Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002221.1 Hibiscus syriacus cultivar Beakdansim tig00004518_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: 74866
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3587 original size:19 final size:18
Alignment explanation
Indices: 3563--3599 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3553 AAAGAAATTC
*
3563 GAGAATTTATTGATAAATG
1 GAGAATTAATTGA-AAATG
3582 GAGAATTAATTGAAAATG
1 GAGAATTAATTGAAAATG
3600 TGATCAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (18 bp):
GAGAATTAATTGAAAATG
Found at i:8240 original size:22 final size:22
Alignment explanation
Indices: 8215--8274 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
8205 TACACCCTTT
8215 AAAGATGATAGATTCACTCTCC
1 AAAGATGATAGATTCACTCTCC
* * *
8237 AAAGATGATAGATTCTCTTTTC
1 AAAGATGATAGATTCACTCTCC
*
8259 AAAGATGAAAGATTCA
1 AAAGATGATAGATTCA
8275 TTGGATTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (22 bp):
AAAGATGATAGATTCACTCTCC
Found at i:8991 original size:45 final size:45
Alignment explanation
Indices: 8921--9090 Score: 250
Period size: 45 Copynumber: 3.8 Consensus size: 45
8911 CTATTTCCCA
*
8921 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCAATAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
*** *
8966 CATTTGTAAGCCCTTCAGAGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCAATAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
*
9011 CATCAATAAGCCCTTCAGTGCATGATTTTTTCAAAGCCTTCGGGT
1 CATCAATAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
* * * *
9056 CATCCATAAGACCTACAGTGCAGGATGTTTTCAAA
1 CATCAATAAGCCCTTCAGTGCATGATGTTTTCAAA
9091 AAGCCTTTGG
Statistics
Matches: 112, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 112 1.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (45 bp):
CATCAATAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
Found at i:9179 original size:45 final size:45
Alignment explanation
Indices: 9109--9211 Score: 152
Period size: 45 Copynumber: 2.3 Consensus size: 45
9099 GGGAGCTTTT
* * * ** *
9109 TGATATTTTCAAAGCCTTCGGGTCATCTGTAATCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGAGTCATCCGTAAGACCTACAGTGCA
9154 TGATGTTTTCAAAGCCTTCGAGTCATCCGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAGCCTTCGAGTCATCCGTAAGACCTACAGTGCA
9199 TGATGTTTTCAAA
1 TGATGTTTTCAAA
9212 AAGCCTTCAG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGAGTCATCCGTAAGACCTACAGTGCA
Found at i:9207 original size:121 final size:121
Alignment explanation
Indices: 8988--9467 Score: 545
Period size: 121 Copynumber: 3.9 Consensus size: 121
8978 CTTCAGAGCA
* ** *
8988 TGATGTTTTCAAAGCCTTCGGGTCATCAATAAGCCCTTCAGTGCATGATTTTTTCAAAGCCTTCG
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCG
* *
9053 GGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGCTTTT
66 GGTCATCCGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTT
*
9109 TGATATTTTCAAAGCCTTCGGGTCATCTGTAATCCCTTCAGTGCATGATGTTTTCAAAGCCTTCG
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCG
* **
9174 AGTCATCCGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTT
66 GGTCATCCGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTT
* * * *
9230 TGATAGTTTCAAAGCCTTCGAGTCATCTGTAAGCCTTTCAGTGCATGATGTTTTCAAAACC-TCT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTC-
* * * **
9294 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC--AAAGCCCGTGGGTCATCTGTAAGCTCT
65 GGGTCATCCGTAAGACCTACAGTGCATGATGTTTTCAAAAAG-CC-----T--T-TGGGAGCT-T
9357 TCAGT
120 T---T
* * *
9362 GCATGATGTTTTCAAAGCCTTCGGGTCCTCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCC
1 ---TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCT
* **
9427 TCGGGTCATCTGTAAG-CCTTTTAGTGCATGATGTTTTCAAA
63 TCGGGTCATCCGTAAGACC-TACAGTGCATGATGTTTTCAAA
9468 GCCTTCGGGC
Statistics
Matches: 308, Mismatches: 30, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
119 4 0.01
120 4 0.01
121 199 0.65
125 1 0.00
127 1 0.00
128 4 0.01
129 2 0.01
132 1 0.00
134 2 0.01
135 87 0.28
136 2 0.01
137 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (121 bp):
TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCG
GGTCATCCGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTT
Found at i:9287 original size:45 final size:45
Alignment explanation
Indices: 9236--9522 Score: 377
Period size: 45 Copynumber: 6.4 Consensus size: 45
9226 TTTTTGATAG
*
9236 TTTCAAAGCCTTCGAGTCATCTGTAAGCCTTTCAGTGCATGATGT
