Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002216.1 Hibiscus syriacus cultivar Beakdansim tig00004510_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: 77084
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:2040 original size:29 final size:29
Alignment explanation
Indices: 2008--2063 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1998 TTATGCCCTT
2008 TATTTTGTAAACATATACGTTATATAATA
1 TATTTTGTAAACATATACGTTATATAATA
*
2037 TATTTTGTAAACATATACGTTGTATAA
1 TATTTTGTAAACATATACGTTATATAA
2064 CATTTTTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (29 bp):
TATTTTGTAAACATATACGTTATATAATA
Found at i:2078 original size:27 final size:29
Alignment explanation
Indices: 2008--2071 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
1998 TTATGCCCTT
*
2008 TATTTTGTAAACATATACGTTATATAATA
1 TATTTTGTAAACATATACGTTATATAACA
*
2037 TATTTTGTAAACATATACGTTGTATAACA
1 TATTTTGTAAACATATACGTTATATAACA
*
2066 TTTTTT
1 TATTTT
2072 ACCCATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (29 bp):
TATTTTGTAAACATATACGTTATATAACA
Found at i:3014 original size:132 final size:131
Alignment explanation
Indices: 2833--3131 Score: 352
Period size: 131 Copynumber: 2.3 Consensus size: 131
2823 GGTATAATAG
* * * * * *
2833 GTCATTTATTTTCGATTGGAAATAATTTGATATTGTCGTTTTCTCTTGAATTAATATCG-ATTTT
1 GTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTTGAATCAATAT-GTAATTT
* * * *
2897 CTTAGACGGAATATTAATA-TCTCTTTATTTCAATTGATGTAATAAATGATTGTTTTAATGCACA
65 -TAAGACGAAATAGTAATATTC-CTTTATTTCAATTGAGGTAATAAATGATTGTTTTAATGCACA
2961 AAAT
128 AAAT
* * * **
2965 GTCGTTTATTCTCGATTGGAAATCATTAGATATTATCATTTT-TGTTTGAATCGCTATGTAATTT
1 GTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCT-CTTGAATCAATATGTAATTT
* *
3029 TAAGACGAAATAGTAATATTCCTTTATTTCAATTGGGGTACTAAATGATTGTTTTAATGCACAAA
65 TAAGACGAAATAGTAATATTCCTTTATTTCAATTGAGGTAATAAATGATTGTTTTAATGCACAAA
3094 AT
130 AT
* * * *
3096 GTTATTTGTTCTCGATTAGAAATAATCAGATATTAT
1 GTCATTTATTCTCGATTGGAAATAATTAGATATTAT
3132 TGTTTTCACT
Statistics
Matches: 141, Mismatches: 23, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
131 90 0.64
132 51 0.36
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.44
Consensus pattern (131 bp):
GTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTTGAATCAATATGTAATTTT
AAGACGAAATAGTAATATTCCTTTATTTCAATTGAGGTAATAAATGATTGTTTTAATGCACAAAA
T
Found at i:4607 original size:2 final size:2
Alignment explanation
Indices: 4600--4642 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
4590 ATAAATTCTT
4600 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
4642 T
1 T
4643 TTTCATTGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5447 original size:37 final size:38
Alignment explanation
Indices: 5362--5447 Score: 106
Period size: 37 Copynumber: 2.3 Consensus size: 38
5352 ATTAAACATT
*
5362 TTTTATATTTTTAATTTTGTAAAAAAAATTATATAAATA
1 TTTTATA-ATTTAATTTTGTAAAAAAAATTATATAAATA
* *
5401 --TTATGAATTTAATTTTTTAAAGAAAA-TATATAAATA
1 TTTTAT-AATTTAATTTTGTAAAAAAAATTATATAAATA
5437 TTTTATAATTT
1 TTTTATAATTT
5448 GTAATATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
36 10 0.24
37 26 0.63
38 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.51
Consensus pattern (38 bp):
TTTTATAATTTAATTTTGTAAAAAAAATTATATAAATA
Found at i:13715 original size:22 final size:21
Alignment explanation
Indices: 13682--13726 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
13672 TTTTTGAATT
*
13682 TTATTTTAAAAAAATCTTAAAA
1 TTATTTTAAAAAAA-CTCAAAA
13704 TTATATTT-AAAAAACTCAAAA
1 TTAT-TTTAAAAAAACTCAAAA
13725 TT
1 TT
13727 TTCAAAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 10 0.48
23 3 0.14
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (21 bp):
TTATTTTAAAAAAACTCAAAA
Found at i:21642 original size:17 final size:16
Alignment explanation
Indices: 21617--21672 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
21607 TAGAAGAAGT
21617 AAAAA-AGAAAGATAA
1 AAAAAGAGAAAGATAA
*
21632 AGAAAAGAGAAAAGATAG
1 A-AAAAGAG-AAAGATAA
* *
21650 AAAAAGAAAAAGAGAA
1 AAAAAGAGAAAGATAA
21666 AAAAAGA
1 AAAAAGA
21673 AAAAATGAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
15 1 0.03
16 17 0.50
17 8 0.24
18 8 0.24
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.04
Consensus pattern (16 bp):
AAAAAGAGAAAGATAA
Found at i:21655 original size:22 final size:23
Alignment explanation
Indices: 21619--21676 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 23
