Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013267.1 Kokia drynarioides strain JFW-HI SEQ_128288, 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: 110180
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:1283 original size:78 final size:78
Alignment explanation
Indices: 1192--1350 Score: 318
Period size: 78 Copynumber: 2.0 Consensus size: 78
1182 AATTGAGTTC
1192 AATTGCTAAAATAAGATTCGTCAATTCGACTAACTCAATTTTTTTATTCAATTCGACTCGATCGA
1 AATTGCTAAAATAAGATTCGTCAATTCGACTAACTCAATTTTTTTATTCAATTCGACTCGATCGA
1257 ATGCTCACCTCTA
66 ATGCTCACCTCTA
1270 AATTGCTAAAATAAGATTCGTCAATTCGACTAACTCAATTTTTTTATTCAATTCGACTCGATCGA
1 AATTGCTAAAATAAGATTCGTCAATTCGACTAACTCAATTTTTTTATTCAATTCGACTCGATCGA
1335 ATGCTCACCTCTA
66 ATGCTCACCTCTA
1348 AAT
1 AAT
1351 AAAGCACAAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 81 1.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (78 bp):
AATTGCTAAAATAAGATTCGTCAATTCGACTAACTCAATTTTTTTATTCAATTCGACTCGATCGA
ATGCTCACCTCTA
Found at i:8675 original size:21 final size:21
Alignment explanation
Indices: 8651--8690 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
8641 ATTAATATAT
**
8651 TAATTTAAATTTATATAATTC
1 TAATTTAAAAATATATAATTC
8672 TAATTTAAAAATATATAAT
1 TAATTTAAAAATATATAAT
8691 ATTAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATTTAAAAATATATAATTC
Found at i:10488 original size:19 final size:19
Alignment explanation
Indices: 10466--10510 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
10456 TTATATTAGG
10466 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
10485 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
10504 ATTTAAT
1 ATTTAAT
10511 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:11350 original size:22 final size:21
Alignment explanation
Indices: 11325--11367 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
11315 TATTTCTTTC
11325 AATTATGTTTTCTTTTATTTTT
1 AATTATG-TTTCTTTTATTTTT
*
11347 AATTCTGTTTCTTTTATTTTT
1 AATTATGTTTCTTTTATTTTT
11368 CCTTAGATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.72
Consensus pattern (21 bp):
AATTATGTTTCTTTTATTTTT
Found at i:12931 original size:97 final size:97
Alignment explanation
Indices: 12746--12939 Score: 214
Period size: 97 Copynumber: 2.0 Consensus size: 97
12736 CAATTTTGAA
* * *
12746 AAGGATGTTCGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTTAGGTACAAATTTAC
1 AAGGATATTCGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTAC
* * * *
12811 AGAATCCAAGATGAGAAACATTGCCTCGATTT
66 AAAATCCAAGATAAAAAACATTGCCTCAATTT
* * ** *
12843 AAGGATATTTGATTAT-TCCGATTTGAAGAAAAA-TCGTGCCTAGTAAGTTAAGGCACAAATTTT
1 AAGGATATTCGATTATCT-CGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTA
* *
12906 CAAAATTCGAA-ATAAAAAAATATTGCCTCAATTT
65 CAAAA-TCCAAGAT-AAAAAACATTGCCTCAATTT
12940 TAAAGTTTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
96 32 0.40
97 48 0.60
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTAC
AAAATCCAAGATAAAAAACATTGCCTCAATTT
Found at i:13452 original size:60 final size:59
Alignment explanation
Indices: 13375--13573 Score: 217
Period size: 59 Copynumber: 3.4 Consensus size: 59
13365 TTTAAAGTTT
* *
13375 AGGGTAAAAATGTAATTTTTGGAAGTTTT-GGGATCAAAATTGGAATTTTTTGG-AAGTTTG
1 AGGGTAAAAATGTAATTTTTGGAAGTTTTAGGG-TCAAAAATGGAA--TTTTGGAAAGTTCG
* *
13435 GGGGTAAAATTGTAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTGGAAAGTTCG
1 AGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTGGAAAGTTCG
* * * ** *
13494 AGGGTAAAAATGAAATTTTTGAAAAG-TTTAGGTTCAAAAATATAATTTTGGAGAA-ATCG
1 AGGGTAAAAATGTAATTTTTG-GAAGTTTTAGGGTCAAAAATGGAATTTTGGA-AAGTTCG
* *
13553 AGGGTCAAAATATAATTTTTG
1 AGGGTAAAAATGTAATTTTTG
13574 AATAGTTTAG
Statistics
Matches: 120, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
58 6 0.05
59 68 0.57
60 43 0.36
61 3 0.03
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (59 bp):
AGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTGGAAAGTTCG
Found at i:13491 original size:30 final size:30
Alignment explanation
Indices: 13318--13542 Score: 152
Period size: 30 Copynumber: 7.6 Consensus size: 30
13308 AGACATTTGG
13318 GGGTAAAAA-GCTAATTTTT-GAAAGTTTTTA
1 GGGTAAAAATG-TAATTTTTGGAAAG-TTTTA
*
13348 -GGTAAAAAAAT-TAAAATTTT--AAAG-TTTA
1 GGGT--AAAAATGT-AATTTTTGGAAAGTTTTA
13376 GGGTAAAAATGTAATTTTTGG-AAGTTTT-
1 GGGTAAAAATGTAATTTTTGGAAAGTTTTA
* * **
13404 GGGATCAAAATTGGAATTTTTTGG-AAGTTTGG
1 GGG-T-AAAAATGTAA-TTTTTGGAAAGTTTTA
*
13436 GGGTAAAATTGTAATTTTTGG-AAGTTTTA
1 GGGTAAAAATGTAATTTTTGGAAAGTTTTA
* **
13465 GGGTCAAAAATGGAA-TTTTGGAAAGTTCGA
1 GGGT-AAAAATGTAATTTTTGGAAAGTTTTA
* *
13495 GGGTAAAAATGAAATTTTTGAAAAG-TTTA