1 TTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTCAGTGCATGATGT
* *
9281 TTTCAAAACC-TCTGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
1 TTTCAAAGCCTTC-GGGTCATCTGTAAGCCTTTCAGTGCATGATGT
*
9326 TTTCAAAGCCCGT-GGGTCATCTGTAAG-CTCTTCAGTGCATGATGT
1 TTTCAAAG-CCTTCGGGTCATCTGTAAGCCT-TTCAGTGCATGATGT
* *
9371 TTTCAAAGCCTTCGGGTCCTCTGTAAGCCCTTCAGTGCATGATGT
1 TTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTCAGTGCATGATGT
* *
9416 TTTCAAAGCCCTCGGGTCATCTGTAAGCCTTTTAGTGCATGATGT
1 TTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTCAGTGCATGATGT
* * * *
9461 TTTCAAAGCCTTCGGG-CATCCGTAAGACC-TACAATGCAGGATGT
1 TTTCAAAGCCTTCGGGTCATCTGTAAG-CCTTTCAGTGCATGATGT
9505 TTTCAAAAAGCCTTCGGG
1 TTTC--AAAGCCTTCGGG
9523 AGGATTTTGA
Statistics
Matches: 215, Mismatches: 18, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
44 30 0.14
45 169 0.79
46 15 0.07
47 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (45 bp):
TTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTCAGTGCATGATGT
Found at i:9584 original size:45 final size:45
Alignment explanation
Indices: 9530--9643 Score: 156
Period size: 45 Copynumber: 2.5 Consensus size: 45
9520 GGGAGGATTT
* * *
9530 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATATTTTCAAAGCCTTCGGGTCATCCGTAAGACCTACAGTGCA
* *
9575 TGATGTTTTCAAAGCCTTCGGATCATCCGTAAGACCTACAGTGCA
1 TGATATTTTCAAAGCCTTCGGGTCATCCGTAAGACCTACAGTGCA
*
9620 GGATATTTTCAAAAAGCCTTCGGG
1 TGATATTTTC--AAAGCCTTCGGG
9644 AGCTTTTTGA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
45 48 0.81
47 11 0.19
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (45 bp):
TGATATTTTCAAAGCCTTCGGGTCATCCGTAAGACCTACAGTGCA
Found at i:9587 original size:76 final size:73
Alignment explanation
Indices: 9455--9595 Score: 201
Period size: 76 Copynumber: 1.9 Consensus size: 73
9445 TTTTAGTGCA
*
9455 TGATGTTTTCAAAGCCTTCGGGCATCCGTAAGACCTACAATGCAGGATGTTTTCAAAAAGCCTTC
1 TGATATTTTCAAAGCCTTCGGGCATCCGTAAGACCTACAATGCAGGATGTTTTC--AAAGCCTTC
9520 GGGAGGATTT
64 GGGAGGATTT
* * * * *
9530 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCG
1 TGATATTTTCAAAGCCTTCGGG-CATCCGTAAGACCTACAATGCAGGATGTTTTCAAAGCCTTCG
9595 G
65 G
9596 ATCATCCGTA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
74 11 0.19
75 21 0.36
76 27 0.46
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (73 bp):
TGATATTTTCAAAGCCTTCGGGCATCCGTAAGACCTACAATGCAGGATGTTTTCAAAGCCTTCGG
GAGGATTT
Found at i:9661 original size:121 final size:120
Alignment explanation
Indices: 9416--9878 Score: 539
Period size: 121 Copynumber: 3.7 Consensus size: 120
9406 TGCATGATGT
* * * * *
9416 TTTCAAAGCCCTCGGGTCATCTGTAAGCCTTTTAGTGCATGATGTTTTCAAAGCCTTCGGGCATC
1 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGTCATC
* ** *
9481 CGTAAGACCTACAATGCAGGATGTTTTCAAAAAGCCTTCGGGAGGATTTTGATAT
66 CGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATAG
*
9536 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGATCAT
1 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG-TCAT
*
9601 CCGTAAGACCTACAGTGCAGGATATTTTCAAAAAGCCTTCGGGAGCTTTTTGATAG
65 CCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATAG
* * *
9657 TTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTTAGTGCATGATGTTTTCAAAACCTCCGAGTCAT
1 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG-GTCAT
* * ** * * * ** **
9722 CTGTAAGCCCTTTAGTGCATGATGTTTTCAAAGACCTCGCCATCTGTAAGCCCTTCAGTGCATTA
65 CCGTAAGACCTACAGTGCAGGATGTTTTCAAA-A---AGCCTTC-GGGAG--CTT-TTTG-A-TA
9787 TG
120 -G
*
9789 TTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTCCAGGTCA
1 -TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC-GGTCA
* *
9854 TCTGTAAGACCTACAGTGCAAGATG
64 TCCGTAAGACCTACAGTGCAGGATG
9879 ATAAGACCTC
Statistics
Matches: 297, Mismatches: 31, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
120 57 0.19
121 139 0.47
122 2 0.01
125 5 0.02
126 3 0.01
128 3 0.01
129 2 0.01
130 1 0.00
131 2 0.01
132 1 0.00
133 81 0.27
134 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (120 bp):
TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGTCATC
CGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATAG
Found at i:9708 original size:45 final size:45
Alignment explanation
Indices: 9657--9878 Score: 288
Period size: 45 Copynumber: 5.0 Consensus size: 45
9647 TTTTTGATAG
* *
9657 TTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTTAGTGCATGATGT
1 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
* * * *
9702 TTTCAAAACCTCCGAGTCATCTGTAAGCCCTTTAGTGCATGATGT
