCGATCGA-TTAACTAACAAAT-ATTAACTTTA
* *
47067 AT-TT-TTGATT-CTTAATTT-TAACTTGATATTTATTTTTATCATTGCTTTTTATTTAATATTA
194 ATATTAATCATTACTTAATTTATAACTTGATATTTATTTTTATCATTGCTTTTTATTTAATATTA
47128 CTTTTGATTCATAGATTTGACTTGCTATTAATATTGATCATTCATATCGATTTAATAAATTTGAA
259 CTTTTGATTCATAGATTTGACTTGCTATTAATATTGATCATTCATATCGATTTAATAAATTTGAA
47193 CTTTTATTTATTGTTTTGTGGGTTTATTCGTAGATTTGAATACATCTCTAAGTTATAATTGTTAC
324 CTTTTATTTATTGTTTTGTGGGTTTATTCGTAGATTTGAATACATCTCTAAGTTATAATTGTTAC
47258 ATATTTTATTTAATTTATTTAATTTTTTTAAATTAAAGGTTCAACTCGGACGAGTACTTGTACAT
389 ATATTTTATTTAATTTATTTAATTTTTTTAAATTAAAGGTTCAACTCGGACGAGTACTTGTACAT
47323 TGATGTTATGACATTTCTATTTAAACAATAAGAAACGAAGCATATGATTTAGAATAATTCGAATT
454 TGATGTTATGACATTTCTATTTAAACAATAAGAAACGAAGCATATGATTTAGAATAATTCGAATT
47388 ATCCCAAAGTAGTTCACCACACAGTCGTAGAATAATTCGAATTAGCAAGTTAGTGAGGTTTCTTC
519 ATCCCAAAGTAGTTCACCACACAGTCGTAGAATAATTCGAATTAGCAAGTTAGTGAGGTTTCTTC
47453 TGTAAGTTTGCGAAATTTATGTATTTCTGTTTGAAAGAGAGAGTGTTATCAAGAATTTG
584 TGTAAGTTTGCGAAATTTATGTATTTCTGTTTGAAAGAGAGAGTGTTATCAAGAATTTG
47512 G
1 G
47513 GTATAATTCT
Statistics
Matches: 623, Mismatches: 14, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
638 425 0.68
640 6 0.01
642 4 0.01
643 5 0.01
644 10 0.02
645 169 0.27
646 4 0.01
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.42
Consensus pattern (642 bp):
GAATTTGTTCGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGGTTGAGAAAG
TCGAACCACTCTAAATCATTGTGCAAATATTTTCAATTTTCTGCAAAAACTTCCACCAAAATTTT
TATTGTCAATTCACCCCCTCTTGGCTATTTCGTCGATCGATTAACTAACAAATATTAACTTTAAT
ATTAATCATTACTTAATTTATAACTTGATATTTATTTTTATCATTGCTTTTTATTTAATATTACT
TTTGATTCATAGATTTGACTTGCTATTAATATTGATCATTCATATCGATTTAATAAATTTGAACT
TTTATTTATTGTTTTGTGGGTTTATTCGTAGATTTGAATACATCTCTAAGTTATAATTGTTACAT
ATTTTATTTAATTTATTTAATTTTTTTAAATTAAAGGTTCAACTCGGACGAGTACTTGTACATTG
ATGTTATGACATTTCTATTTAAACAATAAGAAACGAAGCATATGATTTAGAATAATTCGAATTAT
CCCAAAGTAGTTCACCACACAGTCGTAGAATAATTCGAATTAGCAAGTTAGTGAGGTTTCTTCTG
TAAGTTTGCGAAATTTATGTATTTCTGTTTGAAAGAGAGAGTGTTATCAAGAATTTG
Found at i:47925 original size:714 final size:696
Alignment explanation
Indices: 46874--48149 Score: 2178
Period size: 714 Copynumber: 1.8 Consensus size: 696
46864 CAAGAATTTG
*
46874 GAATTTGTTCGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGGTTGAGAAAG
1 GAATTTATTCGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGGTTGAGAAAG
* *
46939 TCGAACCACTCTAAATCGTTGTGCAAATATTTTCAATTTTCTGCAAAAACTTCCACCAAAATTTT
66 TCGAACCACTCTAAATCGCTGTGCAAATATTTTCAATTTTCTGCAAAAACTTCCACCAAAAATTT
47004 TATTGTCAATTCACCCCCTCTTGGCTATTTCGTCGATCGATTTAATATTGATCATTAACTTTAAT
131 TATTGTCAATTCACCCCCTCTTGGCTATTTCGTCGATCGATTTAATATTGATCATTAACTTTAAT
* * * *
47069 TTTTGATTCTTAATTTTAACTTGATATTTATTTTTATCATTGCTTTTTATTTAATATTACTTTTG
196 TTTTGATGCTTAATTTTAACTTGATATTCATTTTTATCATTGCTTATGATTTAATATTACTTTTG
*
47134 ATTCATAGATTTGACTTGCTATTAATATTGATCATTCATATCGATTTAATAAATTTGAACTTTTA
261 ATACATAGATTTGACTTGCTATTAATATTGATCATTCATATCGATTTAATAAATTTGAACTTTTA
47199 TTTATTGTTTTGTGGGTTTATTCGTAGATTTGAATACATCTCTAAGTTATAATTGTTACATATTT
