Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009592.1 Hibiscus syriacus cultivar Beakdansim tig00116971_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: 7920512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 39
Found at i:3654768 original size:23 final size:23
Alignment explanation
Indices: 3654701--3654769 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
3654691 CACCACAGCT
* *
3654701 CGTATAAATGCACCAAAGTGCAA
1 CGTAGAAATGCACCAAAGTGCCA
* * * *
3654724 CGTAGAATTGTACCTAAGTGCCG
1 CGTAGAAATGCACCAAAGTGCCA
*
3654747 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
3654770 TATAAGATGT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCAAAGTGCCA
Found at i:3681565 original size:20 final size:21
Alignment explanation
Indices: 3681535--3681583 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
3681525 ATCTCTTTAG
3681535 ATTATTTATTTAATTATTATT
1 ATTATTTATTTAATTATTATT
*
3681556 ATTA-TTATTTAATTCTTATCT
1 ATTATTTATTTAATTATTAT-T
*
3681577 TTTATTT
1 ATTATTT
3681584 TAAAAACAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 14 0.58
21 8 0.33
22 2 0.08
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTATTTATTTAATTATTATT
Found at i:3681672 original size:15 final size:16
Alignment explanation
Indices: 3681652--3681681 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3681642 ATATTTCACT
3681652 TTTTATC-TTATTTTG
1 TTTTATCTTTATTTTG
3681667 TTTTATCTTTATTTT
1 TTTTATCTTTATTTT
3681682 CCTACTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATCTTTATTTTG
Found at i:3681700 original size:35 final size:36
Alignment explanation
Indices: 3681649--3681717 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 36
3681639 ACTATATTTC
3681649 ACTTTTTATCTTATTTTGTTTTA-TCTTTATTTTCCT
1 ACTTTTTATCTTATTTTGTTTTACT-TTTATTTTCCT
*
3681685 ACTTTTT-TTTTATTTTGTTTTACTTTTATTTTC
1 ACTTTTTATCTTATTTTGTTTTACTTTTATTTTC
3681718 TCTTTTAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 23 0.74
36 8 0.26
ACGTcount: A:0.13, C:0.12, G:0.03, T:0.72
Consensus pattern (36 bp):
ACTTTTTATCTTATTTTGTTTTACTTTTATTTTCCT
Found at i:3682969 original size:16 final size:16
Alignment explanation
Indices: 3682932--3682969 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
3682922 CCTAACTAAC
3682932 TTTTTCCTTTCATTTT
1 TTTTTCCTTTCATTTT
3682948 TGTTTT-CTTTCATTTT
1 T-TTTTCCTTTCATTTT
3682964 ATTTTT
1 -TTTTT
3682970 ATCGTTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.08, C:0.13, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTTCCTTTCATTTT
Found at i:3684914 original size:14 final size:14
Alignment explanation
Indices: 3684868--3684942 Score: 62
Period size: 15 Copynumber: 5.0 Consensus size: 14
3684858 TGCAAAGATC
3684868 AAATCAAAGCAGAAAGA
1 AAATCAAAG-A-AAA-A
*
3684885 AAATCAAAGAACAA
1 AAATCAAAGAAAAA
*
3684899 AAATCAAAAAGAAAA
1 AAATCAAAGA-AAAA
*
3684914 AAAGCAAAGAGAAAA
1 AAATCAAAGA-AAAA
3684929 TAAA-CAAAGAAAAA
1 -AAATCAAAGAAAAA
3684943 GGGACAAGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
14 14 0.27
15 24 0.47
16 4 0.08
17 9 0.18
ACGTcount: A:0.73, C:0.09, G:0.12, T:0.05
Consensus pattern (14 bp):
AAATCAAAGAAAAA
Found at i:3684922 original size:13 final size:13
Alignment explanation
Indices: 3684878--3684942 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 13
3684868 AAATCAAAGC
3684878 AGAAAGAAAATCAA
1 AGAAA-AAAATCAA
3684892 AGAACAAAAATCAAAA
1 AGAA-AAAAATC--AA
*
3684908 AGAAAAAAAGCAA
1 AGAAAAAAATCAA
*
3684921 AGAGAAAATAAACAA
1 AGA-AAAA-AATCAA
3684936 AGAAAAA
1 AGAAAAA
3684943 GGGACAAGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
13 5 0.11
14 18 0.41
15 15 0.34
16 6 0.14
ACGTcount: A:0.75, C:0.08, G:0.12, T:0.05
Consensus pattern (13 bp):
AGAAAAAAATCAA
Found at i:3686047 original size:31 final size:31
Alignment explanation
Indices: 3685974--3686061 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 31
3685964 AGGAAGAGTG
* *
3685974 GGGGTATCTTTGAAGATTCAACATCAAATATT
1 GGGGCATCTTTG-GGATTCAACATCAAATATT
*
3686006 GGGGCATCTTTGGCGATTCAACATCGAATATT
1 GGGGCATCTTTGG-GATTCAACATCAAATATT
*
3686038 -GTGCATCTTTTGGGATTCAACATC
1 GGGGCATC-TTTGGGATTCAACATC
3686062 CTGATATGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
31 17 0.34
32 33 0.66
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (31 bp):
GGGGCATCTTTGGGATTCAACATCAAATATT
Found at i:3687159 original size:29 final size:30
Alignment explanation
Indices: 3687088--3687147 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
3687078 CAATTTAAGG
3687088 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
3687119 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
3687148 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:3687283 original size:36 final size:36
Alignment explanation
Indices: 3687243--3687314 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
3687233 ATTGCCCAGG
* *
3687243 GGGTATAGATTCCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
*
3687279 GGGTACAGATACCCCCCCAGGGGGTACAGATTCCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
3687315 CTGCAGGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.22, C:0.35, G:0.28, T:0.15
Consensus pattern (36 bp):
GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
Found at i:3687284 original size:15 final size:15
Alignment explanation
Indices: 3687264--3687293 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3687254 CCCCCCCAGG
3687264 GGGTACAGATACCCC
1 GGGTACAGATACCCC
3687279 GGGTACAGATACCCC
1 GGGTACAGATACCCC
3687294 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:3687321 original size:22 final size:21
Alignment explanation
Indices: 3687237--3687315 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
3687227 TTCAAGATTG
* *
3687237 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
3687258 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
3687276 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
*
3687294 CCCAGGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
3687315 C
1 C
3687316 TGCAGGTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
15 11 0.22
18 8 0.16
21 30 0.61
ACGTcount: A:0.22, C:0.37, G:0.28, T:0.14
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:3687389 original size:20 final size:21
Alignment explanation
Indices: 3687349--3687392 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3687339 AACAGAATGT
3687349 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
3687370 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
3687391 CC
1 CC
3687393 TGTTCAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.45, G:0.27, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:3687454 original size:21 final size:21
Alignment explanation
Indices: 3687428--3687470 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3687418 ATTTGAATAT
*
3687428 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3687449 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3687470 T
1 T
3687471 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:3687536 original size:20 final size:22
Alignment explanation
Indices: 3687498--3687537 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
3687488 TTTGAGTATA
3687498 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
3687520 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
3687538 ATATATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:3688705 original size:19 final size:20
Alignment explanation
Indices: 3688681--3688728 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3688671 AATGATTTTC
*
3688681 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
3688700 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
3688720 TTTTGAAAA
1 TTTTGAAAA
3688729 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:3690043 original size:29 final size:31
Alignment explanation
