Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001762.1 Hibiscus syriacus cultivar Beakdansim tig00003559_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: 91798
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:100 original size:13 final size:14
Alignment explanation
Indices: 79--107 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
69 TATTATAAAT
79 AATTATATTTTTAA
1 AATTATATTTTTAA
93 AATT-TATTTTTAA
1 AATTATATTTTTAA
106 AA
1 AA
108 ATAAATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTATATTTTTAA
Found at i:1114 original size:19 final size:21
Alignment explanation
Indices: 1074--1124 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
1064 GATAACAATG
1074 ATTTCTTTCTCACTTTTCTTTT
1 ATTT-TTTCTCACTTTTCTTTT
1096 -TCTTTTTCTC-CTTTT-TTTT
1 AT-TTTTTCTCACTTTTCTTTT
1115 ATTTTTTCTC
1 ATTTTTTCTC
1125 TGGTTCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 12 0.44
20 6 0.22
21 7 0.26
22 2 0.07
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.73
Consensus pattern (21 bp):
ATTTTTTCTCACTTTTCTTTT
Found at i:5574 original size:2 final size:2
Alignment explanation
Indices: 5559--5604 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
5549 CTCCACATAC
* *
5559 AT AT AT AC AC 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
5601 AT AT
1 AT AT
5605 TGTTTGAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:14102 original size:4 final size:4
Alignment explanation
Indices: 14088--14117 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
14078 TTTTTTAGTC
14088 TATT T-TT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
14118 AATCTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TATT
Found at i:14396 original size:25 final size:25
Alignment explanation
Indices: 14362--14420 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
14352 CAATTATTTT
* *
14362 TTTTTAAATCATATCGAACGTTACG
1 TTTTAAAATCATATCGAACGTTACA
*
14387 TTTTAAAATCATATCTAACGTTACA
1 TTTTAAAATCATATCGAACGTTACA
14412 TTGTTAAAA
1 TT-TTAAAA
14421 AATAAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 24 0.80
26 6 0.20
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (25 bp):
TTTTAAAATCATATCGAACGTTACA
Found at i:27247 original size:20 final size:20
Alignment explanation
Indices: 27153--27365 Score: 250
Period size: 20 Copynumber: 10.6 Consensus size: 20
27143 GATTTTCCAT
* ** *
27153 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
27173 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
27193 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
27213 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
27233 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
27253 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
27273 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
27293 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
27313 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
27334 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
27354 AATCGCAACGCG
1 AATCGCAACGCG
27366 ATATTTAAAG
Statistics
Matches: 165, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 145 0.88
21 17 0.10
22 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:27786 original size:33 final size:33
Alignment explanation
Indices: 27747--27817 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
27737 TTCACTTAGA
*
27747 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
27780 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
27813 TTTCA
1 TTTCA
27818 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:27957 original size:14 final size:14
Alignment explanation
Indices: 27938--27992 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
27928 AGAATGACTG
27938 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
27952 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
27971 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
27985 TCGCAACG
1 TCGCAACG
27993 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:27975 original size:33 final size:33
Alignment explanation
Indices: 27938--28008 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
27928 AGAATGACTG
**
27938 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
27971 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
28004 TCGCA
1 TCGCA
28009 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:28026 original size:19 final size:19
Alignment explanation
Indices: 28004--28101 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
27994 GAAACCAAAA
*
28004 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
28023 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
28037 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
28056 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
28070 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
28089 TCGCGTTGCGATT
1 TCGCGTTGCGATT
28102 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:28045 original size:14 final size:14
Alignment explanation
Indices: 28026--28115 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