326 TTTATTGTTTTGTGGGTTTATTCGTAGATTTGAATACATCTCTAAGTTATAATTGTTACATATTT
47264 TATTTAATTTATTTAATTTTTTTAAATTAAAGGTTCAACTCGGACGAGTACTTGTACATTGATGT
391 TATTTAATTTATTTAA---TTTTAAATTAAAGGTTCAACTCGGACGAGTACTTGTACATTGATGT
*
47329 TATGACATTTCTATTTAAACAATAAGAAACGAAGCATATGATTTAGAATAATTCGAATTATCCCA
453 TATGACATTTCTATTTAAACAATAAGAAACGAAG-ATATGATTTAGAATAATTCGAATTAGCCCA
47394 AAGTAGTTCACCACACAGTCGTAGAATAATTCGAATTAGCAAGTTAGTGAGGTTTCTTCTGTAAG
517 AAGTAGTTCACCACACAGTCGTAGAATAATTCGAATTAGCAAGTTAGTGAGGTTTCTTCTGTAAG
47459 TTTGCGAAATTTATGTATTTCTGTTTGAAAGAGAGAGTGTTATCAAGAATTTGGGTATAATTCTT
582 TTTGCGAAATTTATGTATTTCTGTTTGAAAGAGAGAGTGTTATCAAGAATTTGGGTATAATTCTT
47524 AAGGGAGTTGTAAGGTTACTCTTTGTCCTCAAAAGAAAGAACAAATTAGT
647 AAGGGAGTTGTAAGGTTACTCTTTGTCCTCAAAAGAAAGAACAAATTAGT
*
47574 GAATTTATTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGGTTGAGAAAG
1 GAATTTATTCGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGGTTGAGAAAG
*
47639 TCGAACCACTCTAAATCGCTGTGCAAATATTTTCAATTTTCTGCAAAAGCTTCCACCAAAAATTT
66 TCGAACCACTCTAAATCGCTGTGCAAATATTTTCAATTTTCTGCAAAAACTTCCACCAAAAATTT
47704 TATTG-CTAATTCACCCCCCTCTTGGCTATTTCGTCGATCGATTAACTTAACAAATTTAAATATT
131 TATTGTC-AATTCA-CCCCCTCTTGGCTATTTCGTCGATCG-------------ATTT-AATATT
47768 GATCATTAACTTTAA-TTTTGATGCTTAATTTTAACTTGATATTCATTTTTATCATTGCTTATGA
180 GATCATTAACTTTAATTTTTGATGCTTAATTTTAACTTGATATTCATTTTTATCATTGCTTATGA
* * *
47832 TTTAATATTACTTTTGATACGTAGGTTTGACTTGCTATTAGTATTGATCATTCATATCGATTTAA
245 TTTAATATTACTTTTGATACATAGATTTGACTTGCTATTAATATTGATCATTCATATCGATTTAA
47897 TAAATTTGAACTTTTATTTATTGTTTTGTGGGTTTATTCGTAGATTTGAATACATCTCTAAGTTA
310 TAAATTTGAACTTTTATTTATTGTTTTGTGGGTTTATTCGTAGATTTGAATACATCTCTAAGTTA
* * *
47962 TAATTGTTACATATTTTATTTAATTTATTTAATTTTGAATTAAAGGTTCAACTCGGATGATTACT
375 TAATTGTTACATATTTTATTTAATTTATTTAATTTTAAATTAAAGGTTCAACTCGGACGAGTACT
*
48027 TGTACATTGATGTTATTACATTTCTATTTAAACAATAAGAAACGAAGATATGATTTAGAATAATT
440 TGTACATTGATGTTATGACATTTCTATTTAAACAATAAGAAACGAAGATATGATTTAGAATAATT
* *
48092 TGAATTAGCCCAAAGTAGTTCACCACACGGTCGTAGAATAATTCGAATTAGCAAGTTA
505 CGAATTAGCCCAAAGTAGTTCACCACACAGTCGTAGAATAATTCGAATTAGCAAGTTA
48150 AGATTAACGA
Statistics
Matches: 540, Mismatches: 20, Indels: 22
0.93 0.03 0.04
Matches are distributed among these distances:
699 1 0.00
700 136 0.25
701 26 0.05
710 73 0.14
711 76 0.14
714 207 0.38
715 21 0.04
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (696 bp):
GAATTTATTCGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGGTTGAGAAAG
TCGAACCACTCTAAATCGCTGTGCAAATATTTTCAATTTTCTGCAAAAACTTCCACCAAAAATTT
TATTGTCAATTCACCCCCTCTTGGCTATTTCGTCGATCGATTTAATATTGATCATTAACTTTAAT
TTTTGATGCTTAATTTTAACTTGATATTCATTTTTATCATTGCTTATGATTTAATATTACTTTTG
ATACATAGATTTGACTTGCTATTAATATTGATCATTCATATCGATTTAATAAATTTGAACTTTTA
TTTATTGTTTTGTGGGTTTATTCGTAGATTTGAATACATCTCTAAGTTATAATTGTTACATATTT
TATTTAATTTATTTAATTTTAAATTAAAGGTTCAACTCGGACGAGTACTTGTACATTGATGTTAT
GACATTTCTATTTAAACAATAAGAAACGAAGATATGATTTAGAATAATTCGAATTAGCCCAAAGT
AGTTCACCACACAGTCGTAGAATAATTCGAATTAGCAAGTTAGTGAGGTTTCTTCTGTAAGTTTG