Indices: 3689991--3690049 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
3689981 ATTTAAGGCA
3689991 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAATGGTTTTTGGACTTGAATTGAATTTAC
3690022 AAAAT-GTTTTTGGACTT-AATTGAATTTA
1 AAAATGGTTTTTGGACTTGAATTGAATTTA
3690050 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (31 bp):
AAAATGGTTTTTGGACTTGAATTGAATTTAC
Found at i:3690162 original size:20 final size:20
Alignment explanation
Indices: 3690139--3690216 Score: 85
Period size: 20 Copynumber: 4.1 Consensus size: 20
3690129 TTCAAGATTG
*
3690139 CCCAGGGGGTATAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
3690159 CCCAGGGGGTACAGA-T-AC
1 CCCAGGGGGTACAGATTCCC
*
3690177 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGAT-TCCC
3690195 CCCAGGGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
3690215 CC
1 CC
3690217 TGCAGGTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
15 9 0.19
18 8 0.17
19 1 0.02
20 19 0.40
21 10 0.21
ACGTcount: A:0.22, C:0.36, G:0.28, T:0.14
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:3690185 original size:15 final size:15
Alignment explanation
Indices: 3690165--3690194 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3690155 TCCCCCCAGG
3690165 GGGTACAGATACCCC
1 GGGTACAGATACCCC
3690180 GGGTACAGATACCCC
1 GGGTACAGATACCCC
3690195 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:3690290 original size:20 final size:21
Alignment explanation
Indices: 3690250--3690293 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3690240 AACAGAATGT
3690250 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
3690271 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
3690292 CC
1 CC
3690294 TGTTCAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.45, G:0.27, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:3690355 original size:21 final size:21
Alignment explanation
Indices: 3690329--3690371 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3690319 ATTTGAATAT
*
3690329 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3690350 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3690371 T
1 T
3690372 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:3690437 original size:20 final size:22
Alignment explanation
Indices: 3690399--3690438 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
3690389 TTTGAGTATA
3690399 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
3690421 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
3690439 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:3691974 original size:18 final size:18
Alignment explanation
Indices: 3691951--3691993 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3691941 CTTTAGATTA
*
3691951 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
3691969 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
3691987 TTTATTT
1 TTTATTT
3691994 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:3692082 original size:15 final size:16
Alignment explanation
Indices: 3692062--3692091 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3692052 ATATTTCCCT
3692062 TTTTATC-TTATTTTG
1 TTTTATCTTTATTTTG
3692077 TTTTATCTTTATTTT
1 TTTTATCTTTATTTT
3692092 CATACTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATCTTTATTTTG
Found at i:3692101 original size:36 final size:36
Alignment explanation
Indices: 3692060--3692128 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
3692050 TTATATTTCC
3692060 CTTTTTATCTTATTTTGTTTTA-TCTTTATTTTCATA
1 CTTTTTATCTTATTTTGTTTTACT-TTTATTTTCATA
* *
3692096 CTTTTTATTTTGTTTTGTTTTACTTTTATTTTC
1 CTTTTTATCTTATTTTGTTTTACTTTTATTTTC
3692129 TGTTTTAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 29 0.97
37 1 0.03
ACGTcount: A:0.13, C:0.10, G:0.04, T:0.72
Consensus pattern (36 bp):
CTTTTTATCTTATTTTGTTTTACTTTTATTTTCATA
Found at i:3693172 original size:3 final size:3
Alignment explanation
Indices: 3693164--3693222 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
3693154 CTGCAAAATG
*
3693164 TAA TAA TAA TAA TTAA TAA GAA TAA T-A TAA TTAA TAA TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
*
3693210 T-A TAC TAA TAA TA
1 TAA TAA TAA TAA TA
3693223 TTTTTATAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 4 0.08
3 38 0.79
4 6 0.12
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3697426 original size:2 final size:2
Alignment explanation
Indices: 3697419--3697449 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3697409 GTCTTGAATA
3697419 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3697450 ATAGTAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3708560 original size:22 final size:22
Alignment explanation
Indices: 3708533--3708577 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3708523 ATTTAAGAAT
3708533 TTTAAACTCTAAAA-ATTTAATC
1 TTTAAA-TCTAAAATATTTAATC
* *
3708555 TTTAAATTTAAAATCTTTAATC
1 TTTAAATCTAAAATATTTAATC
3708577 T
1 T
3708578 CAAATTCTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTAAATCTAAAATATTTAATC
Found at i:3718981 original size:32 final size:32
Alignment explanation
Indices: 3718945--3719007 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
3718935 AATTAGTTTT
* * * *
3718945 GGTGGAGGAAATGTATTTTTCAAGTTAGATCA
1 GGTGGAAGAAATATACTTTTCAAGTCAGATCA
*
3718977 GGTGGAAGATATATACTTTTCAAGTCAGATC
1 GGTGGAAGAAATATACTTTTCAAGTCAGATC
3719008 GAATTCGAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.33
Consensus pattern (32 bp):
GGTGGAAGAAATATACTTTTCAAGTCAGATCA
Found at i:3720470 original size:2 final size:2
Alignment explanation
Indices: 3720463--3720521 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
3720453 TCGTCCCTTT
3720463 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3720504 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
3720522 GTTTGAAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3720636 original size:36 final size:35
Alignment explanation
Indices: 3720509--3720970 Score: 396
Period size: 36 Copynumber: 12.5 Consensus size: 35
3720499 ATATATATAT
* *
3720509 ATATATATATATAG-TTTGAAAATATTTTTAAAATACATA
1 ATATA-ATATATAGTTTTTAAAATA-TTTT-GAA-A-ATA
* * *
3720548 TATATAATATATAGTTTTGAAAAACATGTTTGAAAACATTT
1 -ATATAATATATAGTTTT-TAAAATAT-TTTG-AAA-A-TA
*
3720589 ATATATTATATAGTTTTTAAAATATTTTGAAAATTA
1 ATATAATATATAGTTTTTAAAATATTTTGAAAA-TA
*
3720625 ATATAATATATAGTTTTTAAAACATTTTTGAAAAT-
1 ATATAATATATAGTTTTTAAAATA-TTTTGAAAATA
* * *
3720660 ATATATTATACAGTTTTTAAAACATTTTTGAAAATA
1 ATATAATATATAGTTTTTAAAATA-TTTTGAAAATA
* *
3720696 TATATATTATATAGTTTTTAAAATATTTTAAAAATAA
1 -ATATAATATATAGTTTTTAAAATATTTTGAAAAT-A
*
3720733 ATATAATATATAGTTTTTAAAACATTTTTGAAAATA
1 ATATAATATATAGTTTTTAAAATA-TTTTGAAAATA
*
3720769 TATATATTATATAGTTTTTAAAATATTTTGAAAATAA
1 -ATATAATATATAGTTTTTAAAATATTTTGAAAAT-A
3720806 ATATAATATATAGTTTTTAAAATA-TTTGAAAAACATA
1 ATATAATATATAGTTTTTAAAATATTTTG--AAA-ATA
* * **
3720843 TATATATTATATAATTTTTAAAACGTTTTGAAAAATA
1 -ATATAATATATAGTTTTTAAAATATTTTG-AAAATA
* *
3720880 TACATAATATATAAGTTTTTAAAACAATTTTTGAAAAT-
1 -ATATAATATAT-AGTTTTTAAAA-TA-TTTTGAAAATA
* *
3720918 ATA-AATTATATAGTTTTGAAAATTATTTTTAAACAT-
1 ATATAA-TATATAGTTTTTAAAA-TATTTTGAAA-ATA
*
3720954 ATATATTATATAGTTTT
1 ATATAATATATAGTTTT
3720971 ATTAATTAGT
Statistics
Matches: 363, Mismatches: 36, Indels: 50
0.81 0.08 0.11
Matches are distributed among these distances:
35 44 0.12
36 120 0.33
37 92 0.25
38 40 0.11
39 23 0.06
40 33 0.09
41 11 0.03
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (35 bp):
ATATAATATATAGTTTTTAAAATATTTTGAAAATA
Found at i:3720766 original size:73 final size:72
Alignment explanation
Indices: 3720509--3720970 Score: 463
Period size: 73 Copynumber: 6.2 Consensus size: 72
3720499 ATATATATAT
* * *
3720509 ATATATATATATAG-TTTGAAAATATTTTT-AAAATACATATATATAATATATAGTTTTGAAAAA
1 ATATA-ATATATAGTTTTTAAAACATTTTTGAAAAT--ATATATAT--TATATAGTTTT-TAAAA
*