21609 GAAGAAGTAA
*
21619 AAAAGAAAGATAAAG-AAAAGAG
1 AAAAGAAAGAAAAAGAAAAAGAG
*
21641 AAAAGATAGAAAAAGAAAAAGAG
1 AAAAGAAAGAAAAAGAAAAAGAG
21664 AAAA-AAAGAAAAA
1 AAAAGAAAGAAAAA
21677 ATGAGAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 21 0.66
23 11 0.34
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (23 bp):
AAAAGAAAGAAAAAGAAAAAGAG
Found at i:21660 original size:16 final size:16
Alignment explanation
Indices: 21624--21676 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
21614 AGTAAAAAAG
21624 AAAGATAAAGAAAAGAGA
1 AAAGATAAA-AAAAGA-A
*
21642 AAAGATAGAAAAAGAA
1 AAAGATAAAAAAAGAA
*
21658 AAAGAGAAAAAAAGAA
1 AAAGATAAAAAAAGAA
21674 AAA
1 AAA
21677 ATGAGAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 18 0.56
17 6 0.19
18 8 0.25
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (16 bp):
AAAGATAAAAAAAGAA
Found at i:24013 original size:42 final size:42
Alignment explanation
Indices: 23954--24707 Score: 526
Period size: 45 Copynumber: 17.8 Consensus size: 42
23944 GAAGCTTCAA
** *
23954 CTTGACTCCCTCGTGAAGAGGAGTCAATGTTTCAATGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAATGTCATT
* * *
23996 CTTGACTTCCTCGTGAAGAGGA-TCCAATCTTTCATTGTCTTT
1 CTTGACTTTCTCGTGAAGAGGAGT-CAATCTTTCAATGTCATT
** *
24038 CTTGACTTTCTCGTGAAGAGGAGTCAAAATTTCAATGTTATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAATGTCATT
* ** *
24080 CTCGACTCCCT-GTGAAGAGGAGTCAATCTTTCAATGTTATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAATGTCATT
* * *
24121 CTTGACTTCCTCGTGAAGA-GAATCAATC-TT---TGTTATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAATGTCATT
*
24158 CTTGAC-TTCTTCGTGAAGAGAAGTCAATCTTT---T-T-ATT
1 CTTGACTTTC-TCGTGAAGAGGAGTCAATCTTTCAATGTCATT
* * *
24195 CTTGACTCTCTCGTGAAGTGGAGTCAATCTTTCAATGTTATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAATGTCATT
* * *
24237 CTTGAGTTCCTCGTGAAGAGAAGTCAATC-TT---TGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAATGTCATT
* *
24275 CTTGACTTTCTCGCGAAGAAGAGTCAATCTTT-AGTGATGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCA---ATGTCATT
* * *
24319 CTTAACTTTCTCGTGAAGATGA-TCAATCTTT-AGTGATTTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCA---ATGTCATT
* * * * * *
24362 CTCGACTTTCTCATGAAGAGAACTCAACCTTTTAGCGATGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATC-TTT--CAATGTCATT
* * * * *
24407 CTTGACTTTCTCATGAAGAGAAGTCAACTTTTTAGCGATGACATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAA-TCTTT--CAATGTCATT
* * *
24452 CTTGACTTTCTCGTGAAGAAGAGTCAATCTTT-AGTGTTGTAATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCA---ATGTCATT
* * * *
24496 CTTGACTTTCTCGTGAAGAAGAGTCAATCTTTTAGTGTTGACTT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAATG-TCA-TT
* * *
24540 CCTTGACTTTCTCGTGAAGAGGAGTCAATATTTTAGTGTTTTC-TT
1 -CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAATG---TCATT
* * *
24585 CCTTGATTTTCTCATAAAGAGGAGTCAATCTTTCAGTATTGTCATT
1 -CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCA--A-TGTCATT
* * * * * *
24631 TTTGATTTTCTCGTGAAGAGAAGTCAATATTTCAGTGTTGTGATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCA---ATGTCATT
* * * *
24676 ATTGACTTTCTTGGGAAGAGGAGTCAACCTTT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTT
24708 TAGTGATGTC
Statistics
Matches: 587, Mismatches: 87, Indels: 73
0.79 0.12 0.10
Matches are distributed among these distances:
36 2 0.00
37 51 0.09
38 40 0.07
39 5 0.01
40 3 0.01
41 49 0.08
42 114 0.19
43 40 0.07
44 74 0.13
45 203 0.35
46 2 0.00
47 2 0.00
48 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (42 bp):
CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAATGTCATT
Found at i:24163 original size:37 final size:37
Alignment explanation
Indices: 23993--24306 Score: 233
Period size: 42 Copynumber: 7.9 Consensus size: 37
23983 TTTCAATGTC
*
23993 ATTCTTGACTTCCTCGTGAAGAGGATCCAATCTTTCATTGTCT
1 ATTCTTGACTTCCTCGTGAAGAGAAT-CAATC--T--TTGT-T
* *
24036 -TTCTTGACTTTCTCGTGAAGAGGAGTCAAAAT-TTCAATGTT
1 ATTCTTGACTTCCTCGTGAAGA-GAATC--AATCTT---TGTT
* * *
24077 ATTCTCGACTCCCT-GTGAAGAGGAGTCAATCTTTCAATGTT
1 ATTCTTGACTTCCTCGTGAAGA-GAATCAATC-TT---TGTT
24118 ATTCTTGACTTCCTCGTGAAGAGAATCAATCTTTGTT
1 ATTCTTGACTTCCTCGTGAAGAGAATCAATCTTTGTT
*
24155 ATTCTTGACTTCTTCGTGAAGAGAAGTCAATCTTT-TT
1 ATTCTTGACTTCCTCGTGAAGAGAA-TCAATCTTTGTT
* *
24192 ATTCTTGAC-TCTCTCGTGAAGTGGAGTCAATCTTTCAATGTT
1 ATTCTTGACTTC-CTCGTGAAG-AGAATCAATC-TT---TGTT
* *
24234 ATTCTTGAGTTCCTCGTGAAGAGAAGTCAATCTTTGTC