CGAAATTTATGTATTTCTGTTTGAAAGAGAGAGTGTTATCAAGAATTTGGGTATAATTCTTAAGG
GAGTTGTAAGGTTACTCTTTGTCCTCAAAAGAAAGAACAAATTAGT
Found at i:49265 original size:20 final size:20
Alignment explanation
Indices: 49240--49281 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
49230 GTTACTATGG
49240 TTATCATTTAACTATTATAT
1 TTATCATTTAACTATTATAT
**
49260 TTATCATTTAGTTATTATAT
1 TTATCATTTAACTATTATAT
49280 TT
1 TT
49282 TTGTATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (20 bp):
TTATCATTTAACTATTATAT
Found at i:49295 original size:19 final size:19
Alignment explanation
Indices: 49252--49318 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
49242 ATCATTTAAC
* * *
49252 TATTATATTTATCATTTAGT
1 TATTATATTT-TTATATAAT
*
49272 TATTATATTTTTGTATAAT
1 TATTATATTTTTATATAAT
49291 TATTATATTTTTATATAAT
1 TATTATATTTTTATATAAT
49310 TATTATATT
1 TATTATATT
49319 ATATTTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 32 0.76
20 10 0.24
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (19 bp):
TATTATATTTTTATATAAT
Found at i:49333 original size:24 final size:24
Alignment explanation
Indices: 49291--49349 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 24
49281 TTTGTATAAT
49291 TATTATATTTTTATATAATTATTA-
1 TATTATATTTTTATATAATT-TTAG
*
49315 TATTATA-TTTTATTTTAATTTTAG
1 TATTATATTTTTA-TATAATTTTAG
49339 TATTGATATTT
1 TATT-ATATTT
49350 GTAACAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 8 0.27
24 17 0.57
25 3 0.10
26 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.64
Consensus pattern (24 bp):
TATTATATTTTTATATAATTTTAG
Found at i:49757 original size:42 final size:42
Alignment explanation
Indices: 49699--49823 Score: 139
Period size: 42 Copynumber: 3.0 Consensus size: 42
49689 GATTTAAATA
*
49699 TATTAATATTATAAAATAATTAAAATAATATATTTATAATTATT
1 TATTAA-ATT-TAAAATAATTAAAATAATATATTTATAATAATT
* * *
49743 TATTAAATTTAAAATAGTTATATTAATATAGTTTATAATAATT
1 TATTAAATTTAAAATAATTAAAATAATATA-TTTATAATAATT
* **
49786 T-TTATATTTTTAATAATT-AAATAATATATTT-TAATAAT
1 TATTAAATTTAAAATAATTAAAATAATATATTTATAATAAT
49824 ATAAAATAAC
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
39 7 0.10
40 3 0.04
41 8 0.11
42 31 0.44
43 15 0.21
44 6 0.09
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (42 bp):
TATTAAATTTAAAATAATTAAAATAATATATTTATAATAATT
Found at i:49801 original size:21 final size:20
Alignment explanation
Indices: 49766--49824 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
49756 ATAGTTATAT
* *
49766 TAATATAGTTT-ATAATAAT
1 TAATATATTTTAATAATAAA
**
49785 TTTTATATTTTTAATAATTAAA
1 TAATATA-TTTTAATAA-TAAA
49807 TAATATATTTTAATAATA
1 TAATATATTTTAATAATA
49825 TAAAATAACA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 5 0.16
20 5 0.16
21 13 0.42
22 8 0.26
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TAATATATTTTAATAATAAA
Found at i:49873 original size:23 final size:24
Alignment explanation
Indices: 49822--49875 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 24
49812 TATTTTAATA
*