1 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
* *
9747 TTTCAAAGACC-TC--GCCATCTGTAAGCCCTTCAGTGCATTATGT
1 TTTCAAAG-CCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
9790 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
1 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
* * * * * *
9835 TTTCAAAACCTCCAGGTCATCTGTAAGACCTACAGTGCAAGATG
1 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
9879 ATAAGACCTC
Statistics
Matches: 156, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
42 2 0.01
43 37 0.24
45 115 0.74
46 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32
Consensus pattern (45 bp):
TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
Found at i:9723 original size:421 final size:420
Alignment explanation
Indices: 8921--9878 Score: 1553
Period size: 421 Copynumber: 2.3 Consensus size: 420
8911 CTATTTCCCA
* * *
8921 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATTTGTAAGCCCTTCAGAG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTG
* ** *
8986 CATGATGTTTTCAAAGCCTTCGGGTCATCAATAAGCCCTTCAGTGCATGATTTTTTCAAAGCCTT
66 CATGATGTTTTCAAAGCCCTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTT
* * *
9051 CGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATATT
131 CGGGTCATCCATAAGACCTACAATGCAGGATGTTTTCAAAAAGCCTTCGGGAGCATTTTGATATT
*
9116 TTCAAAGCCTTCGGGTCATCTGTAATCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGAGTCATC
196 TTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGAGTCATC
* *
9181 CGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATAGTTTCAAAGCC
261 CGTAAGACCTACAGTGCAGGATATTTTCAAAAAGCCTTCAGGAGCTTTTTGATAGTTTCAAAGCC
* *
9246 TTCGAGTCATCTGTAAGCCTTTCAGTGCATGATGTTTTCAAAACCTCTGGGTCATCTGTAAGCCC
326 TTCGAGTCATCTGTAAGCCTTTCAGTGCATGATGTTTTCAAAACCTCCGAGTCATCTGTAAGCCC
* * *
9311 TTCAGTGCATGATGTTTTCAAAGCCCGTGGGT
391 TTCAGTGCATGATGTTTTCAAAGACC-T-CGC
* *
9343 CATCTGTAAGCTCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCCTCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTG
* *
9408 CATGATGTTTTCAAAGCCCTCGGGTCATCTGTAAGCCTTTTAGTGCATGATGTTTTCAAAGCCTT
66 CATGATGTTTTCAAAGCCCTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTT
* *
9473 CGGG-CATCCGTAAGACCTACAATGCAGGATGTTTTCAAAAAGCCTTCGGGAGGATTTTGATATT
131 CGGGTCATCCATAAGACCTACAATGCAGGATGTTTTCAAAAAGCCTTCGGGAGCATTTTGATATT
9537 TTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCG-GATCAT
196 TTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGAG-TCAT
*
9601 CCGTAAGACCTACAGTGCAGGATATTTTCAAAAAGCCTTCGGGAGCTTTTTGATAGTTTCAAAGC
260 CCGTAAGACCTACAGTGCAGGATATTTTCAAAAAGCCTTCAGGAGCTTTTTGATAGTTTCAAAGC
* *
9666 CTTCGGGTCATCTGTAAGCCTTTTAGTGCATGATGTTTTCAAAACCTCCGAGTCATCTGTAAGCC
325 CTTCGAGTCATCTGTAAGCCTTTCAGTGCATGATGTTTTCAAAACCTCCGAGTCATCTGTAAGCC
*
9731 CTTTAGTGCATGATGTTTTCAAAGACCTCGC
390 CTTCAGTGCATGATGTTTTCAAAGACCTCGC
*
9762 CATCTGTAAGCCCTTCAGTGCATTATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTG
* * * * *
9827 CATGATGTTTTCAAA-ACCTCCAGGTCATCTGTAAGACCTACAGTGCAAGATG
66 CATGATGTTTTCAAAGCCCT-CGGGTCATCTGTAAGCCCTTCAGTGCATGATG
9879 ATAAGACCTC
Statistics
Matches: 496, Mismatches: 38, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
418 3 0.01
419 104 0.21
420 2 0.00
421 264 0.53
422 123 0.25
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.33
Consensus pattern (420 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTG
CATGATGTTTTCAAAGCCCTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTT
CGGGTCATCCATAAGACCTACAATGCAGGATGTTTTCAAAAAGCCTTCGGGAGCATTTTGATATT
TTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGAGTCATC
CGTAAGACCTACAGTGCAGGATATTTTCAAAAAGCCTTCAGGAGCTTTTTGATAGTTTCAAAGCC
TTCGAGTCATCTGTAAGCCTTTCAGTGCATGATGTTTTCAAAACCTCCGAGTCATCTGTAAGCCC
TTCAGTGCATGATGTTTTCAAAGACCTCGC
Found at i:9827 original size:88 final size:89
Alignment explanation
Indices: 9674--9878 Score: 279
Period size: 88 Copynumber: 2.3 Consensus size: 89
9664 GCCTTCGGGT
* * *
9674 CATCTGTAAGCCTTTTAGTGCATGATGTTTTCAAAACCTCCGAGTCATCTGTAAGCCCTTTAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTCCGAGTCATCTGTAAGCCCTTCAGTG
9739 CATGATGTTTTCAAAGACCT-C-GC
66 CATGATGTTTTCAAA-ACCTCCAGC
* * * *
9762 CATCTGTAAGCCCTTCAGTGCATTATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTCCGAGTCATCTGTAAGCCCTTCAGTG
*
9827 CATGATGTTTTCAAAACCTCCAGGT
66 CATGATGTTTTCAAAACCTCCA-GC
* * *
9852 CATCTGTAAGACCTACAGTGCAAGATG
1 CATCTGTAAGCCCTTCAGTGCATGATG
9879 ATAAGACCTC