1 GGGTAAAAATGTAATTTTTGGAAAGTTTTA
* *
13524 GGTTCAAAAATATAATTTT
1 GGGT-AAAAATGTAATTTT
13543 GGAGAAATCG
Statistics
Matches: 159, Mismatches: 19, Indels: 34
0.75 0.09 0.16
Matches are distributed among these distances:
27 12 0.08
28 11 0.07
29 47 0.30
30 61 0.38
31 25 0.16
32 3 0.02
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (30 bp):
GGGTAAAAATGTAATTTTTGGAAAGTTTTA
Found at i:13517 original size:29 final size:29
Alignment explanation
Indices: 13313--13585 Score: 134
Period size: 29 Copynumber: 9.3 Consensus size: 29
13303 TTTTTAGACA
* *
13313 TTTGGGGGTAAAAA-GCTAATTTTTGAAAG
1 TTTGAGGGTAAAAATG-AAATTTTTGAAAG
* * *
13342 TTTTTA-GGTAAAAAAATTAAAATTTT-AAAG
1 -TTTGAGGGT--AAAAATGAAATTTTTGAAAG
* *
13372 TTT-AGGGTAAAAATGTAATTTTTGGAAG
1 TTTGAGGGTAAAAATGAAATTTTTGAAAG
* * * *
13400 TTTTG-GGATCAAAATTGGAATTTTTTGGAAG
1 -TTTGAGGGT-AAAAAT-GAAATTTTTGAAAG
* * * *
13431 TTTGGGGGTAAAATTGTAATTTTTGGAAG
1 TTTGAGGGTAAAAATGAAATTTTTGAAAG
* * *
13460 TTTTAGGGTCAAAAATGGAATTTTGGAAAG
1 TTTGAGGGT-AAAAATGAAATTTTTGAAAG
*
13490 TTCGAGGGTAAAAATGAAATTTTTGAAAAG
1 TTTGAGGGTAAAAATGAAATTTTTG-AAAG
* *
13520 TTT-AGGTTCAAAAAT-ATAATTTTGGAGAA-
1 TTTGAGGGT-AAAAATGA-AATTTTTGA-AAG
* * *
13549 ATCGAGGGTCAAAAT-ATAATTTTTGAATAG
1 TTTGAGGGTAAAAATGA-AATTTTTGAA-AG
13579 TTT-AGGG
1 TTTGAGGG
13586 GCCTCTAGAG
Statistics
Matches: 189, Mismatches: 36, Indels: 37
0.72 0.14 0.14
Matches are distributed among these distances:
27 12 0.06
28 5 0.03
29 75 0.40
30 71 0.38
31 26 0.14
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (29 bp):
TTTGAGGGTAAAAATGAAATTTTTGAAAG
Found at i:14678 original size:3 final size:3
Alignment explanation
Indices: 14670--14707 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
14660 TTTTTAATAC
*
14670 TAT TAT TAT TAT TATT TAA TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
14708 CATTTAATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:14689 original size:22 final size:22
Alignment explanation
Indices: 14662--14707 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
14652 CTTTCGATTT
14662 TTTAATACTATTATTATTATTA
1 TTTAATACTATTATTATTATTA
*
14684 TTTAATATTATTATTATTATTA
1 TTTAATACTATTATTATTATTA
14706 TT
1 TT
14708 CATTTAATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTAATACTATTATTATTATTA
Found at i:15363 original size:25 final size:26
Alignment explanation
Indices: 15333--15391 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
15323 GGTTAATTGG
15333 TTTGGGCCTA-TTTGGGCCA-TTGTAA
1 TTTGGGCCTAGTTTGGGCCATTTG-AA
** *
15358 TTTGGGTTTAGTTTGGGTCATTTGAA
1 TTTGGGCCTAGTTTGGGCCATTTGAA
15384 TTTGGGCC
1 TTTGGGCC
15392 CAATTGAGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
25 8 0.30
26 16 0.59
27 3 0.11
ACGTcount: A:0.14, C:0.12, G:0.31, T:0.44
Consensus pattern (26 bp):
TTTGGGCCTAGTTTGGGCCATTTGAA
Found at i:15483 original size:6 final size:6
Alignment explanation
Indices: 15455--15547 Score: 72
Period size: 6 Copynumber: 16.0 Consensus size: 6
15445 TTGTAATAGT
* *
15455 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
15502 -ATAAA TTTAAA TTTTAAA -ATAAA TTT-AA TCTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
15548 ATGAGTTTGG
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
5 23 0.33
6 35 0.51
7 11 0.16
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:15491 original size:17 final size:17
Alignment explanation
Indices: 15455--15547 Score: 134
Period size: 17 Copynumber: 5.4 Consensus size: 17
15445 TTGTAATAGT
15455 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
15473 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
15490 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
15507 TTTAAATTTTAAAATAAA
1 TTTAAA-TTTAAAATAAA
15525 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
15542 TTTAAA
1 TTTAAA
15548 ATGAGTTTGG
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
16 1 0.01
17 43 0.63
18 24 0.35
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:15519 original size:35 final size:34
Alignment explanation
Indices: 15455--15547 Score: 134
Period size: 35 Copynumber: 2.7 Consensus size: 34
15445 TTGTAATAGT
*
15455 TTTAAATTTGAAAATAAATTTAAACTTAAATTAAA
1 TTTAAATTT-AAAATAAATTTAAACTTAAAATAAA
*
15490 TTTAAATTTAAAATAAATTTAAATTTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAA-CTTAAAATAAA
15525 TTT-AATCTTAAAATAAATTTAAA
1 TTTAAAT-TTAAAATAAATTTAAA
15548 ATGAGTTTGG
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
34 17 0.31
35 37 0.69
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATTTAAACTTAAAATAAA
Found at i:15549 original size:11 final size:11
Alignment explanation
Indices: 15457--15529 Score: 66