28016 TTTCATTTCG
28026 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
28040 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
28059 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
28073 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
28090 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
28106 CGTTGCGATT
1 CGTTGCGATT
28116 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:28051 original size:33 final size:33
Alignment explanation
Indices: 28009--28123 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
27999 CAAAATCGCA
28009 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
28042 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
28075 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
28108 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
28124 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:30035 original size:92 final size:93
Alignment explanation
Indices: 29821--30107 Score: 558
Period size: 93 Copynumber: 3.1 Consensus size: 93
29811 TAGATTGCTT
*
29821 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29886 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
29914 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29979 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
30006 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
30071 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
30099 AGTAAATTT
1 AGTAAATTT
30108 ATCCATTCAA
Statistics
Matches: 192, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 92 0.48
93 100 0.52
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:30191 original size:19 final size:19
Alignment explanation
Indices: 30151--30279 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
30141 TAGTTTACTT
* *
30151 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
30171 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
30190 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
30209 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
30223 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
30242 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
30256 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
30275 TCGCA
1 TCGCA
30280 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:30230 original size:33 final size:32
Alignment explanation
Indices: 30187--30279 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
30177 CGCGAAACCA
**
30187 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
30219 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
30252 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
30280 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:30277 original size:52 final size:52
Alignment explanation
Indices: 30151--30279 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
30141 TAGTTTACTT
**
30151 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
30203 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
30256 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
30280 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:30297 original size:19 final size:19
Alignment explanation
Indices: 30275--30391 Score: 112
Period size: 19 Copynumber: 6.7 Consensus size: 19
30265 GAAACCAAAA
*
30275 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
30294 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
30310 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
* *
30326 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
30342 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
30359 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
30378 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
30392 AAGTTTCGTG
Statistics
Matches: 82, Mismatches: 7, Indels: 18
0.77 0.07 0.17
Matches are distributed among these distances:
14 15 0.18
15 3 0.04
16 11 0.13
17 8 0.10
18 7 0.09
19 38 0.46
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:30316 original size:14 final size:14
Alignment explanation
Indices: 30297--30352 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
30287 TTTCATTTCG
30297 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
30311 CGTTGCGATTTCATTT
1 CGTTGCGA-TTC-TTT
*
30327 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
30343 CGTTGCGATT
1 CGTTGCGATT
30353 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 16 0.43
15 3 0.08
16 9 0.24
17 3 0.08
18 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:30361 original size:33 final size:33
Alignment explanation
Indices: 30280--30371 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
30270 CAAAATCGCA
*
30280 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
30313 TTGCGA-TTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
30345 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
30372 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:30397 original size:19 final size:19
Alignment explanation
Indices: 30343--30407 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