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
87 4 0.04
88 74 0.73
90 24 0.24
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32
Consensus pattern (89 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTCCGAGTCATCTGTAAGCCCTTCAGTG
CATGATGTTTTCAAAACCTCCAGC
Found at i:10081 original size:3 final size:3
Alignment explanation
Indices: 10075--10120 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
10065 ATAATAATAA
* *
10075 TAT TAT TAT TAT TAT TAT AAA TAT TAT TAT TAT TAT TA- TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
10121 ATAAATAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:10099 original size:21 final size:21
Alignment explanation
Indices: 10073--10114 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
10063 TAATAATAAT
10073 AATATTATTATTATTATTATA
1 AATATTATTATTATTATTATA
10094 AATATTATTATTATTATTATA
1 AATATTATTATTATTATTATA
10115 TTATTAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AATATTATTATTATTATTATA
Found at i:11479 original size:14 final size:13
Alignment explanation
Indices: 11454--11498 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
11444 CATTGTTTAG
11454 TTATATTTTAATT
1 TTATATTTTAATT
11467 TTATATGTTTAATT
1 TTATAT-TTTAATT
**
11481 CAATATTTTAATT
1 TTATATTTTAATT
11494 ATTAT
1 -TTAT
11499 TATTATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (13 bp):
TTATATTTTAATT
Found at i:11735 original size:141 final size:140
Alignment explanation
Indices: 11555--11945 Score: 400
Period size: 141 Copynumber: 2.8 Consensus size: 140
11545 TATAAGTTGA
**
11555 TAATATTTATTTATTTTAAAAATATTAAGAAAATGCAGTCTTAAAGCAACTAGATGTC-TTATTC
1 TAATATTTATTTATTTT-TTAATATTAAGAAAA-GCAGTCTTAAAGCAACTAGATGTCATT-TTC
* *
11619 TGGTATTTTAAAGAATAATAAATATCATGCTTATA-AAAAATAT-ATATATTTGCT-TTAATTTT
63 TGATATTTTAAA-AA-AATAAATATCATACTTATATAAAAATATAATATATTTGCTATTAATTTT
*
11681 ATATAAATCATGTTT-T
126 ATAGAAAT-AT-TTTAT
11697 TAATATTTATTTATTTTTTAATATTAAGAAAAGACAGTCTTAAAGCAACTAGATGTCATTTTCTG
1 TAATATTTATTTATTTTTTAATATTAAGAAAAG-CAGTCTTAAAGCAACTAGATGTCATTTTCTG
* * * * ** * * ** * *
11762 ATATTTTAAATAAATTAATATCCTACTTTTATATTAATTTAATTTATTTTTTATTATTTTTATGG
65 ATATTTTAAAAAAATAAATATCATACTTATATAAAAATATAATATATTTGCTATTAATTTTATAG
11827 AAATATTTTAT
130 AAATATTTTAT
* * * * * *
11838 TAATATTTATTTATTTTTTAATATTAAGAAAGGGGCTGTCTTAAAGCAACTAGAAGGCCTTTTGT
1 TAATATTTATTTATTTTTTAATATTAAGAAA--AGCAGTCTTAAAGCAACTAGATGTCATTTTCT
* *
11903 GATATTTCTAAATAAAATAAATGTCTTA-TT-TATAAAAATATAA
64 GATATTT-TAAA-AAAATAAATATCATACTTATATAAAAATATAA
11946 AAATATATAT
Statistics
Matches: 209, Mismatches: 30, Indels: 20
0.81 0.12 0.08
Matches are distributed among these distances:
139 15 0.07
140 10 0.05
141 92 0.44
142 74 0.35
143 7 0.03
144 11 0.05
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (140 bp):
TAATATTTATTTATTTTTTAATATTAAGAAAAGCAGTCTTAAAGCAACTAGATGTCATTTTCTGA
TATTTTAAAAAAATAAATATCATACTTATATAAAAATATAATATATTTGCTATTAATTTTATAGA
AATATTTTAT
Found at i:11962 original size:18 final size:18
Alignment explanation
Indices: 11941--11977 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
11931 TTTATAAAAA
11941 TATAAAAA-TATATATATT
1 TATAAAAATTA-ATATATT
11959 TATAAAAATTAATATATT
1 TATAAAAATTAATATATT
11977 T
1 T
11978 TCTAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TATAAAAATTAATATATT
Found at i:17541 original size:18 final size:18
Alignment explanation
Indices: 17518--17565 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
17508 AAATTGTCTT
*
17518 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
17536 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
17553 TATTTATATATTT
1 TA-TTATATATTT
17566 TTTAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:21876 original size:5 final size:5
Alignment explanation
Indices: 21868--21904 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
21858 TAAAACTATC
*
21868 TTATA TTATA TTATA TTATA TTATA TTTATT TTATA T
1 TTATA TTATA TTATA TTATA TTATA -TTATA TTATA T
21905 ATGTTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TTATA
Found at i:21911 original size:15 final size:16
Alignment explanation
Indices: 21868--21914 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 16
21858 TAAAACTATC
*
21868 TTATATTATA-TTATA
1 TTATATTATATTTATT
21883 TTATATTATATTTATT
1 TTATATTATATTTATT
*
21899 TTATA-TATGTTTATT
1 TTATATTATATTTATT
21914 T
1 T
21915 GAATAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 20 0.69
16 9 0.31
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TTATATTATATTTATT