Period size: 11 Copynumber: 6.8 Consensus size: 11
15447 GTAATAGTTT
15457 TAAATTTGAAAA
1 TAAATTT-AAAA
*
15469 TAAATTTAAACT
1 TAAATTTAAA-A
*
15481 TAAA-TTAAATT
1 TAAATTTAAA-A
15492 TAAATTTAAAA
1 TAAATTTAAAA
15503 TAAATTT-AAA
1 TAAATTTAAAA
15513 T---TTTAAAA
1 TAAATTTAAAA
15521 TAAATTTAA
1 TAAATTTAA
15530 TCTTAAAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
7 3 0.06
8 4 0.08
10 4 0.08
11 25 0.48
12 16 0.31
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:16314 original size:206 final size:206
Alignment explanation
Indices: 15951--16891 Score: 1388
Period size: 206 Copynumber: 4.6 Consensus size: 206
15941 CTCTATGTTT
* * * * *
15951 CATCAGGATGACGAATTTGGTTCACTTCTCCGTATCTCATCAGGGAGCTAACCACTTTATTGCTT
1 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
* * * * *
16016 CGA-CTGCTTCTCAGTATCTCATCAGGAAGC-AAGGGTTCGAAGATTTGCTCACATCGAGCGTAG
66 CGACCCGCTTCTCAGTATCTCATCAGGAAGCTGA-GATTCGAAGATTTGCTCACATCGAGCATGG
* * *
16079 GTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGATCGCGTCATTTGTTTCAATTCGC
130 GTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCGTCGTTTGTTTCAATCCGC
*
16144 TTTTCTATATCA
195 TTTTCTGTATCA
*
16156 CATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
1 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
* * * *
16221 CGACCCGCTTCTCGGTATCTCATCAAGAAGTTGAGATTTGAAGATTTGCTCACATCGAGCATGGG
66 CGACCCGCTTCTCAGTATCTCATCAGGAAGCTGAGATTCGAAGATTTGCTCACATCGAGCATGGG
* * *
16286 GTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCGTCGTTTGTTTCAATCCGCT
131 TTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCGTCGTTTGTTTCAATCCGCT
* *
16351 TCTCTGTATCT
196 TTTCTGTATCA
* * * *
16362 CATCAGGAAGACGAATTTAGTCCGCTTCACAGTATCTCATCAGGAAGCTAACTATTTTATTGCTT
1 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
* * *
16427 CGACCCGCTTCTCAGCATCTCATCAGGAAGCTGTGATTCGAAGATTTGCTCACATCGAGCGTGGG
66 CGACCCGCTTCTCAGTATCTCATCAGGAAGCTGAGATTCGAAGATTTGCTCACATCGAGCATGGG
* *
16492 TTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCATCGTTTGTTTCCATCCG-T
131 TTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCGTCGTTTGTTTCAATCCGCT
16556 TTCTCTGTATCA
196 TT-TCTGTATCA
* * *
16568 CATCAAGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAGGAAACTAACCATTTTATTGCTT
1 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
* * * * *
16633 CGACCCGCTTCTCAGTATCTCATCAGAAAGTTGGGATTCTAAGATTTGCTCACATCGAGCATGAG
66 CGACCCGCTTCTCAGTATCTCATCAGGAAGCTGAGATTCGAAGATTTGCTCACATCGAGCATGGG
*
16698 TTTGATTTGGTCTTCTTCTCAGTATCTCATTAGGAAGATGA-CTGCGTCGTTTGTTTCAATCCGC
131 TTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATC-GCGTCGTTTGTTTCAATCCGC
*
16762 TTCTT-TGTATCT
195 TT-TTCTGTATCA
* * *
16774 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAGGAAGCTAACTATTTTATTGCAT
1 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
*
16839 CGACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCAC
66 CGACCCGCTTCTCAGTATCTCATCAGGAAGCTGAGATTCGAAGATTTGCTCAC
16892 CTTTGAGTTG
Statistics
Matches: 660, Mismatches: 70, Indels: 11
0.89 0.09 0.01
Matches are distributed among these distances:
205 65 0.10
206 590 0.89
207 4 0.01
208 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (206 bp):
CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
CGACCCGCTTCTCAGTATCTCATCAGGAAGCTGAGATTCGAAGATTTGCTCACATCGAGCATGGG
TTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCGTCGTTTGTTTCAATCCGCT
TTTCTGTATCA
Found at i:16653 original size:412 final size:411
Alignment explanation
Indices: 15876--16891 Score: 1529
Period size: 412 Copynumber: 2.5 Consensus size: 411
15866 TCTGGTTTCA
* * * * * ** ** *
15876 TTGACTTGGCCTTCTTCTCAGTATC-CAATCAGGAAGGTGACCACATCACTTGTTTTGATCCACT
1 TTGATTTGGTCTTCTTCTCAGTATCTC-ATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCT
* * * * * * * *
15940 TCTCTATGTTTCATCAGGATGACGAATTTGGTTCACTTCTCCGTATCTCATCAGGGAGCTAACCA
65 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACTA
* * * *
16005 CTTTATTGCTTCGA-CTGCTTCTCAGTATCTCATCAGGAAGCAAGGGTTCGAAGATTTGCTCACA
130 TTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAGGAAGC-TGGATTCGAAGATTTGCTCACA
*
16069 TCGAGCGTAGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGATCGCGTCATTTGT
194 TCGAGCGTAGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGATCGCATCATTTGT
* *
16134 TTCAATTCGCTTTTCTATATCACATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAG
259 TTCAATCCGCTTTTCTATATCACATCAAGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAG
* *
16199 GAAGCTAACCATTTTATTGCTTCGACCCGCTTCTCGGTATCTCATCA-AGAAGTTGAGATT-TGA
324 GAAACTAACCATTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAGA-AAGTTGAGATTCT-A