30333 GCGATTCTGT
*
30343 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGA-TTTAAGTTTCG
**
30362 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTAAGTTTCG
30381 CGTTGCGATTTAAGTTTCG
1 CGTTGCGATTTAAGTTTCG
*
30400 TGTTGCGA
1 CGTTGCGA
30408 AAGTAAACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
18 3 0.08
19 37 0.93
ACGTcount: A:0.11, C:0.17, G:0.28, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTAAGTTTCG
Found at i:32347 original size:14 final size:14
Alignment explanation
Indices: 32328--32363 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
32318 ATTGTTTAAT
32328 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
32342 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
32356 TGATTTGT
1 TGATTTGT
32364 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:32486 original size:19 final size:19
Alignment explanation
Indices: 32470--32571 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
32460 AAAAATGACT
32470 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
32489 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
32508 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
32522 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
32541 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
32561 ATCGCAATGCG
1 ATCGCAATGCG
32572 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:32624 original size:19 final size:19
Alignment explanation
Indices: 32600--32901 Score: 313
Period size: 19 Copynumber: 17.4 Consensus size: 19
32590 GATTATCTCG
32600 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
32619 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
32638 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
32652 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
32671 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
32690 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCGCA
*
32709 TTGCGA--TTC-TGTCG-A
1 TTGCGATTTTCATTTCGCA
*
32724 -TGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
32742 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
32756 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
32775 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
32794 TTGCGA--TTC-TATCG--
1 TTGCGATTTTCATTTCGCA
32808 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
32827 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
32841 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
32861 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
32875 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
32894 TTGCGATT
1 TTGCGATT
32902 GTAATTTCCG
Statistics
Matches: 238, Mismatches: 14, Indels: 62
0.76 0.04 0.20
Matches are distributed among these distances:
14 39 0.16
15 1 0.00
16 37 0.16
17 35 0.15
18 4 0.02
19 110 0.46
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:32640 original size:52 final size:52
Alignment explanation
Indices: 32578--32834 Score: 362
Period size: 52 Copynumber: 4.9 Consensus size: 52
32568 TGCGTTTATA
*
32578 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
32630 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* * * *
32682 ATTTCGCATTGCGATTTTCATTTCACATTGCGA--TTC-TGTCG-A-TGTGATTTTC
1 ATTTCGCATTGCGA--TTC---TCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
32734 ATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
32786 ATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
32835 CTCTCGTTGC
Statistics
Matches: 182, Mismatches: 13, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
47 8 0.04
49 3 0.02
50 7 0.04
51 1 0.01
52 144 0.79
53 1 0.01
54 7 0.04
55 3 0.02
57 8 0.04
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:32656 original size:33 final size:33
Alignment explanation
Indices: 32619--32782 Score: 238
Period size: 33 Copynumber: 4.8 Consensus size: 33
32609 TCATTTCGCA
*
32619 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
*
32652 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TGTCG
*
32688 CATTGCGATTTTCATTTCACATTGCGATTCTGTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
* *
32723 ATGTGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
32756 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
32783 TTCATTTCGC
Statistics
Matches: 119, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
33 80 0.67
35 7 0.06
36 8 0.07
38 24 0.20
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
Found at i:32789 original size:85 final size:85
Alignment explanation
Indices: 32671--32873 Score: 352
Period size: 85 Copynumber: 2.4 Consensus size: 85
32661 TCATTTCGCA
* *
32671 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCACATTGCGATTCTGTCGATGTGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCACATTGCGATTCTATCGATGCGATTTTCAT
*
32736 TTCGCATTGCGATTCTGTCG
66 TTCGCATTGCGATTCTCTCG
* *
32756 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCACATTGCGATTCTATCGATGCGATTTTCAT
32821 TTCGCATTGCGATTCTCTCG
66 TTCGCATTGCGATTCTCTCG