3720572 CATGTTTGAAAACATTT
60 CAT-TTT-AAAA-A-TA
* * *
3720589 ATATATTATATAGTTTTTAAAATA-TTTTGAAAAT-TAATATAATATATAGTTTTTAAAACATTT
1 ATATAATATATAGTTTTTAAAACATTTTTGAAAATAT-ATATATTATATAGTTTTTAAAACA-TT
*
3720652 TTGAAAAT-
64 TTAAAAATA
* * *
3720660 ATATATTATACAGTTTTTAAAACATTTTTGAAAATATATATATTATATAGTTTTTAAAATATTTT
1 ATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATATTATATAGTTTTTAAAACATTTT
3720725 AAAAATAA
66 AAAAAT-A
*
3720733 ATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATATTATATAGTTTTTAAAATATTTT
1 ATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATATTATATAGTTTTTAAAACATTTT
*
3720798 GAAAATAA
66 AAAAAT-A
* *** * *
3720806 ATATAATATATAGTTTTTAAAATATTTGAAAAACATATATATATTATATAATTTTTAAAACGTTT
1 ATATAATATATAGTTTTTAAAACATTTTTGAAA-ATATATATATTATATAGTTTTTAAAACATTT
3720871 TGAAAAATA
65 T-AAAAATA
* * *
3720880 TACATAATATATAAGTTTTTAAAACAATTTTTGAAAATATA-A-ATTATATAGTTTTGAAAATTA
1 -ATATAATATAT-AGTTTTTAAAAC-ATTTTTGAAAATATATATATTATATAGTTTTTAAAA-CA
*
3720943 TTTTTAAACAT-
62 -TTTTAAAAATA
*
3720954 ATATATTATATAGTTTT
1 ATATAATATATAGTTTT
3720971 ATTAATTAGT
Statistics
Matches: 334, Mismatches: 33, Indels: 38
0.82 0.08 0.09
Matches are distributed among these distances:
71 31 0.09
72 39 0.12
73 110 0.33
74 49 0.15
75 30 0.09
76 32 0.10
77 8 0.02
78 5 0.01
79 11 0.03
80 19 0.06
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (72 bp):
ATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATATTATATAGTTTTTAAAACATTTT
AAAAATA
Found at i:3720980 original size:13 final size:13
Alignment explanation
Indices: 3720964--3721019 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
3720954 ATATATTATA
3720964 TAGTTTTATTAAT
1 TAGTTTTATTAAT
*
3720977 TAGTATATTATTATTT
1 TAGT-T-TTATTA-AT
*
3720993 TA-TTTTATTTAT
1 TAGTTTTATTAAT
*
3721005 TTGTTTTATTAAT
1 TAGTTTTATTAAT
3721018 TA
1 TA
3721020 ACTTTTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
12 2 0.06
13 19 0.58
14 2 0.06
15 7 0.21
16 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (13 bp):
TAGTTTTATTAAT
Found at i:3728833 original size:165 final size:162
Alignment explanation
Indices: 3728554--3729587 Score: 972
Period size: 165 Copynumber: 6.3 Consensus size: 162
3728544 TGCCATCCCT
* * * ** * *
3728554 AGCTCCAAGGCACATCATTTACAACATAGCTCAAGGAAAG-AGGGTTATTTACCAACAAAAGACC
1 AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGGCGAGAAGGGTTATCT-GC--CAAAAGACC
* * * * * * * *
3728618 TTCGAGTTCGACTACGCTCAACTCCAAGGCACATTATTTGCAGCATAACTTAAGTCGAGAAGGGT
63 TTCGAGTTCGACTACACTCAGCTCTAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGT
* * * * *
3728683 TATTTGCC-GAAGACCCTCGAGTTTGATTACACTC
128 TATTTGCCAAAAGACCTTCGAGTTCGACTACGCTC
* * * * * *
3728717 AGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGAC
1 AGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGGCGAGAAGGGTTATCTG---CCAAAAGAC
* * * * * *
3728782 CTTCGAGTTCGACTACGCTCAGCTCTAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGG
62 CTTCGAGTTCGACTACACTCAGCTCTAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGG
* *
3728847 TTATCTGCCAACCAAAGATCTTCGAGTTCGACTACGCTC
127 TTATTTGCC-A--AAAGACCTTCGAGTTCGACTACGCTC
* ** *
3728886 AGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTTGAGAAGGGCTATCTGCC-AAAGACCCTT
1 AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGGCGAGAAGGGTTATCTGCCAAAAGA-CCTT
* * *
3728950 -GAGTTTC-ATTACACTCAGCTTTGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGT
65 CGAG-TTCGACTACACTCAGCTCT-AAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGT
* *
3729013 TATCTGTCTCCAAAAGACCTTCGAGTTAGACTACGCTC
128 TAT-T-T-GCCAAAAGACCTTCGAGTTCGACTACGCTC
* * * *
3729051 AGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-AAAGACCCTC
1 AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGGCGAGAAGGGTTATCTGCCAAAAGACCTTC
* * * *
3729115 GAGTTCGATTACACTCAGCTTCTAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGAGTTA
66 GAGTTCGACTACACTCAGC-TCTAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
*
3729180 TCTATCACCAAAAGACCTTCGAGTTCGACTACGCTC
130 T-T-T-GCCAAAAGACCTTCGAGTTCGACTACGCTC
* * *
3729216 AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG-CTAAAGACCCTC
1 AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGGCGAGAAGGGTTATCTGCCAAAAGACCTTC
* * * *
3729280 GAGTTCGATTACATTCAGCT-TCGAGTGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTT
66 GAGTTCGACTACACTCAGCTCT-AAG-GCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTT
* * *
3729344 ATCTGTCACAAAAAGGCCTTCGAGTTTGACTACGCTC
129 ATTTG-C-C-AAAAGACCTTCGAGTTCGACTACGCTC
* * * * * * *
3729381 AGCTCTAAGGCATATAATTTGCAGCATAACTTAAGTCGATAAGGGTTATCTGCCAACCAAATACC
1 AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGGCGAGAAGGGTTATCTGCC-A--AAAGA-C
* * * * * * * *
3729446 CTT-GAGTTTGACTACGCTCAGCTTCGAGGGCACATCATTTACGGTATAGCTCAAGGCTAGAAAG
62 CTTCGAGTTCGACTACACTCAGC-TCTAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGG
* * *
3729510 GATATCTACC-AAAGACCTTCGAGTTCGACTACGCTC
126 GTTATTTGCCAAAAGACCTTCGAGTTCGACTACGCTC
* * * *
3729546 AGCTCCAAGGCAAATCATTTACAGCATAGCCTAAGGCAAGAA
1 AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGGCGAGAA
3729588 AGGCTATTTG
Statistics
Matches: 747, Mismatches: 93, Indels: 60
0.83 0.10 0.07
Matches are distributed among these distances:
163 6 0.01
164 61 0.08
165 546 0.73
166 3 0.00
167 4 0.01
168 42 0.06
169 80 0.11
170 5 0.01
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (162 bp):
AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGGCGAGAAGGGTTATCTGCCAAAAGACCTTC
GAGTTCGACTACACTCAGCTCTAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
TTGCCAAAAGACCTTCGAGTTCGACTACGCTC
Found at i:3729032 original size:249 final size:248
Alignment explanation
Indices: 3728554--3729573 Score: 1075
Period size: 249 Copynumber: 4.1 Consensus size: 248
3728544 TGCCATCCCT
* * * * * * * *
3728554 AGCTCCAAGGCACATCATTTACAACATAGCTCAAG--GAAAGAGGGTTATTTACCAACAAAAGAC
1 AGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGA-AGGGTTATCTGCCAACCAAAGAC
* *
3728617 CTTCGAGTTCGACTACGCTCAACTCCAAGGCACATTATTTGCAGCATAACTTAAGTCGAGAAGGG
65 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* * * * *
3728682 TTATTTGCCGAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
130 TTATCTGCCAAAGACCCTTGAGTTTCACTACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
*
3728747 CTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGACCTTCGAGTTCGACTACGCTC
195 CTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTC
* * *
3728802 AGCTCTAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGATC
1 AGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
* * * *
3728867 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTTGAGAAGGGC
66 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGT
* *
3728932 TATCTGCCAAAGACCCTTGAGTTTCATTACACTCAGCTTTGAGGGCACATCATTTACAGCATAAC
131 TATCTGCCAAAGACCCTTGAGTTTCACTACACTCAGCTTCGAGGGCACATCATTTACAGCATAAC
* *
3728997 TCAAGGCTAGAAGGGTTATCTGTCTCCAAAAGACCTTCGAGTTAGACTACGCTC
196 TCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTC
* * *
3729051 AGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACC
1 AGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
* * * * * * * * * * *
3729112 CTCGAGTTCGATTACACTCAGCTTCTAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGAG
66 TTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* * * * *
3729177 TTATCTATCACCAAAAGA-CCTTCGAG-TTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCA
130 TTATC--T-GCC-AAAGACCCTT-GAGTTTC-ACTACACTCAGCTTCGAGGGCACATCATTTACA
* * * * * * * **
3729239 GCATAGCTTAAGTCGAGAAGGGTTATCTG---CTAAAGACCCTCGAGTTCGATTACATTC
189 GCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTC
* * * * * * *
3729296 AGCTTCGAGTGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACAA--AAAG
1 AGCTCCAAG-GCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-CAACCAAAG