*
16262 AGATTTGCTCACATCGAGCATGGGG
387 AGATTTGCTCACATCGAGCATGAGG
*
16287 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
* * *
16352 CTCTGTATCTCATCAGGAAGACGAATTTAGTCCGCTTCACAGTATCTCATCAGGAAGCTAACTAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACTAT
*
16417 TTTATTGCTTCGACCCGCTTCTCAGCATCTCATCAGGAAGCTGTGATTCGAAGATTTGCTCACAT
131 TTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAGGAAGCTG-GATTCGAAGATTTGCTCACAT
* * *
16482 CGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCATCGTTTGTT
195 CGAGCGTAGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGATCGCATCATTTGTT
* *
16547 TCCATCCG-TTTCTCTGTATCACATCAAGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAG
260 TCAATCCGCTTT-TCTATATCACATCAAGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAG
*
16611 GAAACTAACCATTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAGAAAGTTGGGATTCTAAG
324 GAAACTAACCATTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAGAAAGTTGAGATTCTAAG
*
16676 ATTTGCTCACATCGAGCATGAGT
389 ATTTGCTCACATCGAGCATGAGG
* *
16699 TTGATTTGGTCTTCTTCTCAGTATCTCATTAGGAAGATGACTGCGTCGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
* *
16764 CTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAGGAAGCTAACTAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACTAT
*
16829 TTTATTGCATCGACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCAC
131 TTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAGGAAGCT-GGATTCGAAGATTTGCTCAC
16892 CTTTGAGTTG
Statistics
Matches: 548, Mismatches: 50, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
411 122 0.22
412 423 0.77
413 3 0.01
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (411 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACTAT
TTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAGGAAGCTGGATTCGAAGATTTGCTCACATC
GAGCGTAGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGATCGCATCATTTGTTT
CAATCCGCTTTTCTATATCACATCAAGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAGGA
AACTAACCATTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAGAAAGTTGAGATTCTAAGAT
TTGCTCACATCGAGCATGAGG
Found at i:17043 original size:39 final size:39
Alignment explanation
Indices: 17000--17143 Score: 121
Period size: 39 Copynumber: 3.7 Consensus size: 39
16990 GTTGACGATG
17000 ATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGACTGTA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGACTGTA
* ** **** *
17039 ATCTGCCTCTGGCTCGGGGTAAGAGATTGGTTGA-TGATG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGACTG-TA
* * * * *
17078 ATTTGCCCCAGGCTCGGAGTAAAAGATCAAATGGCT-TCA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGACTGT-A
**
17117 ATCTGTTCCAAGCTCGGGGTAAGAGAT
1 ATCTGCCCCAAGCTCGGGGTAAGAGAT
17144 TGGTTGATGA
Statistics
Matches: 77, Mismatches: 25, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
38 3 0.04
39 73 0.95
40 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGACTGTA
Found at i:17087 original size:78 final size:77
Alignment explanation
Indices: 16958--17182 Score: 274
Period size: 78 Copynumber: 2.9 Consensus size: 77
16948 GTGGATAATC
* * * * * *
16958 GTAATCTGCCTCATGATCTGGGTAGGAGTTTGGTTGACGATGATCTGCCCCAAGCTCGGGGTAAG
1 GTAATCTGCCTC-TGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAG
17023 AGATCAAATGACT
65 AGATCAAATGACT
* * *
17036 GTAATCTGCCTCTGGCTCGGGGTAAGAGATTGGTTGATGATGATTTGCCCCAGGCTCGGAGTAAA
1 GTAATCTGCCTCT-GCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAG
*
17101 AGATCAAATGGCT
65 AGATCAAATGACT
** *
17114 -TCAATCTGTTCC-AAGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCTAGGCTCGGGGTA
1 GT-AATCTG--CCTCTGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTA
17177 AGAGAT
63 AGAGAT
17183 TAGTTAACAA
Statistics
Matches: 127, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
77 2 0.02
78 123 0.97
80 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (77 bp):
GTAATCTGCCTCTGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAGA
GATCAAATGACT
Found at i:17599 original size:50 final size:49
Alignment explanation
Indices: 17540--17960 Score: 256
Period size: 49 Copynumber: 8.5 Consensus size: 49
17530 GTATCAGGTT
* ** *
17540 CGCCATTGCGACTTAAACCTTTCCCCTTCAAATCTTTGTGGTACTAGATT
1 CGCCGTTGCGACTTAAACCTTT-CCCTTCATGTCTTTGTGGTACTAGATC
* * * * * *
17590 CGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTTC-ACGGTC
1 CGCCGTTGCGACTTAAACCTTTCCCTTCATGTCTT-TGTGGTACTA-GATC
* * *
17640 CGCCGTTGTGACTTAAACCTTTCCCTT-TTGTATCTTTGTGGTACTGGATC
1 CGCCGTTGCGACTTAAACCTTTCCCTTCATG--TCTTTGTGGTACTAGATC
** * * ** * * *
17690 TACCGTTGCG-GTCTAGATATTTCCCTTTATGTCTTTGAGGTACTAGGTC