1 ATTCTTGACTTCCTCGTGAAGAGAA-TCAATCTTTGTT
* * *
24272 ATTCTTGACTTTCTCGCGAAGAAGAGTCAATCTTT
1 ATTCTTGACTTCCTCGTGAAG-AGAATCAATCTTT
24307 AGTGATGTCA
Statistics
Matches: 229, Mismatches: 21, Indels: 47
0.77 0.07 0.16
Matches are distributed among these distances:
36 2 0.01
37 53 0.23
38 43 0.19
39 7 0.03
40 2 0.01
41 49 0.21
42 66 0.29
43 4 0.02
44 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (37 bp):
ATTCTTGACTTCCTCGTGAAGAGAATCAATCTTTGTT
Found at i:24381 original size:241 final size:240
Alignment explanation
Indices: 23954--24393 Score: 543
Period size: 241 Copynumber: 1.8 Consensus size: 240
23944 GAAGCTTCAA
* *
23954 CTTGACTCCCTCGTGAAGAGGAGTCAATGTTTCAATGTCATTCTTGACTTCCTCGTGAAGAGGAT
1 CTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTCATTCTTGACTTCCTCGTGAAGAGAAT
* * * * *
24019 CCAATCTTTCATTGTCTTTCTTGACTTTCTCGTGAAGAGGAGTCAAAATTTCAATGTTATTCTCG
66 CCAATC-TT-ATTGTCATTCTTGACTTTCTCGCGAAGAAGAGTCAAAATTTCAATGTCATTCTCA
* * *
24084 ACTCCCTGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGAGAA-TCAAT
129 ACTCCCTGTGAAGAGGAGTCAATCTTTCAATGTTATTCTCGACTTCCTCATGAAGAGAACTCAAC
24148 CTTTGTTATTCTTGACTTCTTCGTGAAGAGAAGTCAATCTTTTTATT
194 CTTTGTTATTCTTGACTTCTTCGTGAAGAGAAGTCAATCTTTTTATT
* * * *
24195 CTTGACTCTCTCGTGAAGTGGAGTCAATCTTTCAATGTTATTCTTGAGTTCCTCGTGAAGAGAAG
1 CTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTCATTCTTGACTTCCTCGTGAAGAGAA-
**
24260 T-CAATC-T-TTGTCATTCTTGACTTTCTCGCGAAGAAGAGTCAATCTTT-AGTGATGTCATTCT
65 TCCAATCTTATTGTCATTCTTGACTTTCTCGCGAAGAAGAGTCAAAATTTCA---ATGTCATTCT
* ** * * *
24321 TAACTTTCTCGTGAAGATGA-TCAATCTTT-AGTGATTTCATTCTCGACTTTCTCATGAAGAGAA
127 CAACTCCCT-GTGAAGAGGAGTCAATCTTTCAATG--TT-ATTCTCGACTTCCTCATGAAGAGAA
24384 CTCAACCTTT
188 CTCAACCTTT
24394 TAGCGATGTC
Statistics
Matches: 168, Mismatches: 22, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
236 1 0.01
237 35 0.21
238 3 0.02
239 24 0.14
240 11 0.07
241 85 0.51
242 9 0.05
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (240 bp):
CTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTCATTCTTGACTTCCTCGTGAAGAGAAT
CCAATCTTATTGTCATTCTTGACTTTCTCGCGAAGAAGAGTCAAAATTTCAATGTCATTCTCAAC
TCCCTGTGAAGAGGAGTCAATCTTTCAATGTTATTCTCGACTTCCTCATGAAGAGAACTCAACCT
TTGTTATTCTTGACTTCTTCGTGAAGAGAAGTCAATCTTTTTATT
Found at i:24414 original size:45 final size:45
Alignment explanation
Indices: 24268--24757 Score: 439
Period size: 45 Copynumber: 10.9 Consensus size: 45
24258 AGTCAATCTT
*
24268 TGTCATTCTTGACTTTCTCGCGAAGA-AGAGTCAATC-TTTAGTGA
1 TGTCATTCTTGACTTTCTCGTGAAGAGA-AGTCAATCTTTTAGTGA
*
24312 TGTCATTCTTAACTTTCTCGTGAAGATG-A-TCAATC-TTTAGTGA
1 TGTCATTCTTGACTTTCTCGTGAAGA-GAAGTCAATCTTTTAGTGA
* * * * * *
24355 TTTCATTCTCGACTTTCTCATGAAGAGAACTCAACCTTTTAGCGA
1 TGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGA
* *
24400 TGTCATTCTTGACTTTCTCATGAAGAGAAGTCAA-CTTTTTAGCGA
1 TGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATC-TTTTAGTGA
* *
24445 TGACATTCTTGACTTTCTCGTGAAGA-AGAGTCAATC-TTTAGTGT
1 TGTCATTCTTGACTTTCTCGTGAAGAGA-AGTCAATCTTTTAGTGA
* *
24489 TGTAATTCTTGACTTTCTCGTGAAGA-AGAGTCAATCTTTTAGTGT
1 TGTCATTCTTGACTTTCTCGTGAAGAGA-AGTCAATCTTTTAGTGA
* * * *
24534 TGAC-TTCCTTGACTTTCTCGTGAAGAGGAGTCAATATTTTAGTGT
1 TGTCATT-CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGA
* * * * * *
24579 TTTC-TTCCTTGATTTTCTCATAAAGAGGAGTCAATCTTTCAGT-A
1 TGTCATT-CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGA
* * * * *
24623 TTGTCATTTTTGATTTTCTCGTGAAGAGAAGTCAATATTTCAGTGT
1 -TGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGA
* * * * * *
24669 TGTGATTATTGACTTTCTTGGGAAGAGGAGTCAACCTTTTAGTGA
1 TGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGA
* *
24714 TGTCATTCTCAACTTGACTTTCTCGTAAAGAGTAGTCAA-CTTTT
1 TGTCA-T-T---CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTT
24758 CAGTAGTATC
Statistics
Matches: 375, Mismatches: 52, Indels: 33
0.82 0.11 0.07
Matches are distributed among these distances:
42 1 0.00
43 37 0.10
44 74 0.20
45 231 0.62
46 4 0.01
47 1 0.00
49 5 0.01
50 22 0.06
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.40
Consensus pattern (45 bp):
TGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGA
Found at i:24506 original size:134 final size:133
Alignment explanation
Indices: 23989--24722 Score: 555
Period size: 134 Copynumber: 5.7 Consensus size: 133
23979 AATGTTTCAA
* * * *
23989 TGTCATTCTTGACTTCCTCGTGAAGAGGA-TCCAATCTTTCA---TTGTCTTTCTTGACTTTCTC