Found at i:25253 original size:18 final size:17
Alignment explanation
Indices: 25230--25263 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
25220 AAAATGATAC
25230 AACTAAAAAAATAAAAAG
1 AACT-AAAAAATAAAAAG
*
25248 AACTAAATAATAAAAA
1 AACTAAAAAATAAAAA
25264 AATTCTAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (17 bp):
AACTAAAAAATAAAAAG
Found at i:25727 original size:21 final size:21
Alignment explanation
Indices: 25697--25756 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
25687 CCCAGCTGCA
*
25697 GTGT-ATATGAAATGGCTGTG
1 GTGTCATATGAAATGGCTATG
* *
25717 GTGTCATATGATACGGCTATG
1 GTGTCATATGAAATGGCTATG
*
25738 GTG-CAATCTGAAATGGCTA
1 GTGTC-ATATGAAATGGCTA
25757 CGGAATGTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 5 0.16
21 27 0.84
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.32
Consensus pattern (21 bp):
GTGTCATATGAAATGGCTATG
Found at i:27483 original size:15 final size:14
Alignment explanation
Indices: 27440--27486 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
27430 TTATAACTGC
27440 AAAATTAATAAAA-
1 AAAATTAATAAAAT
* *
27453 AAAAGTTATTATAAT
1 AAAA-TTAATAAAAT
27468 AAAATTTAATAAAAT
1 AAAA-TTAATAAAAT
27483 AAAA
1 AAAA
27487 AATTATTGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 4 0.15
14 7 0.26
15 16 0.59
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (14 bp):
AAAATTAATAAAAT
Found at i:30420 original size:22 final size:22
Alignment explanation
Indices: 30395--30487 Score: 141
Period size: 22 Copynumber: 4.2 Consensus size: 22
30385 ACATTGATCG
30395 TTGACCGGTCTGACCGTTGACT
1 TTGACCGGTCTGACCGTTGACT
*
30417 TTGACCGGTCTGACCGTTGATT
1 TTGACCGGTCTGACCGTTGACT
* *
30439 TTGATCGGTCTGGCCGTTGACT
1 TTGACCGGTCTGACCGTTGACT
* *
30461 TTGACCAGTATGACCGTTGACT
1 TTGACCGGTCTGACCGTTGACT
30483 TTGAC
1 TTGAC
30488 AAAAAAGTCA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.34
Consensus pattern (22 bp):
TTGACCGGTCTGACCGTTGACT
Found at i:34415 original size:61 final size:61
Alignment explanation
Indices: 34327--34441 Score: 178
Period size: 61 Copynumber: 1.9 Consensus size: 61
34317 AAAGGTGGAT
*
34327 ACGACCTTATGTATCATGTCCGGATTAGCACTATAGCATAAGCTTAGTGTAGGTGGTGGGC
1 ACGACCTTATGTATCATGTCCGGATTAGCACTATAGCATAAGCTTAGTGCAGGTGGTGGGC
* * *
34388 ACGACCTTATGTGT-ATTGTCCGGATTAGCACTATGGCGTAAGCTTAGTGCAGGT
1 ACGACCTTATGTATCA-TGTCCGGATTAGCACTATAGCATAAGCTTAGTGCAGGT
34442 TTAGCACTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
60 1 0.02
61 48 0.98
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (61 bp):
ACGACCTTATGTATCATGTCCGGATTAGCACTATAGCATAAGCTTAGTGCAGGTGGTGGGC
Found at i:34632 original size:46 final size:45
Alignment explanation
Indices: 34551--34680 Score: 156
Period size: 46 Copynumber: 2.9 Consensus size: 45
34541 GTAAGCATGC
* * *
34551 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTAATA
1 AAATAAGCCTACAAGCTTATGGAATAAATGGTAAGTATATTAATA
* * * *
34595 AAATTAA-CGTACAAGTTTATGGTATTAAATGGTAAGTATATTGATA
1 AAA-TAAGCCTACAAGCTTATGG-AATAAATGGTAAGTATATTAATA
*
34641 AAATAAGCCTACAAGCTTATGGAATGAATGGTAAGTATAT
1 AAATAAGCCTACAAGCTTATGGAATAAATGGTAAGTATAT
34681 GGTAAAATAT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
44 15 0.21
45 24 0.33
46 33 0.46
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (45 bp):
AAATAAGCCTACAAGCTTATGGAATAAATGGTAAGTATATTAATA
Found at i:36447 original size:45 final size:46
Alignment explanation
Indices: 36364--36454 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 46
36354 AATGATCGAG
36364 AAGCATCTAAGGTTGCACGCTTTCAAGACCAAAACTCTCAGATAAT
1 AAGCATCTAAGGTTGCACGCTTTCAAGACCAAAACTCTCAGATAAT
36410 AAGCATCTAAGGTTGCACG-TTTCAAGACCAAAACTCTCAGATAAT
1 AAGCATCTAAGGTTGCACGCTTTCAAGACCAAAACTCTCAGATAAT
36455 GACAAGTGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 26 0.58
46 19 0.42
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.24
Consensus pattern (46 bp):
AAGCATCTAAGGTTGCACGCTTTCAAGACCAAAACTCTCAGATAAT
Found at i:37537 original size:21 final size:21
Alignment explanation
Indices: 37498--37537 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
37488 GATAAATCTG
**
37498 AGAAATCTTCGAATTGAAGCA
1 AGAAATCTTCGAAGAGAAGCA
*
37519 AGAAGTCTTCGAAGAGAAG
1 AGAAATCTTCGAAGAGAAG
37538 GTCCCACCGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.20
Consensus pattern (21 bp):
AGAAATCTTCGAAGAGAAGCA
Found at i:37922 original size:13 final size:14
Alignment explanation
Indices: 37898--37927 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