1 CGCCGTTGCGACT-TAAACCTTTCCCTTCATGTCTTTGTGGTACTAGATC
* * *
17739 CGCCATTGCGACTTAAACCTTTCCCTTC-TGTCTTTTTGGTACTGGATC
1 CGCCGTTGCGACTTAAACCTTTCCCTTCATGTCTTTGTGGTACTAGATC
* * * * * * *
17787 CGCCGTTGCGACTTAGATCTTTCCCTTCATGTCTTCGCGGCACTAAATT
1 CGCCGTTGCGACTTAAACCTTTCCCTTCATGTCTTTGTGGTACTAGATC
** * * * * * * * * *
17836 CGTTGTTGCGGCTTAGATCTTTCCCGTCATGTCTCTGAGGTACAAGGTT
1 CGCCGTTGCGACTTAAACCTTTCCCTTCATGTCTTTGTGGTACTAGATC
* * * * * * * *
17885 CGTCGTTACGACTTAAACCCTTCCCTTTCGTATCTTTGCGATACTGGATC
1 CGCCGTTGCGACTTAAACCTTTCCC-TTCATGTCTTTGTGGTACTAGATC
* * *
17935 CGCCATTGCGGTCTTAAATCTTTCCC
1 CGCCGTTGC-GACTTAAACCTTTCCC
17961 GTCTTATCTT
Statistics
Matches: 277, Mismatches: 83, Indels: 21
0.73 0.22 0.06
Matches are distributed among these distances:
48 41 0.15
49 118 0.43
50 99 0.36
51 19 0.07
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.38
Consensus pattern (49 bp):
CGCCGTTGCGACTTAAACCTTTCCCTTCATGTCTTTGTGGTACTAGATC
Found at i:17681 original size:100 final size:99
Alignment explanation
Indices: 17535--17822 Score: 336
Period size: 100 Copynumber: 2.9 Consensus size: 99
17525 CTAAAGTATC
* *** *
17535 AGGTTCGCCATTGCGACTTAAACCTTTCCCCTTCAAATCTTTGTGGTACTAGATTCGCCGTTGCG
1 AGGTCCGCCATTGCGACTTAAACCTTT-CCCTTTTGATCTTTGTGGTACTGGATTCGCCGTTGCG
* *
17600 GCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTTC-
65 GCTTAGATCTTTCCCTTCTTGTCTTCTGAGGTACT
* * *
17634 ACGGTCCGCCGTTGTGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGA-TCTACCGTTG
1 A-GGTCCGCCATTGCGACTTAAACCTTTCCCTTTTG-ATCTTTGTGGTACTGGATTC-GCCGTTG
*
17698 CGG-TCTAGATATTTCCCTT-TATGTCTT-TGAGGTACT
63 CGGCT-TAGATCTTTCCCTTCT-TGTCTTCTGAGGTACT
* * * *
17734 AGGTCCGCCATTGCGACTTAAACCTTTCCCTTCTG-TCTTTTTGGTACTGGATCCGCCGTTGCGA
1 AGGTCCGCCATTGCGACTTAAACCTTTCCCTTTTGATCTTTGTGGTACTGGATTCGCCGTTGCGG
*
17798 CTTAGATCTTTCCCTTCATGTCTTC
66 CTTAGATCTTTCCCTTCTTGTCTTC
17823 GCGGCACTAA
Statistics
Matches: 159, Mismatches: 20, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
97 42 0.26
98 2 0.01
99 48 0.30
100 67 0.42
ACGTcount: A:0.15, C:0.27, G:0.19, T:0.39
Consensus pattern (99 bp):
AGGTCCGCCATTGCGACTTAAACCTTTCCCTTTTGATCTTTGTGGTACTGGATTCGCCGTTGCGG
CTTAGATCTTTCCCTTCTTGTCTTCTGAGGTACT
Found at i:17876 original size:146 final size:149
Alignment explanation
Indices: 17694--17960 Score: 346
Period size: 146 Copynumber: 1.8 Consensus size: 149
17684 TGGATCTACC
* * * * * *
17694 GTTGCGGTCTAGATATTTCCCTTTATGTCTTTGAGGTACTAGGTCCGCCATTGCGACTTAAACCT
1 GTTGCGGTCTAGATATTTCCCGTCATGTCTCTGAGGTACAAGGTCCGCCATTACGACTTAAACCC
* * * *
17759 TTCCC-TTCTGTCTTTTTG-G-TACTGGATCCGCCGTTGC-GACTTAGATCTTTCCCTTCATGTC
66 TTCCCTTTC-GTATCTTTGCGATACTGGATCCGCCATTGCGGACTTAAATCTTTCCCTTCATGTC
17820 TTCGCGGCACTAAATTCGTT
130 TTCGCGGCACTAAATTCGTT
* * * *
17840 GTTGCGG-CTTAGATCTTTCCCGTCATGTCTCTGAGGTACAAGGTTCGTCGTTACGACTTAAACC
1 GTTGCGGTC-TAGATATTTCCCGTCATGTCTCTGAGGTACAAGGTCCGCCATTACGACTTAAACC
*
17904 CTTCCCTTTCGTATCTTTGCGATACTGGATCCGCCATTGCGGTCTTAAATCTTTCCC
65 CTTCCCTTTCGTATCTTTGCGATACTGGATCCGCCATTGCGGACTTAAATCTTTCCC
17961 GTCTTATCTT
Statistics
Matches: 101, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
145 1 0.01
146 65 0.64
147 4 0.04
148 17 0.17
149 14 0.14
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (149 bp):
GTTGCGGTCTAGATATTTCCCGTCATGTCTCTGAGGTACAAGGTCCGCCATTACGACTTAAACCC
TTCCCTTTCGTATCTTTGCGATACTGGATCCGCCATTGCGGACTTAAATCTTTCCCTTCATGTCT
TCGCGGCACTAAATTCGTT
Found at i:17976 original size:100 final size:100
Alignment explanation
Indices: 17841--18067 Score: 312
Period size: 100 Copynumber: 2.3 Consensus size: 100
17831 AAATTCGTTG
*
17841 TTGCGG-CTTAGATCTTTCCCGTCATGTCTCTGAGGTACAAGGTTCGTCGTTACGACTTAAACCC
1 TTGCGGTCTTAGATCTTTCCCGTCATATCTCTGAGGTACAAGGTTCGTCGTTACGACTTAAACCC
*
17905 TTCCCTTTCGTATCTTTGCGATACTGGATCCGCCA
66 TTCCCTTTCGTATCATTGCGATACTGGATCCGCCA
* * * * * *
17940 TTGCGGTCTTAAATCTTTCCCGTCTTATCTTTGAGGTATAAGGTTCGTTGTTACGATTTAAACCC
1 TTGCGGTCTTAGATCTTTCCCGTCATATCTCTGAGGTACAAGGTTCGTCGTTACGACTTAAACCC
* * * *
18005 TTCCCTTTTGTATCATTGCGGTACTGGATCTGCCG
66 TTCCCTTTCGTATCATTGCGATACTGGATCCGCCA
* * *
18040 GTGCGGTCTTAGATCTTTCTCATCATAT
1 TTGCGGTCTTAGATCTTTCCCGTCATAT
18068 TTCATAGTGC
Statistics
Matches: 110, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
99 6 0.05
100 104 0.95
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (100 bp):
TTGCGGTCTTAGATCTTTCCCGTCATATCTCTGAGGTACAAGGTTCGTCGTTACGACTTAAACCC
TTCCCTTTCGTATCATTGCGATACTGGATCCGCCA
Found at i:19306 original size:14 final size:15
Alignment explanation
Indices: 19289--19320 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19279 CTTTTTCTCT
19289 TTTTATTA-TTATTA