* * * * * *
3729359 GCCTTCGAGTTTGACTACGCTCAGCTCTAAGGCATATAATTTGCAGCATAACTTAAGTCGATAAG
63 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAG
* * * *
3729424 GGTTATCTGCCAACCAAATACCCTTGAGTTTGACTACGCTCAGCTTCGAGGGCACATCATTTACG
128 GGTTATCTG----CCAAAGACCCTTGAGTTTCACTACACTCAGCTTCGAGGGCACATCATTTACA
* * * *
3729489 GTATAGCTCAAGGCTAGAAAGGATATC--T-ACCAAAGACCTTCGAGTTCGACTACGCTC
189 GCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTC
*
3729546 AGCTCCAAGGCAAATCATTTACAGCATA
1 AGCTCCAAGGCATATCATTTACAGCATA
3729574 GCCTAAGGCA
Statistics
Matches: 639, Mismatches: 108, Indels: 49
0.80 0.14 0.06
Matches are distributed among these distances:
245 55 0.09
246 71 0.11
247 1 0.00
248 30 0.05
249 362 0.57
250 120 0.19
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (248 bp):
AGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGT
TATCTGCCAAAGACCCTTGAGTTTCACTACACTCAGCTTCGAGGGCACATCATTTACAGCATAAC
TCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTC
Found at i:3729162 original size:330 final size:328
Alignment explanation
Indices: 3728611--3729594 Score: 1167
Period size: 330 Copynumber: 3.0 Consensus size: 328
3728601 TTTACCAACA
* * * * * * * * * * *
3728611 AAAGACCTTCGAGTTCGACTACGCTCAAC-TCCAAGGCACATTATTTGCAGCATAACTTAAGTCG
1 AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCT
* * * * * * * *
3728675 AGAAGGGTTAT-T-T-GCC-GAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCAT
66 AGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTTGACTACGCTCAGC-TCCAAGGCATATCAT
* * * * *
3728736 TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGACCTTCGAGTTCGACTACGCT
130 TTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG--ACC-AAAGACCCTCGAGTTCGACTACGCT
* * * * * *
3728801 CAGC-TCTAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGA
192 CAGCTTCTAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCT--C-ACCAAAGA
* * *
3728865 TCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTTGAGAAGG
254 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAAATCATTTGCAGCATAGCTTAAGTCGAGAAGG
3728930 GCTATCTGCC
319 GCTATCTGCC
* *
3728940 AAAGACCCTTGAGTTTC-ATTACACTCAGCTTTGAGGGCACATCATTTACAGCATAACTCAAGGC
1 AAAGACCCTCGAG-TTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGC
* *
3729004 TAGAAGGGTTATCTGTCTCCAAAAGACCTTCGAGTTAGACTACGCTCAGCTCCAAGGCATATCAT
65 TAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCAT
* * * *
3729069 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCTCGAGTTCGATTACACTCAG
130 TTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCCTCGAGTTCGACTACGCTCAG
* *
3729133 CTTCTAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGAGTTATCTATCACCAAAAGACCT
195 CTTCTAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATC--TCACC-AAAGACCT
* *
3729198 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTT
257 TCGAGTTCGACTACGCTCAGCTCCAAGGCAAATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
*
3729263 ATCTGCT
322 ATCTGCC
* * *
3729270 AAAGACCCTCGAGTTCGATTACATTCAGCTTCGAGTGCACATCATTTACAGTATAACTCAAGGCT
1 AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCT
* * * *
3729335 AGAAGGGTTATCTGTCACAAAAAGGCCTTCGAGTTTGACTACGCTCAGCTCTAAGGCATATAATT
66 AGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATT
* * * *
3729400 TGCAGCATAACTTAAGTCGATAAGGGTTATCTGCCAACCAAATACCCTTGAGTTTGACTACGCTC
131 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTG---ACCAAAGACCCTCGAGTTCGACTACGCTC
* * * * * *
3729465 AGCTTCGAGGGCACATCATTTACGGTATAGCTCAAGGCTAGAAAGGATATCT-ACCAAAGACCTT
193 AGCTTCTAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTCACCAAAGACCTT
* * * * *
3729529 CGAGTTCGACTACGCTCAGCTCCAAGGCAAATCATTTACAGCATAGCCTAAGGCAAGAAAGGCTA
258 CGAGTTCGACTACGCTCAGCTCCAAGGCAAATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA
3729594 T
323 T
3729595 TTGTAAATAA
Statistics
Matches: 562, Mismatches: 78, Indels: 29
0.84 0.12 0.04
Matches are distributed among these distances:
329 52 0.09
330 371 0.66
331 4 0.01
332 3 0.01
333 42 0.07
334 90 0.16
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (328 bp):
AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCT
AGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATT
TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCCTCGAGTTCGACTACGCTCAGC
TTCTAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTCACCAAAGACCTTCGA
GTTCGACTACGCTCAGCTCCAAGGCAAATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT
GCC
Found at i:3730520 original size:37 final size:36
Alignment explanation
Indices: 3730181--3730600 Score: 416
Period size: 37 Copynumber: 11.6 Consensus size: 36
3730171 TTTAAAATAC
*
3730181 ATATATATAATATATAGTTTTGAAAAACATGTTTGAAAA
1 ATATATATAATATATAGTTTT-TAAAACAT-TTTG-AAA
* * *
3730220 CATTTATATATTATATAGTTTTTAAAATATTTTGAAA
1 -ATATATATAATATATAGTTTTTAAAACATTTTGAAA
3730257 AT-TA-AT-ATAATATAG-TTTTAAAACATTTTTGAAA
1 ATATATATAAT-ATATAGTTTTTAAAACA-TTTTGAAA
*
3730291 A-A-ATAT-ATATACAGTTTTTAAAACATTTTG-AA
1 ATATATATAATATATAGTTTTTAAAACATTTTGAAA
* *
3730323 A-ATATAT-ATATATAGTTTTTTTAAACATTTTAAAA
1 ATATATATAATATATAG-TTTTTAAAACATTTTGAAA
* *
3730358 ATAAATATAATATATAGTTTTTAAAATATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACA-TTTTGAAA
*
3730395 ATATATATATTATATAGTTTTTAAAACATTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTGAAA
*
3730431 ATAAATATAATATATAGTTTTTAAAACA-TTTGAAAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTG--AAA
* * *
3730468 CATATATATATTATATAATTTTTAAAACGTTTTGAAA
1 -ATATATATAATATATAGTTTTTAAAACATTTTGAAA
3730505 TATATATATAATATATAAGTTTTTAAAACAATTTTTGAAA
1 -ATATATATAATATAT-AGTTTTTAAAAC-A-TTTTGAAA
* * * **
3730545 ATATA-A-ATTATATAGTTTTGAAAATTATTTTTTAA
1 ATATATATAATATATAGTTTTTAAAA-CATTTTGAAA
* *
3730580 ACATATATATTATATAGTTTT
1 ATATATATAATATATAGTTTT
3730601 ATTAATTAGT
Statistics
Matches: 326, Mismatches: 33, Indels: 45
0.81 0.08 0.11
Matches are distributed among these distances:
32 4 0.01
33 32 0.10
34 45 0.14
35 19 0.06
36 62 0.19
37 82 0.25
38 40 0.12
39 15 0.05
40 27 0.08
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTTAAAACATTTTGAAA
Found at i:3730610 original size:13 final size:13
Alignment explanation
Indices: 3730594--3730649 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
3730584 ATATATTATA
3730594 TAGTTTTATTAAT
1 TAGTTTTATTAAT
*
3730607 TAG-TATATT-AT
1 TAGTTTTATTAAT
*
3730618 TA-TTTTATTTAT
1 TAGTTTTATTAAT
*
3730630 TTGTTTTATTAAT
1 TAGTTTTATTAAT
*
3730643 TAATTTT
1 TAGTTTT
3730650 TTTTCTGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
11 9 0.26
12 8 0.24
13 17 0.50
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (13 bp):
TAGTTTTATTAAT
Found at i:3731944 original size:6 final size:5
Alignment explanation
Indices: 3731905--3731975 Score: 63
Period size: 5 Copynumber: 13.6 Consensus size: 5
3731895 TTTTTTAATA
* * **
3731905 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTAT ATTCTT ATTCT -TTTT ACTAA
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT-T ATT-TT ATTTT ATTTT ATTTT
3731956 ATTTT ATTTTCT ATTTT ATT
1 ATTTT A-TTT-T ATTTT ATT
3731976 AATTATATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
4 3 0.06
5 33 0.62
6 14 0.26
7 3 0.06
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.72
Consensus pattern (5 bp):
ATTTT
Found at i:3731979 original size:21 final size:22
Alignment explanation
Indices: 3731905--3731986 Score: 59
Period size: 21 Copynumber: 3.9 Consensus size: 22
3731895 TTTTTTAATA
* *
3731905 ATTTTATTTTATTTTA-TTT-T
1 ATTTTACTTAATTTTATTTTCT
*
3731925 ATTTTATTTATATTCTTA--TTCT
1 ATTTTACTTA-ATT-TTATTTTCT
*
3731947 -TTTTACTAAATTTTATTTTCT
1 ATTTTACTTAATTTTATTTTCT
*
3731968 ATTTTA-TTAATTATATTTT
1 ATTTTACTTAATTTTATTTT
3731987 TTCGATTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
19 3 0.06
20 12 0.24
21 27 0.53
22 9 0.18
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTTTACTTAATTTTATTTTCT
Found at i:3732094 original size:29 final size:29
Alignment explanation
Indices: 3732050--3732111 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
3732040 TTTTTTTTTC
* *
3732050 TTTTTCTCTTTAATTTATT-TAATATTCAT
1 TTTTTCTCCTTAATTTATTAT-ATATTAAT
*
3732079 TTTTTCTCCTTGATTTATTATATATTAAT
1 TTTTTCTCCTTAATTTATTATATATTAAT
3732108 TTTT
1 TTTT
3732112 CTTTTCTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.23, C:0.10, G:0.02, T:0.66
Consensus pattern (29 bp):
TTTTTCTCCTTAATTTATTATATATTAAT
Found at i:3732128 original size:33 final size:31
Alignment explanation
Indices: 3732044--3732134 Score: 80
Period size: 33 Copynumber: 2.9 Consensus size: 31
3732034 TTTTAATTTT
3732044 TTTTTCTTTTTCTCTTTAATTTATT-TA-ATA
1 TTTTTC-TTTTCTCTTTAATTTATTATATATA
* * *
3732074 TTCATT-TTTTCTCCTTGATTTATTATATATTAA
1 TT-TTTCTTTTCTCTTTAATTTATTATATA-T-A
* *
3732107 TTTTTCTTTTCTCTTTTATTTAATATAT
1 TTTTTCTTTTCTCTTTAATTTATTATAT
3732135 CTTCTTCTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
29 16 0.33
30 4 0.08
31 3 0.06
32 3 0.06
33 22 0.46
ACGTcount: A:0.21, C:0.11, G:0.01, T:0.67
Consensus pattern (31 bp):
TTTTTCTTTTCTCTTTAATTTATTATATATA
Found at i:3736444 original size:31 final size:31
Alignment explanation
Indices: 3736408--3736466 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3736398 ATGTAATTGA
*
3736408 AAATGTGATA-AAAATCATTATATTTTAAGTT
1 AAATGTAATATAAAAT-ATTATATTTTAAGTT
*
3736439 AAATGTAATATAAAATATTATTTTTTAA
1 AAATGTAATATAAAATATTATATTTTAA
3736467 TATTTTAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (31 bp):
AAATGTAATATAAAATATTATATTTTAAGTT
Found at i:3741150 original size:16 final size:16
Alignment explanation
Indices: 3741129--3741164 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3741119 ACCTTCTCCC
*
3741129 TACACACATACATACA
1 TACACACAAACATACA
*
3741145 TACACATAAACATACA
1 TACACACAAACATACA
3741161 TACA
1 TACA
3741165 ATTTATATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (16 bp):
TACACACAAACATACA
Found at i:3741576 original size:25 final size:29
Alignment explanation
Indices: 3741547--3741611 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
3741537 AAGACAAATA
3741547 TAATAAATTAA-AT-T-AA-ATTAATATT
1 TAATAAATTAATATATAAATATTAATATT
*
3741572 TAATAATTTTAATATAATAAATATTAATATT
1 TAATAA-ATTAATAT-ATAAATATTAATATT
3741603 TAATAAATT
1 TAATAAATT
3741612 TGTACTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
25 6 0.19
26 4 0.12
27 2 0.06
29 1 0.03
30 4 0.12
31 15 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TAATAAATTAATATATAAATATTAATATT
Found at i:3741608 original size:17 final size:17
Alignment explanation
Indices: 3741563--3741610 Score: 66
Period size: 15 Copynumber: 3.0 Consensus size: 17
3741553 ATTAAATTAA
3741563 ATTAATATTTAAT-AAT
1 ATTAATATTTAATAAAT
*
3741579 TTTAATA--TAATAAAT
1 ATTAATATTTAATAAAT
3741594 ATTAATATTTAATAAAT
1 ATTAATATTTAATAAAT
3741611 TTGTACTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 4 0.15
15 9 0.33
16 6 0.22
17 8 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTAATATTTAATAAAT
Found at i:3746383 original size:2 final size:2
Alignment explanation
Indices: 3746376--3746406 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3746366 ATAATTTGTA
3746376 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3746407 ATTAACTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3759006 original size:90 final size:90
Alignment explanation
Indices: 3758853--3759032 Score: 351
Period size: 90 Copynumber: 2.0 Consensus size: 90
3758843 GTTACAAACC
3758853 GATAATATTAATGATCAATTTGTTACTTTTTAAACTTTAATGGGAAAAATGAATACTTACTCAAA
1 GATAATATTAATGATCAATTTGTTACTTTTTAAACTTTAATGGGAAAAATGAATACTTACTCAAA
3758918 CATTAGTTATCATTGGTGTAGTTTA
66 CATTAGTTATCATTGGTGTAGTTTA
3758943 GATAATATTAATGATCAATTTGTTACTTTTTAAACTTTAATGGGAAAAATGAATACTTACTCAAA
1 GATAATATTAATGATCAATTTGTTACTTTTTAAACTTTAATGGGAAAAATGAATACTTACTCAAA
*
3759008 CATTAGTTATCGTTGGTGTAGTTTA
66 CATTAGTTATCATTGGTGTAGTTTA
3759033 CCCAAGTATA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (90 bp):
GATAATATTAATGATCAATTTGTTACTTTTTAAACTTTAATGGGAAAAATGAATACTTACTCAAA
CATTAGTTATCATTGGTGTAGTTTA
Found at i:3761539 original size:14 final size:16
Alignment explanation
Indices: 3761520--3761557 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
3761510 ACTTACTTCC
3761520 ATCAAAA-TCA-AAAT
1 ATCAAAATTCAGAAAT
3761534 ATCAAAATTCAGAAAT
1 ATCAAAATTCAGAAAT
3761550 ATCCAAAA
1 AT-CAAAA
3761558 CAGTAATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 3 0.14
16 6 0.29
17 5 0.24
ACGTcount: A:0.61, C:0.16, G:0.03, T:0.21
Consensus pattern (16 bp):
ATCAAAATTCAGAAAT
Found at i:3763629 original size:21 final size:21
Alignment explanation
Indices: 3763599--3763639 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3763589 AAATATTAAA
*
3763599 AAATATTAATGTTTTAGATAG
1 AAATAATAATGTTTTAGATAG
3763620 AAATAATAATGTTTTAGATA
1 AAATAATAATGTTTTAGATA
3763640 ATATTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.41
Consensus pattern (21 bp):
AAATAATAATGTTTTAGATAG
Found at i:3779739 original size:20 final size:20
Alignment explanation
Indices: 3779714--3779774 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
3779704 TTTTGGTGCA
*
3779714 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
3779734 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
3779755 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
3779775 CCACAAGGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:3779784 original size:22 final size:22
Alignment explanation
Indices: 3779735--3779797 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
3779725 TACCCCCATG
****
3779735 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCCCCCCACA
3779757 AGGGGAACCGATTCCCCCCCACA
1 A-GGGAACCGATTCCCCCCCACA
* *
3779780 AGGGAATCGATACCCCCC
1 AGGGAACCGATTCCCCCC
3779798 TGGGGTACTG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.25, C:0.38, G:0.22, T:0.14
Consensus pattern (22 bp):
AGGGAACCGATTCCCCCCCACA
Found at i:3782070 original size:27 final size:27
Alignment explanation
Indices: 3782032--3782123 Score: 175
Period size: 27 Copynumber: 3.4 Consensus size: 27
3782022 TAACAAAAAG
3782032 GGGAGAAGTGTGTTAAATGTTTTAAAT
1 GGGAGAAGTGTGTTAAATGTTTTAAAT
3782059 GGGAGAAGTGTGTTAAATGTTTTAAAT
1 GGGAGAAGTGTGTTAAATGTTTTAAAT
3782086 GGGAGAAGTGTGTTAAATGTTTTAAAT
1 GGGAGAAGTGTGTTAAATGTTTTAAAT
*
3782113 GAGAGAAGTGT
1 GGGAGAAGTGT
3782124 TAAACTAAGG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.35
Consensus pattern (27 bp):
GGGAGAAGTGTGTTAAATGTTTTAAAT
Found at i:3782536 original size:20 final size:19
Alignment explanation
Indices: 3782507--3782544 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
3782497 TATGCTCGAA
3782507 GGGAACCGATTCCCCCCAG
1 GGGAACCGATTCCCCCCAG
3782526 GGGATACCGATTCCCCCCA
1 GGGA-ACCGATTCCCCCCA
3782545 CTATTCAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.21, C:0.42, G:0.24, T:0.13
Consensus pattern (19 bp):
GGGAACCGATTCCCCCCAG
Found at i:3790302 original size:15 final size:13
Alignment explanation
Indices: 3790259--3790336 Score: 59
Period size: 13 Copynumber: 6.1 Consensus size: 13
3790249 AAAAAATAAC
*
3790259 AAAAAAAAGGAAA
1 AAAAAAAAGAAAA
* * *
3790272 ACAAAAAAGGAGA
1 AAAAAAAAGAAAA
**
3790285 AAAAAAAAGAACC
1 AAAAAAAAGAAAA
* **
3790298 AAAAAGAA-CCAA
1 AAAAAAAAGAAAA
*
3790310 AAAAAAAAGAAAG
1 AAAAAAAAGAAAA
3790323 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
3790336 A
1 A
3790337 GGAGGGTTCA
Statistics
Matches: 48, Mismatches: 16, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
12 7 0.15
13 41 0.85
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:3790302 original size:25 final size:23
Alignment explanation
Indices: 3790240--3790336 Score: 72
Period size: 25 Copynumber: 4.0 Consensus size: 23
3790230 TTTGAAGATG
* *