37888 ATATATTAGA
37898 AATAATAATTTTAT
1 AATAATAATTTTAT
37912 AATAA-AATTTTAT
1 AATAATAATTTTAT
37925 AAT
1 AAT
37928 GTTTAATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAATAATTTTAT
Found at i:38849 original size:11 final size:11
Alignment explanation
Indices: 38818--38856 Score: 51
Period size: 11 Copynumber: 3.3 Consensus size: 11
38808 ATGAATAGTA
38818 ACTGCTACAGGGT
1 ACTGCTACA--GT
38831 ACCTGCTACAGT
1 A-CTGCTACAGT
38843 ACTGCTACAGT
1 ACTGCTACAGT
38854 ACT
1 ACT
38857 TCCGTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 13 0.52
12 3 0.12
13 1 0.04
14 8 0.32
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (11 bp):
ACTGCTACAGT
Found at i:39455 original size:23 final size:23
Alignment explanation
Indices: 39389--39474 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
39379 TCATATAAAT
*
39389 TTGCACCGAAGTGCCATGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
39412 TTTGTC-CCGAAG-GACCGCGTAGAGA
1 -TTG-CACCGAAGTG-CCACGTAGA-A
39437 -TGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
39459 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
39475 TATAATATCT
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
22 2 0.04
23 31 0.60
24 17 0.33
25 2 0.04
ACGTcount: A:0.27, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:41739 original size:23 final size:23
Alignment explanation
Indices: 41673--41750 Score: 81
Period size: 23 Copynumber: 3.3 Consensus size: 23
41663 TCATATAAAT
*
41673 TTGCACCGAAGTGCCATGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
41696 TTTGTC-CCGAAG-GACCGCGTAGAGA
1 -TTG-CACCGAAGTG-CCACGTAGA-A
41721 -TGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
41743 TTGCACCG
1 TTGCACCG
41751 TATGCCATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
22 2 0.04
23 24 0.53
24 17 0.38
25 2 0.04
ACGTcount: A:0.27, C:0.26, G:0.28, T:0.19
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:48185 original size:21 final size:22
Alignment explanation
Indices: 48159--48202 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
48149 GAATGCAAAT
48159 AGGGAATCG-TTACCCTGCTAC
1 AGGGAATCGATTACCCTGCTAC
*
48180 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGATTACCCTGCTAC
48202 A
1 A
48203 TTACTGCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.23
Consensus pattern (22 bp):
AGGGAATCGATTACCCTGCTAC
Found at i:48819 original size:23 final size:23
Alignment explanation
Indices: 48753--48838 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
48743 TCATATAAAT
*
48753 TTGCACCGAAGTGCCATGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
48776 TTTGTC-CCGAAG-GACCGCGTAGAGA
1 -TTG-CACCGAAGTG-CCACGTAGA-A
48801 -TGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
48823 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
48839 TATAATATGT
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
22 2 0.04
23 31 0.60
24 17 0.33
25 2 0.04
ACGTcount: A:0.27, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:55256 original size:21 final size:22
Alignment explanation
Indices: 55230--55273 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
55220 GAATGCAAAT
55230 AGGGAATCG-TTACCCTGCTAC
1 AGGGAATCGATTACCCTGCTAC
*
55251 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGATTACCCTGCTAC
55273 A
1 A
55274 TTACTGCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.23
Consensus pattern (22 bp):
AGGGAATCGATTACCCTGCTAC
Found at i:55890 original size:23 final size:23
Alignment explanation
Indices: 55824--55909 Score: 97
Period size: 23 Copynumber: 3.7 Consensus size: 23
55814 TCATATAAAT
55824 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
55847 TTTGTC-CCGAAG-GACCGCGTAGAGA
1 -TTG-CACCGAAGTG-CCACGTAGA-A
55872 -TGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
55894 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
55910 TATAATATGT
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
22 2 0.04
23 31 0.58
24 18 0.34
25 2 0.04
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:56616 original size:20 final size:20
Alignment explanation
Indices: 56588--56628 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
56578 TCAACTTTTT
56588 CTTTAGGGGGGAATCGATTC
1 CTTTAGGGGGGAATCGATTC
*
56608 CTTTTGGGGGGAATCGATTC
1 CTTTAGGGGGGAATCGATTC
56628 C
1 C
56629 CCCCCAGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.32
Consensus pattern (20 bp):
CTTTAGGGGGGAATCGATTC
Found at i:64742 original size:44 final size:44