1 TTTTATTATTTATTA
19303 TTTTATTATTTATTA
1 TTTTATTATTTATTA
19318 TTT
1 TTT
19321 GTTTTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTATTATTTATTA
Found at i:19306 original size:15 final size:16
Alignment explanation
Indices: 19288--19320 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
19278 TCTTTTTCTC
19288 TTTTTATTA-TTATTA
1 TTTTTATTATTTATTA
19303 -TTTTATTATTTATTA
1 TTTTTATTATTTATTA
19318 TTT
1 TTT
19321 GTTTTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.50
15 6 0.38
16 2 0.12
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTATTATTTATTA
Found at i:19341 original size:12 final size:12
Alignment explanation
Indices: 19324--19358 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
19314 ATTATTTGTT
19324 TTTTTTCTTTTC
1 TTTTTTCTTTTC
*
19336 TTTTTTCTTTTG
1 TTTTTTCTTTTC
19348 TTTTATTCTTT
1 TTTT-TTCTTT
19359 GAATCCGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.83
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:25077 original size:29 final size:28
Alignment explanation
Indices: 25036--25178 Score: 108
Period size: 29 Copynumber: 4.9 Consensus size: 28
25026 GTAAAAGGGT
* *
25036 AATTTTTTAAAGTTTCTGGGTCAAAATGG
1 AATTTTTGAAAGTTT-AGGGTCAAAATGG
* * * *
25065 AATTTTTGGAAGTTTAGAGGTAAAAAAGT
1 AATTTTTGAAAGTTTAG-GGTCAAAATGG
* *
25094 AA-TTTTGGAAGTTTTAGGGTCAAAAATAG
1 AATTTTTGAAAG-TTTAGGGTC-AAAATGG
* * *
25123 AATTTTTAAAAAGTTTGAGGGTAAAAATGA
1 AATTTTT-GAAAGTTT-AGGGTCAAAATGG
*
25153 AATTTTTGAAAAGTTTGGGGTCAAAA
1 AATTTTTG-AAAGTTTAGGGTCAAAA
25179 ATATAATTTT
Statistics
Matches: 89, Mismatches: 18, Indels: 14
0.74 0.15 0.12
Matches are distributed among these distances:
28 13 0.15
29 42 0.47
30 26 0.29
31 8 0.09
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (28 bp):
AATTTTTGAAAGTTTAGGGTCAAAATGG
Found at i:25157 original size:30 final size:31
Alignment explanation
Indices: 25102--25188 Score: 117
Period size: 30 Copynumber: 2.9 Consensus size: 31
25092 GTAATTTTGG
*
25102 AAGTTTTAGGGTCAAAAATAGAATTTTTAAA
1 AAGTTTGAGGGTCAAAAATAGAATTTTTAAA
*
25133 AAGTTTGAGGGT-AAAAAT-GAAATTTTTGAA
1 AAGTTTGAGGGTCAAAAATAG-AATTTTTAAA
*
25163 AAGTTTG-GGGTCAAAAATATAATTTT
1 AAGTTTGAGGGTCAAAAATAGAATTTT
25189 GGAGAAATCA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
29 5 0.10
30 34 0.68
31 11 0.22
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.36
Consensus pattern (31 bp):
AAGTTTGAGGGTCAAAAATAGAATTTTTAAA
Found at i:26331 original size:3 final size:3
Alignment explanation
Indices: 26325--26365 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
26315 TTTTTAATAC
*
26325 TAT TAT TAT TAT TAT T-T T-T TAA TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
26366 TACTCAATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:26347 original size:25 final size:25
Alignment explanation
Indices: 26314--26366 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
26304 CCTTTCGATT
26314 TTTTTTAATACTATTATTATTATTA
1 TTTTTTAATACTATTATTATTATTA
*
26339 TTTTTTAATATTATTATTATTATTA
1 TTTTTTAATACTATTATTATTATTA
26364 TTT
1 TTT
26367 ACTCAATACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTTTTAATACTATTATTATTATTA
Found at i:26353 original size:22 final size:22
Alignment explanation
Indices: 26325--26367 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
26315 TTTTTAATAC
*
26325 TATTATTATTATTATTTTTTAA
1 TATTATTATTATTATTATTTAA
26347 TATTATTATTATTATTATTTA
1 TATTATTATTATTATTATTTA
26368 CTCAATACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTATTATTATTATTATTTAA
Found at i:27133 original size:18 final size:17
Alignment explanation
Indices: 27095--27170 Score: 91
Period size: 18 Copynumber: 4.4 Consensus size: 17
27085 CTTTATTTAT
* *
27095 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
27112 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
*
27130 TTTAAATTTTAAAACAAA
1 TTTAAA-TTTAAAATAAA
27148 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
27165 TTTAAA
1 TTTAAA
27171 ATGAGTTTGG
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
16 1 0.02
17 23 0.45
18 24 0.47
19 3 0.06
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:32505 original size:30 final size:31
Alignment explanation
Indices: 32471--32533 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
32461 ACAATTTGCA
*
32471 CATTGAACTATT-GAAAGTTTTCATTTAAGT
1 CATTGAACTATTCAAAAGTTTTCATTTAAGT
* *
32501 CATTGGACTATTCAAAAGTTTTTATTTAAGT
1 CATTGAACTATTCAAAAGTTTTCATTTAAGT
32532 CA
1 CA
32534 CTGGGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (31 bp):
CATTGAACTATTCAAAAGTTTTCATTTAAGT
Found at i:39901 original size:22 final size:22
Alignment explanation