32841 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 TTGCGATTTTCATTT-CGCATTGCGATTTTCAT
32874 GTTGGGATTT
Statistics
Matches: 112, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
85 95 0.85
86 17 0.15
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (85 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCACATTGCGATTCTATCGATGCGATTTTCAT
TTCGCATTGCGATTCTCTCG
Found at i:32866 original size:34 final size:33
Alignment explanation
Indices: 32775--32901 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
32765 TCATTTCGCA
*
32775 TTGCGATTTTCATTTCGCATTGCGATTCTATCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
32808 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
32841 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
32875 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
32902 GTAATTTCCG
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
33 58 0.66
34 29 0.33
35 1 0.01
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:32883 original size:67 final size:66
Alignment explanation
Indices: 32775--32901 Score: 202
Period size: 67 Copynumber: 1.9 Consensus size: 66
32765 TCATTTCGCA
32775 TTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 TTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
32840 G
66 G
* * *
32841 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTT-CGCATTGCGATTCT-ATCGTTGCGATTTTCATTTCGCATTGCGATT
32902 GTAATTTCCG
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
66 15 0.27
67 39 0.70
68 2 0.04
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (66 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
G
Found at i:35197 original size:12 final size:12
Alignment explanation
Indices: 35180--35204 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35170 TCTTCGGGGA
35180 CTTTTTCTTCTT
1 CTTTTTCTTCTT
35192 CTTTTTCTTCTT
1 CTTTTTCTTCTT
35204 C
1 C
35205 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:35413 original size:24 final size:24
Alignment explanation
Indices: 35379--35425 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
35369 CTGAAACATC
35379 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
35403 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
35426 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:36136 original size:20 final size:20
Alignment explanation
Indices: 36108--36497 Score: 457
Period size: 20 Copynumber: 19.4 Consensus size: 20
36098 AAATTTCAGT
* * * *
36108 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
36128 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
36148 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
36168 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
36188 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
36208 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
36228 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
36248 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
36268 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
36288 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
36308 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
36328 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
36349 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
36369 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
36389 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
36409 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
36429 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
36449 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
36469 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
36489 GTTGCGATT
1 GTTGCGATT
36498 ATGGAAAATC
Statistics
Matches: 323, Mismatches: 36, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.02
20 295 0.91
21 19 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:37297 original size:19 final size:21
Alignment explanation
Indices: 37264--37312 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 21
37254 TAATGTTATT
*
37264 TAATA-TATCAAATATA-ATA
1 TAATATTATAAAATATATATA
*
37283 TAA-ATTATAAAATATATTTA
1 TAATATTATAAAATATATATA
37303 TAATATTATA
1 TAATATTATA
37313 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 1 0.04
19 13 0.52
20 5 0.20
21 6 0.24
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATATTATAAAATATATATA
Found at i:38076 original size:14 final size:13
Alignment explanation
Indices: 38053--38094 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
38043 TTTGTATTTC
38053 TTGAATTTATATA
1 TTGAATTTATATA
*
38066 TT-ATTATTTATACA
1 TTGA--ATTTATATA
38080 TTGAATTTATATA
1 TTGAATTTATATA
38093 TT
1 TT
38095 TTTCTTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
12 1 0.04
13 12 0.50
14 10 0.42
15 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (13 bp):
TTGAATTTATATA
Found at i:39040 original size:2 final size:2
Alignment explanation
Indices: 39033--39069 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
39023 CCATCCATGT
39033 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