1 TGTCATTCTTGACTTTCTCGTGAAGAGAAGT-CAATCTTTTAGTGTTGTCATTCTTGACTTTCTC
* * * * * ** *
24050 GTGAAGAGGAGTCAAAATTTCA---ATGTTATTCTCGACTCCCT-GTGAAGAGGAGTCAATCTTT
65 GTGAAGAGAAGTC-AATTTTTAGTGATGTCATTCTTGACTTTCTCGTGAAGAAGAGTCAATCTTT
*
24111 CAATG-
129 -AGTGT
*
24116 T-T-ATTCTTGACTTCCTCGTGAAGAGAA-TCAATC--TT--TG-T-T-ATTCTTGAC-TTCTTC
1 TGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTC-TC
* * **
24170 GTGAAGAGAAGTCAA-TCTT--T--T-T-ATTCTTGACTCTCTCGTGAAGTGGAGTCAATCTTTC
65 GTGAAGAGAAGTCAATTTTTAGTGATGTCATTCTTGACTTTCTCGTGAAGAAGAGTCAATCTTT-
*
24228 AATG-
129 AGTGT
* *
24232 T-T-ATTCTTGAGTTCCTCGTGAAGAGAAGTCAATC------T-TTGTCATTCTTGACTTTCTCG
1 TGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCG
* * * *
24288 CGAAGA-AGAGTCAATCTTTAGTGATGTCATTCTTAACTTTCTCGTGAAGATGA-TCAATCTTTA
66 TGAAGAGA-AGTCAATTTTTAGTGATGTCATTCTTGACTTTCTCGTGAAGAAGAGTCAATCTTTA
24351 GTGAT
130 GTG-T
* * * * * * *
24356 T-TCATTCTCGACTTTCTCATGAAGAGAACTCAACCTTTTAGCGATGTCATTCTTGACTTTCTCA
1 TGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCG
* *
24420 TGAAGAGAAGTCAACTTTTTAGCGATGACATTCTTGACTTTCTCGTGAAGAAGAGTCAATCTTTA
66 TGAAGAGAAGTCAA-TTTTTAGTGATGTCATTCTTGACTTTCTCGTGAAGAAGAGTCAATCTTTA
24485 GTGT
130 GTGT
* *
24489 TGTAATTCTTGACTTTCTCGTGAAGA-AGAGTCAATCTTTTAGTGTTGAC-TTCCTTGACTTTCT
1 TGTCATTCTTGACTTTCTCGTGAAGAGA-AGTCAATCTTTTAGTGTTGTCATT-CTTGACTTTCT
* * * * * * *
24552 CGTGAAGAGGAGTCAATATTTTAGTGTTTTC-TTCCTTGATTTTCTCATAAAGAGGAGTCAATCT
64 CGTGAAGAGAAGTCAAT-TTTTAGTGATGTCATT-CTTGACTTTCTCGTGAAGAAGAGTCAATCT
*
24616 TTCAGTAT
127 TT-AGTGT
* * * * * * *
24624 TGTCATTTTTGATTTTCTCGTGAAGAGAAGTCAATATTTCAGTGTTGTGATTATTGACTTTCTTG
1 TGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCG
* * *
24689 GGAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
66 TGAAGAGAAGTCAA-TTTTTAGTGATGTCATTCT
24723 CAACTTGACT
Statistics
Matches: 501, Mismatches: 65, Indels: 74
0.78 0.10 0.12
Matches are distributed among these distances:
115 14 0.03
116 53 0.11
117 30 0.06
118 7 0.01
119 5 0.01
120 23 0.05
121 1 0.00
122 6 0.01
123 10 0.02
124 28 0.06
125 51 0.10
126 1 0.00
127 1 0.00
132 30 0.06
133 43 0.09
134 112 0.22
135 81 0.16
136 5 0.01
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (133 bp):
TGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCG
TGAAGAGAAGTCAATTTTTAGTGATGTCATTCTTGACTTTCTCGTGAAGAAGAGTCAATCTTTAG
TGT
Found at i:24810 original size:51 final size:50
Alignment explanation
Indices: 24691--24813 Score: 135
Period size: 51 Copynumber: 2.4 Consensus size: 50
24681 CTTTCTTGGG
* *
24691 AAGAGGAGTCAACCTTTT-AGT-GATGTCATTCTCAACTTGACTTTCTCGTA
1 AAGAGGAGTCAA-CTTTTCAGTAG-TATCATTCTCAACTTGACTTTCTCATA
* *
24741 AAGAGTAGTCAACTTTTCAGTAGTATCATTCCTCAACTTGACTTTCTCATG
1 AAGAGGAGTCAACTTTTCAGTAGTATCATT-CTCAACTTGACTTTCTCATA
* *
24792 CAGAGGAGTTAA-TATTTCAGTA
1 AAGAGGAGTCAACT-TTTCAGTA
24814 ATGTTCCTTG
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
49 5 0.08
50 21 0.34
51 36 0.58
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (50 bp):
AAGAGGAGTCAACTTTTCAGTAGTATCATTCTCAACTTGACTTTCTCATA
Found at i:25599 original size:133 final size:134
Alignment explanation
Indices: 25410--25908 Score: 578
Period size: 133 Copynumber: 3.7 Consensus size: 134
25400 GTCTGGTATT
* * * * * *
25410 CCCTAAAGAGTAGTGGAGTAGATCTCCATTTTTATTTCAAATTTGGTCTTCCTGAAGAGAAGTGA
1 CCCTAAAGAGTAGTGGAGCAAAT-T-C-TCTTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGTGA
* *
25475 AGCAAATCATATTTGATTCAATCTTCCCTGAAGAGCATCGAAATGGATCAAAATTTTCTCGAG-C
63 AGCAAATCATATTCGATTCAATCTTCCCTGAAGAGCATCGAAGTGGATCAAAATTTTCTCGAGTC
25539 TGATCTC
128 TGATCTC
* * * * *
25546 CCCTAAAGATTAGTGGAGCATATTCTCTTTCTTTCAGATTTGGTCTTCTTGAAGAGCAGGGAATC
1 CCCTAAAGAGTAGTGGAGCAAATTCTCTTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGC
* * ** *
25611 AAATCATGTTCGATTCAATCTTCCCTGAAAAGCGGCGAAGTGGATCAAAATTATCTCGAGTCTGA
66 AAATCATATTCGATTCAATCTTCCCTGAAGAGCATCGAAGTGGATCAAAATTTTCTCGAGTCTGA
*
25676 TATC
131 TCTC
* * *
25680 CCCTAAAGAGTAGTGGAGCAAATTCTCCTTCTTTCAGATTTGGTCTTCCTTAAGAGCAGTGAAGA
1 CCCTAAAGAGTAGTGGAGCAAATTCTCTTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGC
* * * ** * * *
25745 AAATGAT-TAT-GATTCAATATTCCCTGATGAATAGT-GAAGTGAATCAAATTTTTCTCAAGTCT
66 AAATCATAT-TCGATTCAATCTTCCCTGAAGAGCA-TCGAAGTGGATCAAAATTTTCTCGAGTCT
25807 GATCTC
129 GATCTC
* * *
25813 CCCTAAAGAGTAGTGGAGCAGATTCT-TCTTCTTTCAGATTTGGTATTCCTAAAGAGCAGTGAAG
1 CCCTAAAGAGTAGTGGAGCAAATTCTCT-TTCTTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAG
* *
25877 CAAAT-AGATTCCGATTCAATCTTCCCTAAAGA
65 CAAATCATATT-CGATTCAATCTTCCCTGAAGA
25909 ACAGTGGAAT
Statistics
Matches: 308, Mismatches: 48, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
132 2 0.01
133 196 0.64
134 89 0.29
135 1 0.00
136 20 0.06
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (134 bp):
CCCTAAAGAGTAGTGGAGCAAATTCTCTTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGC
AAATCATATTCGATTCAATCTTCCCTGAAGAGCATCGAAGTGGATCAAAATTTTCTCGAGTCTGA
TCTC
Found at i:25829 original size:267 final size:267
Alignment explanation
Indices: 25400--25903 Score: 651
Period size: 267 Copynumber: 1.9 Consensus size: 267
25390 TATTTGAAAG
* * * *
25400 GTCTGGTATTCCCTAAAGAGTAGTGGAGTAGATCTCCATTTTTATTTCAAATTTGGTCTTCCTGA
1 GTCTGATATCCCCTAAAGAGTAGTGGAGCAAATCTCC---TTTATTTCAAATTTGGTCTTCCTGA
* * * * *
25465 AGAGAAGTGAAGCAAATCATATTTGATTCAATCTTCCCTGAAGAGCATCGAAATGGATCAAAATT
63 AGAGAAGTGAAGAAAATCATATATGATTCAATATTCCCTGAAGAACATCGAAATGAATCAAAATT
* * * *
25530 TTCTCGAGCTGATCTCCCCTAAAGATTAGTGGAGCATATTC-TCTTTCTTTCAGATTTGGTCTTC
128 TTCTCAAGCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTC-TTCTTTCAGATTTGGTATTC
* * *
25594 TTGAAGAGCAGGGAATCAAATCATG-TT-CGATTCAATCTTCCCTGAAAAGCGGCGAAGTGGATC
192 CTAAAGAGCAGGGAAGCAAAT-A-GATTCCGATTCAATCTTCCCTGAAAAGCGGCGAAGTGGATC
25657 AAAATTATCTCGA
255 AAAATTATCTCGA
* * *
25670 GTCTGATATCCCCTAAAGAGTAGTGGAGCAAATTCTCC-TTCTTTCAGATTTGGTCTTCCTTAAG
1 GTCTGATATCCCCTAAAGAGTAGTGGAGCAAA-TCTCCTTTATTTCAAATTTGGTCTTCCTGAAG
* * * * * *
25734 AGCAGTGAAGAAAATGAT-TATGATTCAATATTCCCTGATGAATAGT-GAAGTGAATCAAATTTT
65 AGAAGTGAAGAAAATCATATATGATTCAATATTCCCTGAAGAACA-TCGAAATGAATCAAAATTT
25797 TCTCAAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTATTCC
129 TCTCAAG-CTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTATTCC
*
25862 TAAAGAGCAGTGAAGCAAATAGATTCCGATTCAATCTTCCCT
193 TAAAGAGCAGGGAAGCAAATAGATTCCGATTCAATCTTCCCT
25904 AAAGAACAGT
Statistics
Matches: 202, Mismatches: 26, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
265 1 0.00
266 44 0.22
267 122 0.60
268 2 0.01
270 28 0.14
271 5 0.02
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (267 bp):
GTCTGATATCCCCTAAAGAGTAGTGGAGCAAATCTCCTTTATTTCAAATTTGGTCTTCCTGAAGA
GAAGTGAAGAAAATCATATATGATTCAATATTCCCTGAAGAACATCGAAATGAATCAAAATTTTC
TCAAGCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTATTCCTAA
AGAGCAGGGAAGCAAATAGATTCCGATTCAATCTTCCCTGAAAAGCGGCGAAGTGGATCAAAATT
ATCTCGA
Found at i:27239 original size:16 final size:16
Alignment explanation
Indices: 27220--27251 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27210 ATTAAAATGG
*
27220 AAAAAATGAAAAAAGA
1 AAAAAAAGAAAAAAGA
27236 AAAAAAAGAAAAAAGA
1 AAAAAAAGAAAAAAGA
27252 TGATATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAAAAAGAAAAAAGA
Found at i:29498 original size:35 final size:34
Alignment explanation
Indices: 29459--29531 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 34
29449 TTGCAAATTC
29459 AAATAA-AAAACAAATTAAATAAATTAAAAT-TAAGA
1 AAATAACAAAA-AAA-TAAATAAATTAAAATCTAA-A
**
29494 AAATAACAAAAAAATATTTAAATTAAAATCTAAA
1 AAATAACAAAAAAATAAATAAATTAAAATCTAAA
29528 AAAT
1 AAAT
29532 TAAATATGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 18 0.53
35 12 0.35
36 4 0.12
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (34 bp):
AAATAACAAAAAAATAAATAAATTAAAATCTAAA
Found at i:32627 original size:5 final size:6
Alignment explanation
Indices: 32586--32627 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
32576 TTCATTTTCA
*
32586 CTTTTT CTTTATT CTTTATT CTTCTT -TTTTT CTTTTT CTTTT
1 CTTTTT CTTT-TT CTTT-TT CTTTTT CTTTTT CTTTTT CTTTT
32628 AACAGTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 4 0.12
6 16 0.50
7 12 0.38
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:51381 original size:30 final size:31
Alignment explanation
Indices: 51347--51411 Score: 114
Period size: 30 Copynumber: 2.1 Consensus size: 31
51337 AAAATTAATA
51347 ATTTAATACAAATTGTTACAT-AAATTTGTG
1 ATTTAATACAAATTGTTACATAAAATTTGTG
*
51377 ATTTAATACAAATTTTTACATAAAATTTGTG
1 ATTTAATACAAATTGTTACATAAAATTTGTG
51408 ATTT
1 ATTT
51412 CAACAGAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 20 0.61
31 13 0.39
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (31 bp):
ATTTAATACAAATTGTTACATAAAATTTGTG
Found at i:56235 original size:42 final size:42
Alignment explanation
Indices: 56146--56235 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