Alignment explanation
Indices: 64678--64785 Score: 108
Period size: 44 Copynumber: 2.5 Consensus size: 44
64668 ATGCTGGAGA
* * * * * ** *
64678 AAGAAATGATGAATGGTGGGGCACTTTCCAAGGCCCGTGTCATC
1 AAGAAATAATAAATGTTGGGGCACTTTCAAAGGCCCATAACAAC
* * *
64722 TAGAAATAATAAATGTTGGGGCATTTTGAAAGGCCCATAACAAC
1 AAGAAATAATAAATGTTGGGGCACTTTCAAAGGCCCATAACAAC
*
64766 AAAAAATAATAAATGTTGGG
1 AAGAAATAATAAATGTTGGG
64786 ACATTTTTTT
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (44 bp):
AAGAAATAATAAATGTTGGGGCACTTTCAAAGGCCCATAACAAC
Found at i:65871 original size:62 final size:65
Alignment explanation
Indices: 65713--65884 Score: 190
Period size: 67 Copynumber: 2.7 Consensus size: 65
65703 GAAACTTCAA
* * *
65713 CTTGACTTCCTCGTGAAGAGAAATGAATATTTGTTATTTCTGACTCCCTCACGAAGAGGTGTTAA
1 CTTGACTTCCTCGTGAAGAGAAATAAATCTTTGTTATTCCTGACTCCCTCACGAAGA-G-GTTAA
65778 TC
64 TC
* * * * * *
65780 CTTGACTTCCTCGTGAAGGGAAGTCAATCTTTGTTATCCCTGACTCCC-CA-GCAGA-GTTAGTC
1 CTTGACTTCCTCGTGAAGAGAAATAAATCTTTGTTATTCCTGACTCCCTCACGAAGAGGTTAATC
* *
65842 CTT-AGCTTTCTCGTGAAGAGAAATAAATCTTTATTATTCCTGA
1 CTTGA-CTTCCTCGTGAAGAGAAATAAATCTTTGTTATTCCTGA
65885 AGAGGAGTCA
Statistics
Matches: 90, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
61 1 0.01
62 41 0.46
65 4 0.04
66 2 0.02
67 42 0.47
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.34
Consensus pattern (65 bp):
CTTGACTTCCTCGTGAAGAGAAATAAATCTTTGTTATTCCTGACTCCCTCACGAAGAGGTTAATC
Found at i:66082 original size:82 final size:82
Alignment explanation
Indices: 65944--66234 Score: 395
Period size: 82 Copynumber: 3.5 Consensus size: 82
65934 AAATTAATCC
* * *
65944 TCAAGTCTGATCTCCCCTGAAAGAATAGTGGAGCATACCTATCTTCTAAAATTGATCTGAATACT
1 TCAAGTCTAATCTCCCCTGAAAGAATAGTGGAGCATACCTGTCTTCCAAAATTGATCTGAATACT
66009 CGAAAAAGAGGAACATA
66 CGAAAAAGAGGAACATA
* * * * ** * * *
66026 TCAAGTTTGATCTCCCCTGAAAAAATAGTGAAGCATATTTGTCTTCCAAAAGTGATCTGATTACC
1 TCAAGTCTAATCTCCCCTGAAAGAATAGTGGAGCATACCTGTCTTCCAAAATTGATCTGAATACT
*
66091 CGAAAAAGAGGAACAAA
66 CGAAAAAGAGGAACATA
* * * *
66108 TCAAGTCTAATCTCCCCTGAAAGAATCA-TGGAGCAAACCCGTCTTCCAAAATTCATCTGACTAC
1 TCAAGTCTAATCTCCCCTGAAAGAAT-AGTGGAGCATACCTGTCTTCCAAAATTGATCTGAATAC
66172 TCGAAAAAGAGGAACATA
65 TCGAAAAAGAGGAACATA
* *
66190 TCAAGTCTAATCTCCCCTGAAAGAATAGTGGAGCAGACCCGTCTT
1 TCAAGTCTAATCTCCCCTGAAAGAATAGTGGAGCATACCTGTCTT
66235 TGGTCACTGA
Statistics
Matches: 182, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
81 1 0.01
82 180 0.99
83 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (82 bp):
TCAAGTCTAATCTCCCCTGAAAGAATAGTGGAGCATACCTGTCTTCCAAAATTGATCTGAATACT
CGAAAAAGAGGAACATA
Found at i:66363 original size:31 final size:33
Alignment explanation
Indices: 66328--66388 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 33
66318 TTAATTATTT
* *
66328 TTAATTTAATTACT-TAACTTTC-AATTTACTC
1 TTAATTTAATCACTCTAACATTCAAATTTACTC
66359 TTAATTTAATCACTCTAACATTCAAATTTA
1 TTAATTTAATCACTCTAACATTCAAATTTA
66389 TTTTTTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 13 0.50
32 7 0.27
33 6 0.23
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (33 bp):
TTAATTTAATCACTCTAACATTCAAATTTACTC
Found at i:66703 original size:26 final size:24
Alignment explanation
Indices: 66660--66713 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 24
66650 AGTATAATTT
66660 TAAAACAAATAAAAATTTAAATAC
1 TAAAACAAATAAAAATTTAAATAC
**
66684 TAAAACAAAACTAAAAATTTGGATAC
1 TAAAAC-AAA-TAAAAATTTAAATAC
66710 TAAA
1 TAAA
66714 CGTATAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 6 0.23
25 3 0.12
26 17 0.65
ACGTcount: A:0.63, C:0.09, G:0.04, T:0.24
Consensus pattern (24 bp):
TAAAACAAATAAAAATTTAAATAC
Found at i:68576 original size:14 final size:15
Alignment explanation
Indices: 68557--68593 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
68547 CATTGTTGCA
68557 TTTGCATCTCACA-T
1 TTTGCATCTCACATT
*
68571 TTTGCA-CTCCCATT
1 TTTGCATCTCACATT
68585 TTTGCATCT
1 TTTGCATCT
68594 TTACATTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 13 0.65
15 2 0.10
ACGTcount: A:0.16, C:0.30, G:0.08, T:0.46
Consensus pattern (15 bp):
TTTGCATCTCACATT
Found at i:70934 original size:76 final size:76
Alignment explanation
Indices: 70805--70993 Score: 233
Period size: 76 Copynumber: 2.5 Consensus size: 76
70795 ATCTCACTTG
* * * * * * *
70805 AGATTGTTTTTCTTTAAAAC-TGATTTTGTCTCACTTGAGACAGTTTTTTCTCGAAATAAGATAT
1 AGATTGTTTTTC-TTAAAACAAGATTTT-TCTCGCTTGAGACAATTTTTACTCGAAAGAAAACAT
70869 TTCATTTCACTCA