39070 GAAAATAGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40075 original size:15 final size:15
Alignment explanation
Indices: 40037--40076 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 15
40027 CTTAGTTAAT
40037 ATAAATATTAA--TA
1 ATAAATATTAACCTA
40050 ATAAATATTAACCTA
1 ATAAATATTAACCTA
40065 ATATAAT-TTAAC
1 ATA-AATATTAAC
40077 ACTATCAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.46
15 10 0.42
16 3 0.12
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAATATTAACCTA
Found at i:42957 original size:3 final size:3
Alignment explanation
Indices: 42944--42997 Score: 56
Period size: 3 Copynumber: 17.3 Consensus size: 3
42934 TATATGTAAC
* *
42944 ATA ATTA ATA ATA ACA ATA A-A CAAA ATA ATA ATA ATAA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA ATA
42991 ATA ATA A
1 ATA ATA A
42998 ATAAAAAAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
2 1 0.02
3 36 0.82
4 7 0.16
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:43001 original size:13 final size:13
Alignment explanation
Indices: 42967--42994 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42957 ACAATAAACA
42967 AAATAATAATAAT
1 AAATAATAATAAT
42980 AAATAATAATAAT
1 AAATAATAATAAT
42993 AA
1 AA
42995 TAAATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:43419 original size:41 final size:41
Alignment explanation
Indices: 43281--43477 Score: 245
Period size: 41 Copynumber: 4.8 Consensus size: 41
43271 ATCTTTAGGA
* *** *
43281 AGGGCGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT
1 AGGG-GATGACACGGTTCCTACGTGATGAGGAAATCTGG---TCG
* * * * *
43326 AGGGG-TGATACGGCTCCTACGTGATGAAGAGATCTAGTCG
1 AGGGGATGACACGGTTCCTACGTGATGAGGAAATCTGGTCG
43366 -GGGGATGACACGGTTCCTACGTGATGAGGAAATCTGGTCG
1 AGGGGATGACACGGTTCCTACGTGATGAGGAAATCTGGTCG
43406 AGGGGATGACACGGTTCCTACGTGATGAGGAAATCTGGTCG
1 AGGGGATGACACGGTTCCTACGTGATGAGGAAATCTGGTCG
*
43447 AGGGGATGACACGGTTCCTACATGATGAGGA
1 AGGGGATGACACGGTTCCTACGTGATGAGGA
43478 CGGCTGGCCA
Statistics
Matches: 135, Mismatches: 15, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
39 4 0.03
40 32 0.24
41 70 0.52
43 24 0.18
44 1 0.01
45 4 0.03
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (41 bp):
AGGGGATGACACGGTTCCTACGTGATGAGGAAATCTGGTCG
Found at i:43543 original size:28 final size:28
Alignment explanation
Indices: 43503--43573 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
43493 AGGAGTTATG
* *
43503 GTTTCAAGAGAAACCA-AATTAAAGATTT
1 GTTTCAAAAGAAA-CAGAATCAAAGATTT
*
43531 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGAATCAAAGATTT
43559 GTTTCAAGAA-AAACA
1 GTTTCAA-AAGAAACA
43574 AGCTCAAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 2 0.05
28 34 0.89
29 2 0.05
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.25
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGAATCAAAGATTT
Found at i:43579 original size:28 final size:28
Alignment explanation
Indices: 43523--43584 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
43513 AAACCAAATT
43523 AAAGATTTGTTTCAAAAGAAACAGACTC
1 AAAGATTTGTTTCAAAAGAAACAGACTC
43551 AAAGATTTGTTTCAAGAA-AAACA-AGCTC
1 AAAGATTTGTTTCAA-AAGAAACAGA-CTC
43579 AAAGAT
1 AAAGAT
43585 AACGTGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 1 0.03
28 29 0.91
29 2 0.06
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAGACTC
Found at i:44116 original size:63 final size:63
Alignment explanation
Indices: 44005--44216 Score: 207
Period size: 67 Copynumber: 3.3 Consensus size: 63
43995 TTTCAAAATG
* * * * * *
44005 AACATATTCAAAGATTTACTTCAAGAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT-AAGAG
1 AACAGATTCAAAGATTTA-TTCAAAAGAAATTATCTTAAGAGAGACAAAATT-ATGTTTCAA-AG
44068 A
63 A
*
44069 AACAGATTCAAAGATTT-TTCCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGA
1 AACAGATTCAAAGATTTATT-CAAAAGAAATTATCTTAAGAGAGACAAAATTATGTTT-CAAAGA
* * *
44133 AACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAA
1 AACAGATTCAAAGA--TTT-ATTCAAAAGAAATTATCTTAAGAGAGACAAAATTATGTTT-CAAA
44198 GA
62 GA
*
44200 AACCA-ACTCAAAGATTT
1 AA-CAGATTCAAAGATTT
44217 TTGTTTCAAA
Statistics
Matches: 131, Mismatches: 8, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
62 3 0.02
63 29 0.22
64 32 0.24
65 5 0.04
66 3 0.02
67 55 0.42
68 4 0.03
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (63 bp):
AACAGATTCAAAGATTTATTCAAAAGAAATTATCTTAAGAGAGACAAAATTATGTTTCAAAGA
Found at i:44152 original size:30 final size:30
Alignment explanation
Indices: 44118--44246 Score: 100
Period size: 30 Copynumber: 4.1 Consensus size: 30
44108 AGAGACAAAA
*
44118 TTTTGTTTCCAAAGAAA-CAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAACCA-ACTCAAAGAT
** * * *
44148 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACCAAC-TCA-A-AG----AT
*
44185 TTTTGTTTCCAAAGAAACCAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACCAACTCAAAGAT
44215 TTTTGTTTCAAAAGAAA-CAATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACCAA-CTCAAAGAT
44245 TT
1 TT
44247 GTTTACAAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
29 3 0.04
30 45 0.58