49822 ATATAAA-ATAACATTATTAAAAT
1 ATATAAATATAACATTATAAAAAT
*
49845 AT-TAAATATAATA-TATAAAAAT
1 ATATAAATATAACATTATAAAAAT
49867 ATATAAATA
1 ATATAAATA
49876 AAAATTAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
ATATAAATATAACATTATAAAAAT
Found at i:49876 original size:14 final size:15
Alignment explanation
Indices: 49848--49880 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
49838 TTAAAATATT
*
49848 AAATATAATATATAA
1 AAATATAATAAATAA
49863 AAATAT-ATAAATAA
1 AAATATAATAAATAA
49877 AAAT
1 AAAT
49881 TAACTAGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATATAATAAATAA
Found at i:52281 original size:37 final size:37
Alignment explanation
Indices: 52208--52282 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
52198 GTTGTAAAAT
*
52208 ATTTATATATTTTATTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTATTTAAAAAAATTAAAATCATAAA
* *
52245 ATTTATATAATTTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTATTTAAAAAAATT-AAAATCATAAA
52282 A
1 A
52283 AAATTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTATTTAAAAAAATTAAAATCATAAA
Found at i:53648 original size:45 final size:45
Alignment explanation
Indices: 53597--53683 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
53587 GACAATCAAC
53597 ATTGAAATTGGTGTAATAGGAAAAAAATTAAATTTAATAAAAATT
1 ATTGAAATTGGTGTAATAGGAAAAAAATTAAATTTAATAAAAATT
* *
53642 ATTGAAATTGGTGTAGTAGGAAAAAAATTAAATTTGATAAAA
1 ATTGAAATTGGTGTAATAGGAAAAAAATTAAATTTAATAAAA
53684 TTTCTATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (45 bp):
ATTGAAATTGGTGTAATAGGAAAAAAATTAAATTTAATAAAAATT
Found at i:54913 original size:50 final size:50
Alignment explanation
Indices: 54838--54933 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
54828 CCCACACAAT
** * *
54838 ATGATCGACCACCGTGCTGTCTATCATTCTGACTACTGCCATCAATTATC
1 ATGATCGACCACCGCACTGTCTATCACTCTGACTACCGCCATCAATTATC
54888 ATGATCGACCACCGCACTGTCTATCACTCTGACTACCGCCATCAAT
1 ATGATCGACCACCGCACTGTCTATCACTCTGACTACCGCCATCAAT
54934 GATAATTGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.25, C:0.33, G:0.14, T:0.28
Consensus pattern (50 bp):
ATGATCGACCACCGCACTGTCTATCACTCTGACTACCGCCATCAATTATC
Found at i:58622 original size:25 final size:24
Alignment explanation
Indices: 58568--58633 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
58558 TTAGATCTTT
* * *
58568 ATTTTATGTTTATTTTATTTTATAT
1 ATTTAATGTTT-TTTAATTTTATAA
*
58593 TTTTAATGTTTTTTAATTTTCATAA
1 ATTTAATGTTTTTTAATTTT-ATAA
58618 ATTTAATTGTTTTTTA
1 ATTTAA-TGTTTTTTA
58634 GATTAATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 8 0.24
25 17 0.50
26 9 0.26
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.68
Consensus pattern (24 bp):
ATTTAATGTTTTTTAATTTTATAA
Found at i:62425 original size:13 final size:13
Alignment explanation
Indices: 62409--62456 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
62399 GAAAAGAAGC
62409 AAAGAAAGAGCAA
1 AAAGAAAGAGCAA
*
62422 AAAGAAA-AGAAA
1 AAAGAAAGAGCAA
*
62434 GAAACAAAGAGCAA
1 -AAAGAAAGAGCAA
62448 AAAGAAAGA
1 AAAGAAAGA