64 TTCATTTCACTCA
*
70882 ATATTGTTTTTCTTAAAACAAGATTTTTCTCGCTTGAGACAATTTTTACTCGAAAGAAAACATTT
1 AGATTGTTTTTCTTAAAACAAGATTTTTCTCGCTTGAGACAATTTTTACTCGAAAGAAAACATTT
* *
70947 TATTTTACTCA
66 CATTTCACTCA
*
70958 AGATTG--TTT-TTAAAACAAGATTTATCTCGCTTGAGA
1 AGATTGTTTTTCTTAAAACAAGATTTTTCTCGCTTGAGA
70994 TTGTTTCACT
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
73 26 0.26
74 3 0.03
76 53 0.54
77 17 0.17
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (76 bp):
AGATTGTTTTTCTTAAAACAAGATTTTTCTCGCTTGAGACAATTTTTACTCGAAAGAAAACATTT
CATTTCACTCA
Found at i:71029 original size:39 final size:39
Alignment explanation
Indices: 70974--71271 Score: 390
Period size: 39 Copynumber: 7.7 Consensus size: 39
70964 TTTTTAAAAC
70974 AAGA-TTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* * * *
71012 AATATTTCATCTTGCTTGAG-TTAGTTTCACTTGAAACAG
1 AAGATTTTATCTCGCTTGAGATT-GTTTCACTCGAAACAG
* *
71051 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAT
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* *
71090 AATATTTTATCTCGCTTGAGATTATTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* *
71129 AAGATTTTATCTCACTTGAGATTGTTTCACTCGAAATAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* *
71168 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAATAA
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* *
71207 AAGATTTTATCTAGCTTGAGATAT-TTTCACTTGAAACCA-
1 AAGATTTTATCTCGCTTGAGAT-TGTTTCACTCGAAA-CAG
* *
71246 AAGA-TTTATCTCACTTGAGGTTGTTT
1 AAGATTTTATCTCGCTTGAGATTGTTT
71272 TTCTTAAAAC
Statistics
Matches: 228, Mismatches: 26, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
37 1 0.00
38 22 0.10
39 202 0.89
40 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
Found at i:71597 original size:131 final size:132
Alignment explanation
Indices: 71296--71640 Score: 408
Period size: 131 Copynumber: 2.6 Consensus size: 132
71286 TATTCCTCAA
* * * * * *
71296 TTGAGGGATTAACATTTCAAATGGAGAGTTTATAATGAGAAGAGCTCATACGATAGAGGGAGAAA
1 TTGAGGGATTGA-ATTTCAAATGGAGAGTTCATAATGAGAAAAACTCATCCGATAGAGGGAGAAG
* * * * * *
71361 AAGTTCATAATGAGAAGAGCTTGTTCGACCTATCGCTTGAGTCACGACATTTCGAATCAGAGATG
65 AAGTTCATAAT--GAAGACCTTGTTCGACCTATCGATCGAGTCACAACACTTCGAATCAGACA-G
71426 CCTCGC
127 CCTCGC
* * *
71432 TTGAGGGATTAGCATTTCAAATGGAGAGTTCATAATGAGAAAAACTCATCCGATAGAGGCAGAGG
1 TTGAGGGATT-GAATTTCAAATGGAGAGTTCATAATGAGAAAAACTCATCCGATAGAGGGAGAAG
* * * *
71497 ATGTTCATAATGAAGACCTTGTTCGACCTATTGATCGATTCACAACACTTCGAATTAG-CA-CCT
65 AAGTTCATAATGAAGACCTTGTTCGACCTATCGATCGAGTCACAACACTTCGAATCAGACAGCCT
71560 CGC
130 CGC
* **
71563 TTGAGGGATTGAATTTTCAAATGGAGAGTTCATAAT-AAAAAGAACTCATCCGACCGAGGGAGAA
1 TTGAGGGATTGAA-TTTCAAATGGAGAGTTCATAATGAGAAA-AACTCATCCGATAGAGGGAGAA
71627 GAAGTTCATAATGA
64 GAAGTTCATAATGA
71641 GAAGAACTCA
Statistics
Matches: 180, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
130 6 0.03
131 69 0.38
133 1 0.01
134 39 0.22
136 65 0.36
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (132 bp):
TTGAGGGATTGAATTTCAAATGGAGAGTTCATAATGAGAAAAACTCATCCGATAGAGGGAGAAGA
AGTTCATAATGAAGACCTTGTTCGACCTATCGATCGAGTCACAACACTTCGAATCAGACAGCCTC
GC
Found at i:71679 original size:40 final size:40
Alignment explanation
Indices: 71589--71685 Score: 176
Period size: 40 Copynumber: 2.4 Consensus size: 40
71579 TCAAATGGAG
* *
71589 AGTTCATAATAAAAAGAACTCATCCGACCGAGGGAGAAGA
1 AGTTCATAATGAGAAGAACTCATCCGACCGAGGGAGAAGA
71629 AGTTCATAATGAGAAGAACTCATCCGACCGAGGGAGAAGA
1 AGTTCATAATGAGAAGAACTCATCCGACCGAGGGAGAAGA
71669 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
71686 GCTTGTTCAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.43, C:0.15, G:0.25, T:0.16
Consensus pattern (40 bp):
AGTTCATAATGAGAAGAACTCATCCGACCGAGGGAGAAGA
Found at i:74447 original size:75 final size:75
Alignment explanation
Indices: 74320--74463 Score: 207
Period size: 75 Copynumber: 1.9 Consensus size: 75
74310 CGTGTCCTCG
* ** * *
74320 TTGAAATCCGAATTTCTTTACGTTAGTTGTTTATTTTATTAATGGTACCCACCCTGAAATTATAT
1 TTGAAATCCGAATTTCTTTACGTTAGCTGTACATTTTATTAATGGTAACCACCCTAAAATTATAT
74385 TTGTGTCACC
66 TTGTGTCACC
* * * *
74395 TTGAAATCTGAATTTCTTTATGTTAGCTGTACATTTTATTAATGGTAACCACCTTAAAATTTTAT
1 TTGAAATCCGAATTTCTTTACGTTAGCTGTACATTTTATTAATGGTAACCACCCTAAAATTATAT
74460 TTGT
66 TTGT
74464 ATTTGTCTCA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 60 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (75 bp):
TTGAAATCCGAATTTCTTTACGTTAGCTGTACATTTTATTAATGGTAACCACCCTAAAATTATAT
TTGTGTCACC
Done.