31 3 0.04
32 1 0.01
33 2 0.03
34 2 0.03
35 1 0.01
36 2 0.03
37 19 0.24
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACCAACTCAAAGAT
Found at i:44176 original size:67 final size:67
Alignment explanation
Indices: 44066--44231 Score: 277
Period size: 67 Copynumber: 2.5 Consensus size: 67
44056 TCATTTTAAG
* *
44066 AGAAACAGATTCAAAGA--TTT-TTCCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
44128 AA
66 AA
44130 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
44195 AA
66 AA
44197 AGAAACCA-ACTCAAAGATTTTTGTTTCAAAAGAAA
1 AGAAA-CAGACTCAAAGATTTTTGTTTCAAAAGAAA
44232 CAATCTCAAA
Statistics
Matches: 96, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
64 16 0.17
66 3 0.03
67 75 0.78
68 2 0.02
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30
Consensus pattern (67 bp):
AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
AA
Found at i:44316 original size:52 final size:53
Alignment explanation
Indices: 44236--44338 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 53
44226 AAGAAACAAT
*
44236 CTCAAAGATTTGTTTACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGATTTGTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
44289 CTCAAAGATTT-TTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTGTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
44339 AAATAAATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 37 0.77
53 11 0.23
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (53 bp):
CTCAAAGATTTGTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:44505 original size:29 final size:29
Alignment explanation
Indices: 44349--44513 Score: 187
Period size: 27 Copynumber: 5.8 Consensus size: 29
44339 AAATAAATAG
* *
44349 ACTCAAAGATTTTTGTTTCAAACGAAAC-A
1 ACTCAAAGATTTTT-TTTCAAAAGGAACAA
* ** *
44378 ACTCAAAAAAATTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTTTTCAAAAGGAACAA
* *
44407 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTTTTCAAAAGGAACAA
*
44436 ACTCAAAGA--TTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTTTCAAAAGGAACAA
*
44463 ACTCAAAGA--TTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTTTCAAAAGGAACAA
44490 ACTCAAAGATTTTTTTCTCAAAAG
1 ACTCAAAGATTTTTTT-TCAAAAG
44514 AAATTGTCTT
Statistics
Matches: 118, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
27 52 0.44
28 10 0.08
29 50 0.42
30 6 0.05
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (29 bp):
ACTCAAAGATTTTTTTTCAAAAGGAACAA
Found at i:44839 original size:36 final size:36
Alignment explanation
Indices: 44755--44858 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
44745 GAGAAAATGA
* * *
44755 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
44789 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
44825 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
44859 ACGATCTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:44886 original size:36 final size:36
Alignment explanation
Indices: 44756--44874 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
44746 AGAAAATGAT
* * * *
44756 GTCTCAAGCGAGACGAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGA-AAAC
* **
44790 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
44826 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
44861 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
44875 TCAACTTTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 19 0.28
35 12 0.17
36 38 0.55
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:44943 original size:102 final size:104
Alignment explanation
Indices: 44826--45058 Score: 287
Period size: 105 Copynumber: 2.2 Consensus size: 104
44816 TAGAGAAATT
* *
44826 GTCTCAAGCGAGACAAAGTTTGTTTTTG-AG-AA-AACGATCTCAA-GTGAGATCAACTTTGTTT
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAAGAAACAACAATCT-AAGGTGAGATCAACTTTGTTT
* *
44887 A-ATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
64 ATA-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* * *
44928 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTAATTTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTTG-AAGAAACAACAATCTAAGGTGAGATCAACTTTGTTTA
* * *
44993 TAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
65 TAGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
**
45033 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
45059 AAAATTCTCA
Statistics
Matches: 113, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
101 5 0.04
102 21 0.19
103 2 0.02
104 4 0.04
105 80 0.71
106 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (104 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAAGAAACAACAATCTAAGGTGAGATCAACTTTGTTTAT
AGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:45536 original size:4 final size:4
Alignment explanation
Indices: 45527--45576 Score: 86
Period size: 4 Copynumber: 13.0 Consensus size: 4
45517 TTTATGTATC
45527 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
45573 ATGT
1 ATGT
45577 GTATACTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.05
4 42 0.95