62457 AACAAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 4 0.14
13 21 0.72
14 4 0.14
ACGTcount: A:0.73, C:0.06, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAGCAA
Found at i:62427 original size:26 final size:26
Alignment explanation
Indices: 62398--62462 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
62388 CAAATCGAAG
*
62398 AGAAAAGAAGCAAAGAAAGAGCAAAA
1 AGAAAAGAAGCAAACAAAGAGCAAAA
62424 AGAAAAGAAAG-AAACAAAGAGCAAAA
1 AGAAAAG-AAGCAAACAAAGAGCAAAA
*
62450 AG-AAAGAAACAAA
1 AGAAAAGAAGCAAA
62463 TAAAAAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 2 0.06
25 7 0.20
26 23 0.66
27 3 0.09
ACGTcount: A:0.72, C:0.08, G:0.20, T:0.00
Consensus pattern (26 bp):
AGAAAAGAAGCAAACAAAGAGCAAAA
Found at i:62432 original size:18 final size:19
Alignment explanation
Indices: 62395--62435 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
62385 AATCAAATCG
*
62395 AAGAGAAAAGAAGCAAAGA
1 AAGAGAAAAGAAGAAAAGA
*
62414 AAGAGCAAA-AAGAAAAGA
1 AAGAGAAAAGAAGAAAAGA
62432 AAGA
1 AAGA
62436 AACAAAGAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.71, C:0.05, G:0.24, T:0.00
Consensus pattern (19 bp):
AAGAGAAAAGAAGAAAAGA
Found at i:64027 original size:36 final size:36
Alignment explanation
Indices: 63910--64526 Score: 770
Period size: 36 Copynumber: 16.9 Consensus size: 36
63900 TTAAAGAAGA
* * *
63910 TTTGATCTCGCTTGAGATAGTTTCCCTAGAAACAGAAGAT
1 TTTG-TCTCCCTTGAGACAGTTTCCCTTGAAAC--AA-AT
** * * ** * *
63950 TTTGTCTCGTTTGAGATAGTTTCACTCAAAAAAAAA
1 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
* *
63986 ATTGTCTCCCTTGAGACAGTTTCCCTTGAAATAAAT
1 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
**
64022 TTTGTCTCATTTGAGACAGTTTCCCTTGAAACAAAT
1 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
*
64058 TTAGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
1 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
*
64094 TTAGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
1 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
*
64130 TTAGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
1 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
* *
64166 TTAGTCTCCTTTGAGACAGTTTCCCTTGAAACAAAT
1 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
* *
64202 TTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAT
1 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
*
64238 TTTGTCTCCCTTGAGACAGTTTCCATTGAAACAAAT
1 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
* * *
64274 TTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAGT
1 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
* **
64310 TTTGTCTCCCTTGAGACAATTTTTCTTGAAACAAAT
1 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
*
64346 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAGCAAAT
1 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
*
64382 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAATAAAT
1 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
* *
64418 TTTGTCTCCCTTGAGATAG-TTCCCTCGAAACAAAAGAT