3790240 AAAAAGATAA-AAAAATAACAAAA
1 AAAAAGA-AACAAAAAAAAGAAAA
* *
3790263 AAAAGGAAAACAAAAAAGGAGAAAA
1 AAAAAG-AAACAAAAAA-AAGAAAA
*
3790288 AAAAAGAACCAAAAAGAACCA-AAAA
1 AAAAAGAAACAAAAA-AA--AGAAAA
*
3790313 AAAAAGAAAGAAAAAAAAGAAAA
1 AAAAAGAAACAAAAAAAAGAAAA
3790336 A
1 A
3790337 GGAGGGTTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
22 1 0.02
23 12 0.21
24 16 0.28
25 28 0.48
26 1 0.02
ACGTcount: A:0.80, C:0.06, G:0.11, T:0.02
Consensus pattern (23 bp):
AAAAAGAAACAAAAAAAAGAAAA
Found at i:3790322 original size:19 final size:19
Alignment explanation
Indices: 3790239--3790337 Score: 57
Period size: 19 Copynumber: 5.4 Consensus size: 19
3790229 GTTTGAAGAT
*
3790239 GAAAAAGATAA-AAAAATAA
1 GAAAAAGA-AAGAAAAAAAA
* * *
3790258 CAAAAA-AAAGGAAAACAA
1 GAAAAAGAAAGAAAAAAAA
* *
3790276 -AAAAGGAGA-AAAAAAAA
1 GAAAAAGAAAGAAAAAAAA
* *
3790293 GAACCAA-AAAGAACCAAAAA
1 GAA-AAAGAAAGAA-AAAAAA
3790313 -AAAAAGAAAGAAAAAAAA
1 GAAAAAGAAAGAAAAAAAA
3790331 GAAAAAG
1 GAAAAAG
3790338 GAGGGTTCAA
Statistics
Matches: 59, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
17 12 0.20
18 20 0.34
19 22 0.37
20 5 0.08
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.02
Consensus pattern (19 bp):
GAAAAAGAAAGAAAAAAAA
Found at i:3790326 original size:9 final size:9
Alignment explanation
Indices: 3790240--3790336 Score: 54
Period size: 10 Copynumber: 10.2 Consensus size: 9
3790230 TTTGAAGATG
3790240 AAAAAGATAA
1 AAAAAGA-AA
*
3790250 AAAAATAACA
1 AAAAAGAA-A
*
3790260 AAAAA-AAG
1 AAAAAGAAA
* *
3790268 GAAAACAAA
1 AAAAAGAAA
*
3790277 AAAGGAGAAAA
1 AAA-AAG-AAA
*
3790288 AAAAAGAACC
1 AAAAAGAA-A
3790298 AAAAAGAACCA
1 AAAAAGAA--A
3790309 AAAAA-AAA
1 AAAAAGAAA
*
3790317 AGAAAGAAA
1 AAAAAGAAA
3790326 AAAAAGAAA
1 AAAAAGAAA
3790335 AA
1 AA
3790337 GGAGGGTTCA
Statistics
Matches: 68, Mismatches: 12, Indels: 15
0.72 0.13 0.16
Matches are distributed among these distances:
8 9 0.13
9 22 0.32
10 25 0.37
11 12 0.18
ACGTcount: A:0.80, C:0.06, G:0.11, T:0.02
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:3790331 original size:38 final size:38
Alignment explanation
Indices: 3790242--3790333 Score: 98
Period size: 38 Copynumber: 2.4 Consensus size: 38
3790232 TGAAGATGAA
* **
3790242 AAAGATAAAAAAATAACAAAAAAAAGGAAAACAAAAAAG
1 AAAGA-AAAAAAAGAACAAAAAAAACCAAAACAAAAAAG
* *
3790281 -GAGAAAAAAAAAGAACCAAAAAGAACCAAAA-AAAAAAG
1 AAAG-AAAAAAAAGAA-CAAAAAAAACCAAAACAAAAAAG
3790319 AAAGAAAAAAAAGAA
1 AAAGAAAAAAAAGAA
3790334 AAAGGAGGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
38 29 0.66
39 15 0.34
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (38 bp):
AAAGAAAAAAAAGAACAAAAAAAACCAAAACAAAAAAG
Found at i:3791671 original size:54 final size:54
Alignment explanation
Indices: 3791591--3791992 Score: 605
Period size: 54 Copynumber: 7.5 Consensus size: 54
3791581 GTGAAGCAGA
* * *
3791591 AGAAGAT-GTTCGAGTTTCTACTCCCTAAAGAAAAAGGGAGCGAACCCGT-TGAC
1 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG-C
* * * *
3791644 AGAAGATTGTTCGAGTTTCTACTCCCTAAAAAAAAGAGGGAGTGAACCCGTAAGC
1 AGAAGATCGTTCGAGTTCCTACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAAGC
* *
3791699 AAAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAACGAACCCGTAAGC
1 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGC
*
3791753 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGGGGGAGCGAACCCGTAAGC
1 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGC
*
3791807 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGAAGCGAACCCGT-AGAC
1 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG-C
* *
3791861 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGTGAACCCGTAAGC
1 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGC
*
3791915 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAAC
1 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGC
* *
3791969 AGAAGATTGTTCAAGTT-CTACTCC
1 AGAAGATCGTTCGAGTTCCTACTCC
3791993 TTGAAGTGAT
Statistics
Matches: 321, Mismatches: 23, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
53 16 0.05
54 257 0.80
55 47 0.15
56 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.19
Consensus pattern (54 bp):
AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGC
Found at i:3792744 original size:127 final size:130
Alignment explanation
Indices: 3792586--3792842 Score: 493
Period size: 127 Copynumber: 2.0 Consensus size: 130
3792576 ACCACTAGGG
3792586 TTTTGCCCTATGCCCAGCGCCGCCAAAGCCTACACCGTTGGATCTGATGAGATCCAGCGGCTCTC
1 TTTTGCCCTATGCCCAGCGCCGCCAAAGCCTACACCGTTGGATCTGATGAGATCCAGCGGCTCTC
3792651 AACGATCACAGAGTACCAAAACAACACCCACC-TGCATTCC-CGGGACAGCACGAAG-CATGCCT
66 AACGATCACAGAGTACCAAAACAACACCCACCATGCATTCCTCGGGACAGCACGAAGCCATGCCT
3792713 TTTTGCCCTATGCCCAGCGCCGCCAAAGCCTACACCGTTGGATCTGATGAGATCCAGCGGCTCTC
1 TTTTGCCCTATGCCCAGCGCCGCCAAAGCCTACACCGTTGGATCTGATGAGATCCAGCGGCTCTC
3792778 AACGATCACAGAGTACCAAAACAACACCCACCATGCATTCCTCGGGACAGCACGAAGCCATGCCT
66 AACGATCACAGAGTACCAAAACAACACCCACCATGCATTCCTCGGGACAGCACGAAGCCATGCCT
3792843 GTCGGCCATC
Statistics
Matches: 127, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
127 97 0.76
128 8 0.06
129 15 0.12
130 7 0.06
ACGTcount: A:0.27, C:0.35, G:0.20, T:0.18
Consensus pattern (130 bp):
TTTTGCCCTATGCCCAGCGCCGCCAAAGCCTACACCGTTGGATCTGATGAGATCCAGCGGCTCTC
AACGATCACAGAGTACCAAAACAACACCCACCATGCATTCCTCGGGACAGCACGAAGCCATGCCT
Found at i:3793476 original size:16 final size:17
Alignment explanation
Indices: 3793455--3793489 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3793445 GTTTACTAAA
3793455 AATGAAA-CTAGGTTAG
1 AATGAAATCTAGGTTAG
*
3793471 AATGAAATTTAGGTTAG
1 AATGAAATCTAGGTTAG
3793488 AA
1 AA
3793490 ATAAACCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.46, C:0.03, G:0.23, T:0.29
Consensus pattern (17 bp):
AATGAAATCTAGGTTAG
Found at i:3794035 original size:58 final size:59
Alignment explanation
Indices: 3793984--3794101 Score: 211
Period size: 58 Copynumber: 2.0 Consensus size: 59
3793974 TATTTTCGTT
3793984 TACACAGCAAATTTTATGTAGTATATTTAAGCCTTTGCAATAAG-ATATTATTTTATTA
1 TACACAGCAAATTTTATGTAGTATATTTAAGCCTTTGCAATAAGTATATTATTTTATTA
**
3794042 TTTACAGCAAATTTTATGTAGTATATTTAAGCCTTTGCAATAAGTATATTATTTTATTA
1 TACACAGCAAATTTTATGTAGTATATTTAAGCCTTTGCAATAAGTATATTATTTTATTA
3794101 T
1 T
3794102 TTATTAGTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
58 42 0.74
59 15 0.26
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.46
Consensus pattern (59 bp):
TACACAGCAAATTTTATGTAGTATATTTAAGCCTTTGCAATAAGTATATTATTTTATTA
Found at i:3795005 original size:18 final size:19
Alignment explanation
Indices: 3794975--3795022 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 19
3794965 TCATTAATTT
3794975 TTTTAATATTAT-AATTTTA
1 TTTTAA-ATTATAAATTTTA
3794994 TTTTAAATTATAAATTTTA
1 TTTTAAATTATAAATTTTA
3795013 TTTTAAATTA
1 TTTTAAATTA
3795023 ACCATTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAAATTATAAATTTTA
Found at i:3796171 original size:2 final size:2
Alignment explanation
Indices: 3796164--3796188 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3796154 TAATAATTAG
3796164 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3796189 AGCAAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3796701 original size:27 final size:27
Alignment explanation
Indices: 3796657--3796708 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
3796647 TATTTACATC
*
3796657 ATAAATCCAATCCGACCACATGCTCAA
1 ATAAATCCAATCCAACCACATGCTCAA
3796684 ATAAATCCAA-CCTAACCACATGCTC
1 ATAAATCCAATCC-AACCACATGCTC
3796709 TAATTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.40, C:0.35, G:0.06, T:0.19
Consensus pattern (27 bp):
ATAAATCCAATCCAACCACATGCTCAA
Found at i:3796791 original size:14 final size:13
Alignment explanation
Indices: 3796759--3796792 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
3796749 TTTGAATCGG