56136 ACAAACGCAT
* * * * ** *
56146 CAATAGAGTAGTAATTTCGCGGTGTTTTTAGCCCAAACGCCG
1 CAATAAAGTAGTAATTTAGCGGCGTTTGTAGCAAAAACACCG
* *
56188 TAATAAAGTAGTAATTTAGTGGCGTTTGTAGCAAAAACACCG
1 CAATAAAGTAGTAATTTAGCGGCGTTTGTAGCAAAAACACCG
56230 CAATAA
1 CAATAA
56236 GGTTTTTTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (42 bp):
CAATAAAGTAGTAATTTAGCGGCGTTTGTAGCAAAAACACCG
Found at i:56327 original size:207 final size:206
Alignment explanation
Indices: 55973--56350 Score: 562
Period size: 207 Copynumber: 1.8 Consensus size: 206
55963 GTTTCTTGTA
* * * * * *
55973 CAAACGCCGTAATAGAGTAGTAATTTAGCGTGTTTTTACTACAAACGCCGCAATAGGGTTGTTTA
1 CAAACGCCGTAATAAAGTAGTAATTTAGCGCGTTTGTACTAAAAACACCGCAATAAGGTTGTTTA
* * *
56038 TAGTGGTGTTTTTCCAACAAACGCCGCAATAAAGATTACTTTAGCGTCATTTTTAGACAAACGTC
66 TAGTGGTGTTTTTCCAACAAACGCCACAATAAAGAATACTTTAGCGTCATTTTTAGACAAACGCC
*
56103 ACAGTAGGATTAATCAATAGTGGCGTTTCCTGTACAAACGCATCAATAGAGTAGTAATTTCGCGG
131 ACAATAGGATTAATCAATAGTGGCGTTTCCTGTACAAACGCATCAATAGAGTAGTAATTTCGCGG
56168 TGTTTTTAGCC
196 TGTTTTTAGCC
* *
56179 CAAACGCCGTAATAAAGTAGTAATTTAGTGGCGTTTGTAGC-AAAAACACCGCAATAAGGTTTTT
1 CAAACGCCGTAATAAAGTAGTAATTTAG-CGCGTTTGTA-CTAAAAACACCGCAATAAGGTTGTT
** * *
56243 TATAGTGGTGTTTTTTGAACAAACGTCACAATAAAGAATACTTTAGCGTCGTTTTTAGACAAACG
64 TATAGTGGTGTTTTTCCAACAAACGCCACAATAAAGAATACTTTAGCGTCATTTTTAGACAAACG
*
56308 CCACAATAGTG-TTAATCAATAGTGGCGTTTCTTGTACAAACGC
129 CCACAATAG-GATTAATCAATAGTGGCGTTTCCTGTACAAACGC
56351 CGCAAAAACA
Statistics
Matches: 152, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
206 27 0.18
207 123 0.81
208 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (206 bp):
CAAACGCCGTAATAAAGTAGTAATTTAGCGCGTTTGTACTAAAAACACCGCAATAAGGTTGTTTA
TAGTGGTGTTTTTCCAACAAACGCCACAATAAAGAATACTTTAGCGTCATTTTTAGACAAACGCC
ACAATAGGATTAATCAATAGTGGCGTTTCCTGTACAAACGCATCAATAGAGTAGTAATTTCGCGG
TGTTTTTAGCC
Found at i:60371 original size:16 final size:17
Alignment explanation
Indices: 60332--60365 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
60322 CTTGCTCCCA
60332 TAAAA-TTTTATCAATT
1 TAAAAGTTTTATCAATT
60348 TAAAAGTTTTAT-AATT
1 TAAAAGTTTTATCAATT
60364 TA
1 TA
60366 GGAGTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TAAAAGTTTTATCAATT
Found at i:65723 original size:21 final size:22
Alignment explanation
Indices: 65682--65733 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
65672 GTAAGGGAAT
65682 TAGAGAGAGTAGCAATGGAAGCA
1 TAGAGAGAGTAGCAA-GGAAGCA
65705 TAGAGAGCAGTAGC-A-GAAGCA
1 TAGAGAG-AGTAGCAAGGAAGCA
*
65726 CAGAGAGA
1 TAGAGAGA
65734 ATCAACCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 1 0.04
21 12 0.44
23 8 0.30
24 6 0.22
ACGTcount: A:0.44, C:0.12, G:0.35, T:0.10
Consensus pattern (22 bp):
TAGAGAGAGTAGCAAGGAAGCA
Found at i:66281 original size:44 final size:44
Alignment explanation
Indices: 66168--66307 Score: 127
Period size: 44 Copynumber: 3.2 Consensus size: 44
66158 AAAAGCTTCA
* * ** * * * * *
66168 CTATATCCCAGACCTTTAGCGGCGTTTATATATAATAAACGGCG
1 CTATATACAAGACCTTTAGAAGTGTTTATATAAAAAAAAAGCCG
*** *
66212 CTATATACAAGACCTTTAGAAGTGTTTATATCCGAAAAATGCCG
1 CTATATACAAGACCTTTAGAAGTGTTTATATAAAAAAAAAGCCG
* ** *
66256 CTATATACAAGACCTTTTGCGGTGTTTGTATAAAAAAAAAGCCG
1 CTATATACAAGACCTTTAGAAGTGTTTATATAAAAAAAAAGCCG
66300 CTATATAC
1 CTATATAC
66308 CAGATCTATT
Statistics
Matches: 77, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 77 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (44 bp):
CTATATACAAGACCTTTAGAAGTGTTTATATAAAAAAAAAGCCG
Found at i:66337 original size:44 final size:44
Alignment explanation
Indices: 66234--66338 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 44
66224 CCTTTAGAAG
* * * * *
66234 TGTTTATATCCGAAAAATGCCGCTATATACAAGACCTTTTGCGG
1 TGTTTATATCCAAAAAAAGCCGCTATATACAAGACCTATTCCGC
* ** * *
66278 TGTTTGTATAAAAAAAAAGCCGCTATATACCAGATCTATTCCGC
1 TGTTTATATCCAAAAAAAGCCGCTATATACAAGACCTATTCCGC
*
66322 TGTTTTTATCCAAAAAA
1 TGTTTATATCCAAAAAA
66339 CTCCGCTAAA
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.32
Consensus pattern (44 bp):
TGTTTATATCCAAAAAAAGCCGCTATATACAAGACCTATTCCGC
Found at i:66478 original size:43 final size:43
Alignment explanation
Indices: 66411--66497 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
66401 TTGCGATGCC
*
66411 TGTGGGACAAACGTCACTAAATCTCAACACCTATTGTGGCGTT
1 TGTGGGACAAACGTCACTAAATCTCAACACCTATTGCGGCGTT
* * **
66454 TGTGGGACAAACG-CTGCTATATCTCTTCACCTATTGCGGCGTT
1 TGTGGGACAAACGTC-ACTAAATCTCAACACCTATTGCGGCGTT