1 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC--AA-AT
* * *
64456 TTTGTCT-TCTTGAGATAGTTTCCCTCGAAACAGAAGAT
1 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC--AA-AT
* * * *
64494 TTTATCTCACTTGAGATAGTTTCCCTCGAAACA
1 TTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
64527 GAAGATTTTA
Statistics
Matches: 519, Mismatches: 53, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
35 10 0.02
36 411 0.79
37 15 0.03
38 33 0.06
39 46 0.09
40 4 0.01
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (36 bp):
TTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
Found at i:64069 original size:21 final size:21
Alignment explanation
Indices: 64043--64179 Score: 85
Period size: 21 Copynumber: 7.4 Consensus size: 21
64033 TGAGACAGTT
64043 TCCCTTGAAACAAATTTAGTC
1 TCCCTTGAAACAAATTTAGTC
* *
64064 TCCCTTGAGAC------AGTT
1 TCCCTTGAAACAAATTTAGTC
64079 TCCCTTGAAACAAATTTAGTC
1 TCCCTTGAAACAAATTTAGTC
* *
64100 TCCCTTGAGAC------AGTT
1 TCCCTTGAAACAAATTTAGTC
64115 TCCCTTGAAACAAATTTAGTC
1 TCCCTTGAAACAAATTTAGTC
* *
64136 TCCCTTGAGAC------AGTT
1 TCCCTTGAAACAAATTTAGTC
64151 TCCCTTGAAACAAATTTAGTC
1 TCCCTTGAAACAAATTTAGTC
*
64172 TCCTTTGA
1 TCCCTTGA
64180 GACAGTTTCC
Statistics
Matches: 85, Mismatches: 13, Indels: 36
0.63 0.10 0.27
Matches are distributed among these distances:
15 39 0.46
21 46 0.54
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTAGTC
Found at i:64872 original size:41 final size:42
Alignment explanation
Indices: 64778--64872 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 42
64768 AGTCATTGGG
* * * * *
64778 GCCAT-CAGTAAGTCTTTCGAGCATGATGCGTAAGTTCTTCGG
1 GCCATCCA-TAAGTCTTTCGAGCAAGAAGCATAAGTCCTTCGA
* *
64820 GCTATCTATAAGTCTTTCGAGCAAGAAG-ATAAGTCCTTCGA
1 GCCATCCATAAGTCTTTCGAGCAAGAAGCATAAGTCCTTCGA
64861 GCCATCCATAAG
1 GCCATCCATAAG
64873 ACCTTCGGGC
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
41 20 0.47
42 22 0.51
43 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (42 bp):
GCCATCCATAAGTCTTTCGAGCAAGAAGCATAAGTCCTTCGA
Found at i:65141 original size:36 final size:36
Alignment explanation
Indices: 65062--65170 Score: 128
Period size: 36 Copynumber: 3.0 Consensus size: 36
65052 AAAAAATATG
* * * * *
65062 AATTTTGTCTCACTTGAGACAATTTTTACTCGAAACC
1 AATTTTGTCTCGCTTGAGAC-AGTTTCACTTGAAACA
* *
65099 AGTTTTGTCTCGCTTGAAACAGTTTCACTTGAAACA
1 AATTTTGTCTCGCTTGAGACAGTTTCACTTGAAACA
* *
65135 AATTTTGTCTCGCTTGAGTCAGTTTCTCTTGAAACA
1 AATTTTGTCTCGCTTGAGACAGTTTCACTTGAAACA
65171 CAAAATCTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
36 44 0.72
37 17 0.28
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (36 bp):
AATTTTGTCTCGCTTGAGACAGTTTCACTTGAAACA
Found at i:65212 original size:29 final size:28
Alignment explanation
Indices: 65154--65234 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 28
65144 TCGCTTGAGT
* *
65154 CAGTTTCTCTTGAAACACAAAATCTTTGAA
1 CAGTTTCCCTTG-AA-ACAAAATCGTTGAA
65184 CCAGTTTCCCTTGAAACAAAATCGTTGAA
1 -CAGTTTCCCTTGAAACAAAATCGTTGAA
*
65213 TATGTTTCCCTTGAAACAAAAT