Indices: 39875--39942 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
39865 ATCAAAACCG
39875 AATCATCATTTATTCTAACCAC
1 AATCATCATTTATTCTAACCAC
* * *
39897 AATCATGA---A-TCAAAACC-G
1 AATCATCATTTATTC-TAACCAC
*
39915 AATCAACATTTATTCTAACCAC
1 AATCATCATTTATTCTAACCAC
39937 AATCAT
1 AATCAT
39943 GAATCAAGAC
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
18 8 0.25
19 5 0.16
21 5 0.16
22 14 0.44
ACGTcount: A:0.43, C:0.25, G:0.03, T:0.29
Consensus pattern (22 bp):
AATCATCATTTATTCTAACCAC
Found at i:39925 original size:40 final size:40
Alignment explanation
Indices: 39842--39949 Score: 191
Period size: 40 Copynumber: 2.7 Consensus size: 40
39832 TACCAATAAC
* *
39842 CATTTATTCTAACCAAAATCATG-ATCAAAACCGAATCAT
1 CATTTATTCTAACCACAATCATGAATCAAAACCGAATCAA
39881 CATTTATTCTAACCACAATCATGAATCAAAACCGAATCAA
1 CATTTATTCTAACCACAATCATGAATCAAAACCGAATCAA
39921 CATTTATTCTAACCACAATCATGAATCAA
1 CATTTATTCTAACCACAATCATGAATCAA
39950 GACTCAGTTG
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
39 22 0.33
40 44 0.67
ACGTcount: A:0.44, C:0.24, G:0.05, T:0.28
Consensus pattern (40 bp):
CATTTATTCTAACCACAATCATGAATCAAAACCGAATCAA
Found at i:41678 original size:51 final size:52
Alignment explanation
Indices: 41616--41714 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 52
41606 AAAACAGTTA
*
41616 AAAAATAAAAATAT-CAAATATT-TAAAATATTAAAATTGATATAAATTTATT
1 AAAAATAAAAATATACAAATATTATAAAATATAAAAATTGATA-AAATTTATT
* * *
41667 AAAAATAAAAATATATAAATATTATAAATTATAAAAATTTATAAAATT
1 AAAAATAAAAATATACAAATATTATAAAATATAAAAATTGATAAAATT
41715 AATATTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 14 0.33
52 12 0.29
53 16 0.38
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (52 bp):
AAAAATAAAAATATACAAATATTATAAAATATAAAAATTGATAAAATTTATT
Found at i:41690 original size:43 final size:44
Alignment explanation
Indices: 41620--41712 Score: 120
Period size: 43 Copynumber: 2.1 Consensus size: 44
41610 CAGTTAAAAA
* * *
41620 ATAAAAATATCAAATATTTAAAATATTA-AAATTGATATAAATTT
1 ATAAAAATATAAAATATATAAAATATTATAAATT-ATAAAAATTT
41664 ATTAAAAATA-AAAATATAT-AAATATTATAAATTATAAAAATTT
1 A-TAAAAATATAAAATATATAAAATATTATAAATTATAAAAATTT
41707 ATAAAA
1 ATAAAA
41713 TTAATATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
42 5 0.11
43 18 0.41
44 13 0.30
45 8 0.18
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (44 bp):
ATAAAAATATAAAATATATAAAATATTATAAATTATAAAAATTT
Found at i:41695 original size:17 final size:17
Alignment explanation
Indices: 41678--41711 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
41668 AAAATAAAAA
*
41678 TATATAAATATTATAAAT
1 TATAAAAAT-TTATAAAT
41696 TATAAAAATTTATAAA
1 TATAAAAATTTATAAA
41712 ATTAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAAAAATTTATAAAT
Found at i:41729 original size:26 final size:26
Alignment explanation
Indices: 41620--41715 Score: 85
Period size: 26 Copynumber: 3.8 Consensus size: 26
41610 CAGTTAAAAA
* *
41620 ATAAAAATAT-CAAATATT-TAAAAT
1 ATAAAAATATATAAATATTATAAATT
* *
41644 ATTAAAATTGATATAAAT-TTATTAAA-A
1 A-TAAAAAT-ATATAAATATTA-TAAATT
41671 ATAAAAATATATAAATATTATAAATT
1 ATAAAAATATATAAATATTATAAATT
*
41697 ATAAAAATTTATAAA-ATTA
1 ATAAAAATATATAAATATTA
41716 ATATTTTTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
24 1 0.02
25 22 0.37
26 27 0.46
27 5 0.08
28 4 0.07
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (26 bp):
ATAAAAATATATAAATATTATAAATT
Found at i:41832 original size:12 final size:12
Alignment explanation
Indices: 41815--41839 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41805 ATGTAAACTT
41815 AAAAAATTATAA
1 AAAAAATTATAA
41827 AAAAAATTATAA
1 AAAAAATTATAA
41839 A
1 A
41840 TCTAACACGT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAAATTATAA
Found at i:47343 original size:5 final size:6
Alignment explanation
Indices: 47318--47346 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
47308 TAATATATAA
47318 AATTTT AATTTT AATTTT AA-TTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
47347 CACATAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
AATTTT
Found at i:47343 original size:11 final size:12
Alignment explanation
Indices: 47318--47346 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
47308 TAATATATAA
47318 AATTTTAATTTT
1 AATTTTAATTTT
47330 AATTTTAA-TTT
1 AATTTTAATTTT
47341 AATTTT
1 AATTTT
47347 CACATAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
AATTTTAATTTT
Found at i:47542 original size:25 final size:25
Alignment explanation
Indices: 47508--47560 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
47498 AGTTTTAGTT
47508 GAACAAACCCAACATAACTAAAAAA
1 GAACAAACCCAACATAACTAAAAAA