66497 T
1 T
66498 TTTGTTATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
42 1 0.03
43 37 0.97
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (43 bp):
TGTGGGACAAACGTCACTAAATCTCAACACCTATTGCGGCGTT
Found at i:68792 original size:106 final size:107
Alignment explanation
Indices: 68596--68898 Score: 369
Period size: 106 Copynumber: 2.8 Consensus size: 107
68586 TGATTAAATG
* *
68596 CATATGTTAATGAACGACCGTATAGGCACTATGTGTGCAACCTACGAAATTCATCATATGTTGAT
1 CATA-GTTGATGAACGACCGTATAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGAT
* * * * *
68661 GAACAACCATATAGGCACTATGTGTGCAACCCACGTAATTCTT
65 GAACGACCATACAGGCACTAAGTGTGCAACCCACGAAATTCAT
* *
68704 CATA-TTGATGAACAACCATATAGGCACTATGTGTGCAACCCAC-AGAATTCATCATATGTTGAT
1 CATAGTTGATGAACGACCGTATAGGCACTATGTGTGCAACCCACGA-AATTCATCATATGTTGAT
* *
68767 GAACGACCATACATGCTCTAAGTGTGCAACCCACGAAATTCAT
65 GAACGACCATACAGGCACTAAGTGTGCAACCCACGAAATTCAT
* * * * * * *
68810 CATATGTTGAT-AACGATCGTATAGGCACTAAGTGTGCAACCCATGTAATTCATAATTTGTTTAT
1 CATA-GTTGATGAACGACCGTATAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGAT
* * *
68874 GAACGACCGTATAAGCACTAAGTGT
65 GAACGACCATACAGGCACTAAGTGT
68899 ATAACCCCTT
Statistics
Matches: 167, Mismatches: 24, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
105 1 0.01
106 93 0.56
107 64 0.38
108 9 0.05
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.28
Consensus pattern (107 bp):
CATAGTTGATGAACGACCGTATAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATG
AACGACCATACAGGCACTAAGTGTGCAACCCACGAAATTCAT
Found at i:68905 original size:54 final size:54
Alignment explanation
Indices: 68596--68898 Score: 371
Period size: 54 Copynumber: 5.7 Consensus size: 54
68586 TGATTAAATG
* * * *
68596 CATATGTTAATGAACGACCGTATAGGCACTATGTGTGCAACCTACGAAATTCAT
1 CATATGTTGATGAACGACCATATAGGCACTAAGTGTGCAACCCACGAAATTCAT
* * * *
68650 CATATGTTGATGAACAACCATATAGGCACTATGTGTGCAACCCACGTAATTCTT
1 CATATGTTGATGAACGACCATATAGGCACTAAGTGTGCAACCCACGAAATTCAT
* *
68704 CATA--TTGATGAACAACCATATAGGCACTATGTGTGCAACCCAC-AGAATTCAT
1 CATATGTTGATGAACGACCATATAGGCACTAAGTGTGCAACCCACGA-AATTCAT
* * *
68756 CATATGTTGATGAACGACCATACATGCTCTAAGTGTGCAACCCACGAAATTCAT
1 CATATGTTGATGAACGACCATATAGGCACTAAGTGTGCAACCCACGAAATTCAT
* * * *
68810 CATATGTTGAT-AACGATCGTATAGGCACTAAGTGTGCAACCCATGTAATTCAT
1 CATATGTTGATGAACGACCATATAGGCACTAAGTGTGCAACCCACGAAATTCAT
* * * * *
68863 AATTTGTTTATGAACGACCGTATAAGCACTAAGTGT
1 CATATGTTGATGAACGACCATATAGGCACTAAGTGT
68899 ATAACCCCTT
Statistics
Matches: 219, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
52 49 0.22
53 43 0.20
54 126 0.58
55 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.28
Consensus pattern (54 bp):
CATATGTTGATGAACGACCATATAGGCACTAAGTGTGCAACCCACGAAATTCAT
Found at i:69007 original size:58 final size:60
Alignment explanation
Indices: 68912--69024 Score: 167
Period size: 58 Copynumber: 1.9 Consensus size: 60
68902 ACCCCTTTTC
* *
68912 AATGCCTAACGGTGTATTTTTGGCAGAAAGGTACCACTAATG-CAGTTAGATGAAAAGTCA
1 AATGCCTAACAGTGTA-TTTTGGCAGAAAGGTACCACTAATGTAAGTTAGATGAAAAGTCA
* *
68972 AATGCCTAACATTGTA-TTTGGCAGAAAGGTGCCACTAATGTAAGTTAGATGAA
1 AATGCCTAACAGTGTATTTTGGCAGAAAGGTACCACTAATGTAAGTTAGATGAA
69025 GAATGGTGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
58 23 0.48
59 11 0.23
60 14 0.29
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.27
Consensus pattern (60 bp):
AATGCCTAACAGTGTATTTTGGCAGAAAGGTACCACTAATGTAAGTTAGATGAAAAGTCA
Found at i:70041 original size:22 final size:22
Alignment explanation
Indices: 70016--70072 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
70006 CTTTAAATTT
70016 TATTTTATTTTAATTTAGCCAC
1 TATTTTATTTTAATTTAGCCAC
* *
70038 TA-TTTATTTCTGATTTAGCTAC
1 TATTTTATTT-TAATTTAGCCAC
70060 TAACTTTTATTTT
1 T-A-TTTTATTTT
70073 CATGCATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 7 0.24
22 13 0.45
23 1 0.03
24 1 0.03
25 7 0.24
ACGTcount: A:0.25, C:0.12, G:0.05, T:0.58
Consensus pattern (22 bp):
TATTTTATTTTAATTTAGCCAC
Found at i:74610 original size:37 final size:37
Alignment explanation
Indices: 74539--74612 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
74529 AGGGATCAAC
* * *
74539 ATCTCGCTTGAGATAGTTCACTTGAAATAGAAGATTT
1 ATCTCACTTGAGATAGTTCACTCGAAACAGAAGATTT
*
74576 ATCTCACTTGAGATAGTTTCGCTCGAAACA-AAGATTT
1 ATCTCACTTGAGATAG-TTCACTCGAAACAGAAGATTT
74613 TAAGAAACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 22 0.69
38 10 0.31
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (37 bp):