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:46783 original size:12 final size:11
Alignment explanation
Indices: 46755--46792 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
46745 CCTCTTTTTG
*
46755 TTCTTTGCTTT
1 TTCTTTGATTT
46766 TTCTTTGATTT
1 TTCTTTGATTT
46777 TTGCTTTGATTT
1 TT-CTTTGATTT
46789 TTCT
1 TTCT
46793 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:46796 original size:13 final size:12
Alignment explanation
Indices: 46750--46797 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
46740 TTTGTCCTCT
46750 TTTTGTTCTTTG-
1 TTTT-TTCTTTGA
*
46762 CTTTTTCTTTGA
1 TTTTTTCTTTGA
*
46774 TTTTTGCTTTGA
1 TTTTTTCTTTGA
46786 TTTTTCTCTTTG
1 TTTTT-TCTTTG
46798 CTCTTTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 7 0.23
12 18 0.60
13 5 0.17
ACGTcount: A:0.04, C:0.12, G:0.12, T:0.71
Consensus pattern (12 bp):
TTTTTTCTTTGA
Found at i:47496 original size:46 final size:46
Alignment explanation
Indices: 47403--47497 Score: 120
Period size: 47 Copynumber: 2.1 Consensus size: 46
47393 ATAAATGCAG
* * * *
47403 TGTTTCAAGGTGGAAAGAATGTTTCAAGGCCTTAAAGAGAGGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGGAGAA
* *
47449 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGA-TAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGCCTCAAAGAGAGGAGAA
47495 TGT
1 TGT
47498 CAAAATTTGG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
46 17 0.40
47 25 0.60
ACGTcount: A:0.37, C:0.09, G:0.27, T:0.26
Consensus pattern (46 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGGAGAA
Found at i:48946 original size:31 final size:32
Alignment explanation
Indices: 48890--48951 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
48880 TGACAAAATG
48890 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
48922 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
48952 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:52531 original size:3 final size:3
Alignment explanation
Indices: 52518--52571 Score: 56
Period size: 3 Copynumber: 17.3 Consensus size: 3
52508 TATATGTAAC
* *
52518 ATA ATTA ATA ATA ACA ATA A-A CAAA ATA ATA ATA ATAA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA ATA
52565 ATA ATA A
1 ATA ATA A
52572 ATAAAAAAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
2 1 0.02
3 36 0.82
4 7 0.16
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:52575 original size:13 final size:13
Alignment explanation
Indices: 52541--52568 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52531 ACAATAAACA
52541 AAATAATAATAAT
1 AAATAATAATAAT
52554 AAATAATAATAAT
1 AAATAATAATAAT
52567 AA
1 AA
52569 TAAATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:57568 original size:28 final size:28
Alignment explanation
Indices: 57536--57624 Score: 108
Period size: 28 Copynumber: 3.0 Consensus size: 28
57526 TTTATGTTTG
*
57536 TATATCTATGCTACCGATAGGATGATAT
1 TATATCTATGCTGCCGATAGGATGATAT
57564 TATATCTCA-GCTGCCGATAGGATGATATCAT
1 TATATCT-ATGCTGCCGATAGGATG--AT-AT
*
57595 ATATATCTCTGCTGCCGATAGGATGATAT
1 -TATATCTATGCTGCCGATAGGATGATAT
57624 T
1 T
57625 TCAAGTAATC
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
28 22 0.42
29 3 0.06
30 4 0.08
31 2 0.04
32 22 0.42
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (28 bp):
TATATCTATGCTGCCGATAGGATGATAT
Found at i:57609 original size:32 final size:30
Alignment explanation
Indices: 57536--57623 Score: 117
Period size: 32 Copynumber: 2.9 Consensus size: 30
57526 TTTATGTTTG
* *
57536 TATATCTATGCTACCGATAGGATG--ATAT
1 TATATCTCTGCTGCCGATAGGATGATATAT
*
57564 TATATCTCAGCTGCCGATAGGATGATATCAT
1 TATATCTCTGCTGCCGATAGGATGATAT-AT
57595 ATATATCTCTGCTGCCGATAGGATGATAT
1 -TATATCTCTGCTGCCGATAGGATGATAT
57624 TTCAAGTAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
28 21 0.40
30 2 0.04
31 2 0.04
32 27 0.52
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (30 bp):
TATATCTCTGCTGCCGATAGGATGATATAT
Found at i:79700 original size:12 final size:12
Alignment explanation
Indices: 79683--79707 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
79673 ACTATTAAGA
79683 AAAAATATTATT
1 AAAAATATTATT
79695 AAAAATATTATT
1 AAAAATATTATT
79707 A
1 A
79708 TTTTTTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAAATATTATT
Found at i:83666 original size:12 final size:12
Alignment explanation
Indices: 83649--83673 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
83639 AAGCTCCTTA
83649 ATTAGCGGAAGG
1 ATTAGCGGAAGG
83661 ATTAGCGGAAGG
1 ATTAGCGGAAGG
83673 A
1 A
83674 GGAAAAGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.40, T:0.16
Consensus pattern (12 bp):
ATTAGCGGAAGG
Found at i:91014 original size:21 final size:21
Alignment explanation
Indices: 90990--91036 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
90980 ATCGGAAACA
90990 TTATTATTTCTATCGATTTTG
1 TTATTATTTCTATCGATTTTG
* *
91011 TTATTTTTTCTATTGATTTTG
1 TTATTATTTCTATCGATTTTG
91032 TTATT
1 TTATT
91037 GTTCGACACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.06, G:0.09, T:0.68
Consensus pattern (21 bp):
TTATTATTTCTATCGATTTTG
Done.