1 CA-GTTTCCCTTGAAACAAAAT
65235 TTTTCTTCCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 1 0.02
29 32 0.70
30 2 0.04
31 11 0.24
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (28 bp):
CAGTTTCCCTTGAAACAAAATCGTTGAA
Found at i:65738 original size:91 final size:91
Alignment explanation
Indices: 65583--65756 Score: 330
Period size: 91 Copynumber: 1.9 Consensus size: 91
65573 GAAACCCATC
*
65583 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTTATCCAACGAGGGAGAAGAAGTTCATAAT
1 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAAT
65648 GAGAAGAACTTGTTCAACATTGGCTT
66 GAGAAGAACTTGTTCAACATTGGCTT
65674 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAAT
1 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAAT
*
65739 GGGAAGAACTTGTTCAAC
66 GAGAAGAACTTGTTCAAC
65757 CTTAGCTCAA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 81 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.24
Consensus pattern (91 bp):
AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACATTGGCTT
Found at i:65887 original size:20 final size:20
Alignment explanation
Indices: 65825--65887 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
65815 CATTGGAGAG
*
65825 TTCATAATGAGAAGAACTCA
1 TTCATAATGAGAAGAACTAA
*
65845 TTC--AATGAGGGAGAA-TAA
1 TTCATAATGA-GAAGAACTAA
*
65863 GTTCATAATGAGAAGAACTTA
1 -TTCATAATGAGAAGAACTAA
65884 TTCA
1 TTCA
65888 ACCTTAACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
18 7 0.21
19 8 0.24
20 12 0.35
21 7 0.21
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (20 bp):
TTCATAATGAGAAGAACTAA
Found at i:66186 original size:52 final size:52
Alignment explanation
Indices: 66108--66206 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 52
66098 AGGGAGAAGA
* * *
66108 AGTTCATAATGAAAAGAACTTATTCAACCGTGGTTCAAGATTTCCAGTGGAG
1 AGTTCATAATGAAAAGAACTTATTCAACAGTGGATCAACATTTCCAGTGGAG
* * *
66160 AGTTCATAATGAGAAGAACTTGTTCAACATTGGATCAACATTTCCAG
1 AGTTCATAATGAAAAGAACTTATTCAACAGTGGATCAACATTTCCAG
66207 AAGAACCCAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (52 bp):
AGTTCATAATGAAAAGAACTTATTCAACAGTGGATCAACATTTCCAGTGGAG
Found at i:84091 original size:18 final size:18
Alignment explanation
Indices: 84068--84102 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
84058 TTTCTAGCTG
84068 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
* *
84086 CCCATGTTGGACTACTG
1 CCCATGCTGGACCACTG
84103 TCCAATCCTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.37, G:0.23, T:0.23
Consensus pattern (18 bp):
CCCATGCTGGACCACTGC
Found at i:93506 original size:20 final size:19
Alignment explanation
Indices: 93460--93508 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
93450 AGAACTTTTC
*
93460 CAAATTCATA-ATTTATTT
1 CAAATTCATAGATTTATAT
* *
93478 CAGATTCATAGTTTTACTAT
1 CAAATTCATAGATTTA-TAT
93498 CAAATTCATAG
1 CAAATTCATAG
93509 CCTAATGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 9 0.36
19 4 0.16
20 12 0.48
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (19 bp):
CAAATTCATAGATTTATAT
Done.