47533 GAACAAACCCAACATAACTAAAAAA
1 GAACAAACCCAACATAACTAAAAAA
47558 GAA
1 GAA
47561 GAACAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.64, C:0.23, G:0.06, T:0.08
Consensus pattern (25 bp):
GAACAAACCCAACATAACTAAAAAA
Found at i:50403 original size:60 final size:60
Alignment explanation
Indices: 50336--50448 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
50326 AAGAACTATT
* * * ** *
50336 TCAATTCAAGTTTCGGACCAACTAATTGAATTAAAATTCATATATAACAATAATTTTGCA
1 TCAATTCAAATTACGGACCAACTAATTGAACTAAAACCCATACATAACAATAATTTTGCA
**
50396 TCAATTCAAATTACGGATTAACTAATTGAACTAAAACCCATACATAACAATAA
1 TCAATTCAAATTACGGACCAACTAATTGAACTAAAACCCATACATAACAATAA
50449 CTCATGATAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (60 bp):
TCAATTCAAATTACGGACCAACTAATTGAACTAAAACCCATACATAACAATAATTTTGCA
Found at i:75923 original size:90 final size:90
Alignment explanation
Indices: 75789--75965 Score: 257
Period size: 90 Copynumber: 2.0 Consensus size: 90
75779 TTTTGTCCAA
* ** *
75789 GTTAATTCTTAAATTTGACAACTGTTCTCATGTTGGGGCCTACACATGACAATAA-TTTCCACAT
1 GTTAATTCTTAAATTTGACAACTGTTCTCACGTTGAAGCCTACACATGACAATAAGTCT-CACAT
* *
75853 TGAGACCAACTTGGATAAAGAAACAC
65 TAAAACCAACTTGGATAAAGAAACAC
* * *
75879 GTTAATTCTTAAATTTGACAATTGTTCTCACGTTGAAGCCTACACTTGACAATTAGTCTCACATT
1 GTTAATTCTTAAATTTGACAACTGTTCTCACGTTGAAGCCTACACATGACAATAAGTCTCACATT
75944 AAAACCAACTTGGATAAAGAAA
66 AAAACCAACTTGGATAAAGAAA
75966 ATCGTTTAGG
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 75 0.97
91 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (90 bp):
GTTAATTCTTAAATTTGACAACTGTTCTCACGTTGAAGCCTACACATGACAATAAGTCTCACATT
AAAACCAACTTGGATAAAGAAACAC
Found at i:78004 original size:23 final size:23
Alignment explanation
Indices: 77912--78011 Score: 94
Period size: 23 Copynumber: 4.3 Consensus size: 23
77902 ACTAGCACGT
* *
77912 TCTCTGTTTAGCAC-GTCTCGTGC
1 TCTCTGTTTAGCACTGTGT-GTAC
* * *
77935 TCTCTGATTAGCACTTTGTGTGC
1 TCTCTGTTTAGCACTGTGTGTAC
* * * *
77958 TCTCTGATTAGTACTTTGTATAC
1 TCTCTGTTTAGCACTGTGTGTAC
77981 TCTCTGTTTAGCACTGTGTGTAC
1 TCTCTGTTTAGCACTGTGTGTAC
*
78004 TTTCTGTT
1 TCTCTGTT
78012 GCCCAGCACT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 63 0.97
24 2 0.03
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (23 bp):
TCTCTGTTTAGCACTGTGTGTAC
Found at i:81496 original size:15 final size:15
Alignment explanation
Indices: 81476--81524 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
81466 TGTTTCAATC
*
81476 TCTTCATATTCTTCT
1 TCTTCATCTTCTTCT
*
81491 TCTTCATCTTCATCT
1 TCTTCATCTTCTTCT
**
81506 TGATCATCTTCTTCT
1 TCTTCATCTTCTTCT
81521 TCTT
1 TCTT
81525 TGTCTTCCAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.12, C:0.29, G:0.02, T:0.57
Consensus pattern (15 bp):
TCTTCATCTTCTTCT
Found at i:84734 original size:22 final size:22
Alignment explanation
Indices: 84709--84750 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
84699 AAATTTTTTT
84709 TTAAAAAAAATAAAATTATAAG
1 TTAAAAAAAATAAAATTATAAG
* **
84731 TTAATAATGATAAAATTATA
1 TTAAAAAAAATAAAATTATA
84751 TTTTAATTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (22 bp):
TTAAAAAAAATAAAATTATAAG
Found at i:108390 original size:4 final size:4
Alignment explanation
Indices: 108381--108451 Score: 81
Period size: 4 Copynumber: 17.5 Consensus size: 4
108371 CAAATAAACG
* * *
108381 AGAA AGAA AGAA AGGAA AGAA AGAA AGAA AGAA AGGA AGAA GGAGA GGAA
1 AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA AGAA AGA-A AGAA
*
108431 AGAA AG-A AGAA GGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AG
108452 GTAATGTGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
3 3 0.05
4 47 0.81
5 8 0.14
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:108403 original size:17 final size:17
Alignment explanation
Indices: 108381--108451 Score: 94
Period size: 17 Copynumber: 4.4 Consensus size: 17
108371 CAAATAAACG
108381 AGAAAGAAAGAAAGGAA
1 AGAAAGAAAGAAAGGAA
108398 AGAAAGAAAGAAA-GAA
1 AGAAAGAAAGAAAGGAA
* * *
108414 AGGAAGAAGGAGAGGAA
1 AGAAAGAAAGAAAGGAA
108431 AGAAAG-AAG-AAGGAA
1 AGAAAGAAAGAAAGGAA
108446 AGAAAG
1 AGAAAG
108452 GTAATGTGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
15 11 0.23
16 15 0.32
17 21 0.45
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAGAAAGGAA
Found at i:108525 original size:19 final size:18
Alignment explanation
Indices: 108492--108535 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
108482 TATGATATAT
108492 TTTTTAAATCGTATTTTA
1 TTTTTAAATCGTATTTTA
** *
108510 TTTATTAAATTTTATTTAA
1 TTT-TTAAATCGTATTTTA
108529 TTTTTAA
1 TTTTTAA
108536 CAGATTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTTAAATCGTATTTTA
Done.