ATCTCACTTGAGATAGTTCACTCGAAACAGAAGATTT
Found at i:74884 original size:39 final size:39
Alignment explanation
Indices: 74840--75053 Score: 315
Period size: 39 Copynumber: 5.5 Consensus size: 39
74830 AGGGATCTAC
*
74840 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAATATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
74879 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
74918 ATCTTGCTTGAGATAGTTTCACTCG-AACAGAAGACTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
74956 ATCTCGCTTGAAATAGTTTCACTCGAAATAGAAGATTTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTT
* *
74996 ATCTCACTTGAGATA-TTTCACTCGAAACAGTAGATTTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTT
* *
75035 ATCTCACTTGAGATTGTTT
1 ATCTCGCTTGAGATAGTTT
75054 TTCTTAAAAT
Statistics
Matches: 160, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
38 35 0.22
39 106 0.66
40 19 0.12
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (39 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
Found at i:74973 original size:77 final size:79
Alignment explanation
Indices: 74840--75045 Score: 310
Period size: 77 Copynumber: 2.6 Consensus size: 79
74830 AGGGATCTAC
* *
74840 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAATATTTTATCTCGCTTGAGATAGTTTCACTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAAATAGTTTCACTCGA
74905 AACAGAAGA-TTTT
66 AACAGAAGATTTTT
* *
74918 ATCTTGCTTGAGATAGTTTCACTCG-AACAGAAGACTTTATCTCGCTTGAAATAGTTTCACTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAAATAGTTTCACTCGA
*
74982 AATAGAAGATTTTT
66 AACAGAAGATTTTT
* * *
74996 ATCTCACTTGAGATA-TTTCACTCGAAACAGTAGATTTTTATCTCACTTGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTTATCTCGCTTGA
75046 GATTGTTTTT
Statistics
Matches: 115, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
77 53 0.46
78 49 0.43
79 13 0.11
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (79 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAAATAGTTTCACTCGA
AACAGAAGATTTTT
Found at i:75341 original size:92 final size:90
Alignment explanation
Indices: 75158--75407 Score: 312
Period size: 92 Copynumber: 2.8 Consensus size: 90
75148 CATTTCCTGT
* * *
75158 GCTCGATTCACAA-CACTTT-GAATCAACCACGCCT-AACATGAGGGACCAACATTCCAGTAGAG
1 GCTCGATTCA-AAGCA-TTTCGAATCAGCGACGCCTCAA-TTGAGGGA-CAACATTCCAGTAGAG
75220 AATTCATGAGAAGAACTTATTCAACCTTG
62 AATTCATGAGAAGAACTTATTCAACCTTG
* ** * *
75249 GCTCGATTTATGGCATTTCGAATCAGTGACGCCTTAATTGAGGGATCAACATTCCTAGTAGAGAA
1 GCTCGATTCAAAGCATTTCGAATCAGCGACGCCTCAATTGAGGGA-CAACATTCC-AGTAGAGAA
*
75314 TTCATGAGAATAACTTATTCAACCTTG
64 TTCATGAGAAGAACTTATTCAACCTTG
*
75341 GCTCGATTCAAAGCATTTCGAATCAGCGACGCCTCACTTGA--GACAACATTTCCAGTAGAGAAT
1 GCTCGATTCAAAGCATTTCGAATCAGCGACGCCTCAATTGAGGGACAACA-TTCCAGTAGAGAAT
75404 TCAT
65 TCAT
75408 AAAGAATAGC
Statistics
Matches: 139, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
89 19 0.14
90 9 0.06
91 39 0.28
92 72 0.52
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (90 bp):
GCTCGATTCAAAGCATTTCGAATCAGCGACGCCTCAATTGAGGGACAACATTCCAGTAGAGAATT
CATGAGAAGAACTTATTCAACCTTG
Found at i:76929 original size:15 final size:14
Alignment explanation
Indices: 76902--76928 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
76892 GTTTATTTAT
76902 TTTTTTCTATTTTG
1 TTTTTTCTATTTTG
76916 TTTTTTCTATTTT
1 TTTTTTCTATTTT
76929 TATTATTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.07, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTTTCTATTTTG
Found at i:76935 original size:23 final size:23
Alignment explanation
Indices: 76891--76935 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
76881 CTTGTACTTG
*
76891 TGTTTATTTATTTTTTTCTATTT
1 TGTTTATTTATTTTTATCTATTT
*
76914 TGTTTTTTCTATTTTTAT-TATT
1 TGTTTATT-TATTTTTATCTATT
76936 GTTATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.78
Consensus pattern (23 bp):
TGTTTATTTATTTTTATCTATTT
Found at i:76950 original size:23 final size:21
Alignment explanation
Indices: 76904--76961 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
76894 TTATTTATTT
*
76904 TTTTCTATT-TTGTTTTTTCTA
1 TTTT-TATTATTGTTTTTTATA
76925 TTTTTATTATTGTTATTTTATAA
1 TTTTTATTATTGTT-TTTTAT-A
*
76948 TTTTAATTA-TGTTT
1 TTTTTATTATTGTTT
76962 ATTAATTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 4 0.12
21 10 0.31
22 9 0.28
23 9 0.28
ACGTcount: A:0.19, C:0.03, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTTTATTATTGTTTTTTATA
Done.