3796759 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
3796772 TCTTTCTTTTTCTCT
1 T-TTTCTTTTTCT-T
3796787 TTTTCT
1 TTTTCT
3796793 GCTTGAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 16 0.84
15 2 0.11
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTCTTTTTCTT
Found at i:3798213 original size:21 final size:20
Alignment explanation
Indices: 3798170--3798254 Score: 70
Period size: 21 Copynumber: 4.3 Consensus size: 20
3798160 TTTTCCCAAT
*
3798170 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* *
3798190 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAA-TAAGAAAA
**
3798211 TCGCAATGCG-AT--GACTA
1 TCGCAATGCGAATAAGAAAA
3798228 TCGCAATGCGATAATAA-AAAA
1 TCGCAATGCG--AATAAGAAAA
3798249 TCGCAA
1 TCGCAA
3798255 CGATACTTAC
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
17 13 0.25
19 1 0.02
20 14 0.27
21 23 0.45
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:3798506 original size:22 final size:22
Alignment explanation
Indices: 3798478--3798521 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3798468 CACTCTCTCA
3798478 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
3798500 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
3798522 TATCTAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:3800129 original size:18 final size:18
Alignment explanation
Indices: 3800103--3800147 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3800093 CTCACTTCGG
*
3800103 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
3800121 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
3800139 GAGCCATCA
1 GAGCCATCA
3800148 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:3800666 original size:19 final size:20
Alignment explanation
Indices: 3800612--3800678 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
3800602 TAGTTTACTT
* *
3800612 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
3800632 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
3800652 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
3800671 TCGCAACG
1 TCGCAACG
3800679 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:3800686 original size:14 final size:14
Alignment explanation
Indices: 3800667--3800724 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3800657 ATGCGAAATG
3800667 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3800681 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
3800697 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
3800713 AAAATCGCAACG
1 AAAATCGCAACG
3800725 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3800709 original size:32 final size:32
Alignment explanation
Indices: 3800651--3800740 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
3800641 GGAAATGGCT
*
3800651 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
3800684 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
3800716 ATCGCAACGCGAAATGAAATCGCAA
1 ATCGCAACGCGAAATGAAATCGCAA
3800741 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 41 0.73
33 15 0.27
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:3800798 original size:32 final size:33
Alignment explanation
Indices: 3800756--3800824 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3800746 TTTGTTTCGC
*
3800756 GCGA-TTTGTCGTTGCGA-TTTCATTTCGCGTT
1 GCGATTTTGTCGTTGCGATTTTCATTTCGCATT
3800787 GCGATTTTGTCGTTGCGATTTTCATTTCGCATT
1 GCGATTTTGTCGTTGCGATTTTCATTTCGCATT
3800820 GCGAT
1 GCGAT
3800825 AGCCATTCAC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 4 0.11
32 13 0.37
33 18 0.51
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.45
Consensus pattern (33 bp):
GCGATTTTGTCGTTGCGATTTTCATTTCGCATT
Found at i:3800802 original size:14 final size:14
Alignment explanation
Indices: 3800756--3800808 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
3800746 TTTGTTTCGC
3800756 GCGA-TTTGTCGTT
1 GCGATTTTGTCGTT
*
3800769 GCGATTTCATTTCGCGTT
1 GCGATTT--TGT--CGTT
3800787 GCGATTTTGTCGTT
1 GCGATTTTGTCGTT
3800801 GCGATTTT
1 GCGATTTT
3800809 CATTTCGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
13 4 0.12
14 14 0.42
16 4 0.12
18 11 0.33
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.47
Consensus pattern (14 bp):
GCGATTTTGTCGTT
Found at i:3800823 original size:19 final size:19
Alignment explanation
Indices: 3800765--3800880 Score: 84
Period size: 18 Copynumber: 6.4 Consensus size: 19
3800755 CGCGATTTGT
3800765 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3800783 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
3800797 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* *** *
3800816 CATTGCGATAGCCA-TTCA
1 CGTTGCGATTTTCATTTCG
**
3800834 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3800853 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
3800873 TGTTGCGA
1 CGTTGCGA
3800881 AAGTAAACTA
Statistics
Matches: 77, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.03
17 2 0.03
18 26 0.34
19 24 0.31
20 12 0.16
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:3802702 original size:14 final size:14
Alignment explanation
Indices: 3802683--3802718 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3802673 GATTGTTAAT
3802683 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3802697 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3802711 TGATTTGT
1 TGATTTGT
3802719 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3802891 original size:19 final size:19
Alignment explanation
Indices: 3802835--3802883 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
3802825 ATCGCAACGA
3802835 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
3802854 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
3802873 GAAAATCGCAA
1 GAAAATCGCAA
3802884 CGAGAAATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:3802945 original size:20 final size:20
Alignment explanation
Indices: 3802920--3802976 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
3802910 TCGCATTGCG
*
3802920 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
3802940 ATTTTCGCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
*
3802960 ATTTTCGCATTGCGATA
1 ATTTTCGCGTTGCGATA
3802977 GTCAAATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAACC
Found at i:3803938 original size:14 final size:14
Alignment explanation
Indices: 3803919--3803954 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3803909 ATTGTTTAAT
3803919 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3803933 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3803947 TGATTTGT
1 TGATTTGT
3803955 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3805097 original size:14 final size:14
Alignment explanation
Indices: 3805078--3805113 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3805068 ATTGTTTAAT
3805078 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3805092 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3805106 TGATTTGT
1 TGATTTGT
3805114 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3805664 original size:14 final size:14
Alignment explanation
Indices: 3805645--3805680 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3805635 ATTGTTTAAT
3805645 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3805659 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3805673 TGATTTGT
1 TGATTTGT
3805681 TTAATGATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3807139 original size:576 final size:587
Alignment explanation
Indices: 3802940--3807196 Score: 7678
Period size: 578 Copynumber: 7.4 Consensus size: 587
3802930 TGCGATAACC
*
3802940 ATTTTCGCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
3803005 AACTGAACAGATCATAGC-ATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
*
3803069 AAGTGCACACATAAATACACATAATGCAAGTTTTGTTAAATATATACTCCTTTTGGTTTGAAAAT
131 AAGTGCACACATAAATACACATAATGCAAGTTTTGTT-AACATATACTCCTTTTGGTTTGAAAAT
*
3803134 GTTTGGTTAAGTATCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTT
195 GTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTT
3803199 GTTTGAGCAAATG-TTGGTTTCTGCA-GTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTACGG
260 GTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTACGG
3803262 GGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTA-TTTT
325 GGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTT
3803326 TGATTG-TTAATTGATTTGTAAAAGATGA-TTGTAAATGTTGA-TTGTTTAATTGATGTGTACAT
390 TGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACAT
3803388 AATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGC-AAA-
455 AATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAAC
3803451 AGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCATT
520 AGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCATT
3803516 GCG
585 GCG
3803519 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
3803584 AA-TGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
3803648 AAGTGCACACATAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAA
131 AAGTGCACACATAAATACACATAATGCAAGTTTTGTTAAC--ATATACTCCTTTTGGTTTGAAAA
* *
3803713 TGTTTGGTTCAGTACCTAGAATTCAATAATTTGTTGTTTGTAGGTTTTAGATGTGTA-GAAGTCT
194 TGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCT
*
3803777 TGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCGTTAAGTGAGCTGTGTGAAATGGATGTACG
259 TGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTACG
3803842 GGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTA-TATTTT
324 GGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTT
3803906 TTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACA
389 TTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACA
3803971 TAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAA
454 TAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAA
3804036 CAGACTATCGCAACGCGAAATGGC--TCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCAT
519 CAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCAT
3804099 TGCG
584 TGCG
3804103 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
3804168 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
3804233 AAGTGCACACATAAAT--ACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAA
131 AAGTGCACACATAAATACACATAATGCAAGTTTTGTTAAC--ATATACTCCTTTTGGTTTGAAAA
3804296 TGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCT
194 TGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCT
3804361 TGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC-
259 TGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTACG
3804425 GGGTCACAAAGTTGTTGA-TCATTGATTCAATAATTGATGAAGAAATAAGAATTATTA-TA-TTT
324 GGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTT
3804487 TTGATTGTTTAATTGA-TTGTAAAAGATGATTTGTAAATGTTGA-TTGTTTAATTGATGTGTACA
389 TTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACA
3804550 T-ATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGC-TT-TGTTGAAGGCAAAA
454 TAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAA
3804612 CAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCAT
519 CAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCAT
3804677 TGCG
584 TGCG
3804681 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
3804746 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAA-ACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
*
3804810 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATA-TACTCTTTGGTTTGAAAA
131 AAGTGCACACAT-AAATACACATAATGCAAGTTTTGTTAACATATACTCCT-TTTGGTTTGAAAA
*
3804874 TGTTTGGTTAAGTACCTAGAATTCAATAATTTGTTGTTTGTAGGTTTTAGATGTGTAGGAAGTCT
194 TGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCT
*
3804939 TGTTTGAGCAAA----TGGTTTCTGCAGGTTAATCGTTAAGTGAGCTGTGTGAAATGGATGTACG
259 TGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTACG
3805000 GGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTT
324 GGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTT
3805065 TTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC-
389 TTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACA
3805129 -AATTTGTG-TGAAATGTAATAGTTGATTTGTTGA-TTTCAATCTGCTTTATGTTGAAGGCAAAA
454 TAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAA
3805191 CAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGA-TTTCGTTTCGCAT
519 CAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCAT
3805255 TGCG
584 TGCG
3805259 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTC-AATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
3805323 AACTGAACAGATCATAGCAATGTTCAAACTC-AGTTACTAAT-CATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
*
3805386 AAGTGCTCACATAAATACACATAATGCAAG-TTTGTTAACATATACTCC-TTTGGTTTG-AAATG
131 AAGTGCACACATAAATACACATAATGCAAGTTTTGTTAACATATACTCCTTTTGGTTTGAAAATG
3805448 TTTGGTTAAGTACCTAGAATTCAATAA-TTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC-TG
196 TTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTG
3805511 TTTGAGCAAATGTTT-GTTTCTGCA-GTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTACGGG
261 TTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTACGGG
3805574 GTCACAAAGTTGTTGATT--TTGATTCAATAATTGATGAAGAAATAAG-ATTA-T-TTATTTTTT
326 GTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTT
3805634 GATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAA-TGA--TGTACATA
391 GATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATA
*
3805696 ATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTTC-TTATGTTGAAGGCAAAACA
456 ATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACA
*
3805760 GACTATCGCAACGTGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCATTG
521 GACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCATTG
3805825 CG
586 CG
3805827 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
*
3805892 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTATTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
3805957 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACAT-AAATACACATAATGCAAGTTTTGTTAAC--ATATACTCCTTTTGGTTTGAAA
3806022 ATGTTTGGTTAAGTACCTAGAATTC-A-AATTTGCTGTTTGTAGGTTTTAGA--TGTAGGAAGTC
193 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
3806083 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGA-CTGTG-GAAATGGATGTAC
258 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
3806146 GGGGTCACAAAGTTG-TGATTCATTGATTC---AATTGATG-AG-AATAAGAATTA-TATTATTT
323 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
3806204 TTTGATTGTTTAATTGA-TTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
388 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
3806268 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
453 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
3806333 AC--ACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
518 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
3806396 TTGCG
583 TTGCG
3806401 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTC-AATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
3806465 -ACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
3806529 AAGTGCACACATAAATACACATAATGCAAGTTTTGTTAACATATACTCCTTTTGGTTTG-AAATG
131 AAGTGCACACATAAATACACATAATGCAAGTTTTGTTAACATATACTCCTTTTGGTTTGAAAATG
3806593 TTTGGTT-AGTACCTAGAATTCAATAA-TTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTG
196 TTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTG
3806656 -TTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC-GG
261 TTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTACGGG
*
3806719 GTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTATTT
326 GTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTT
3806784 GATTGTTTAATTGATTTGTAAAAGATGA-TTGTAAATGTTGATTTGTTTAA-TGATGTGTACATA
391 GATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATA
3806847 ATTTGTGTTGAAATGTAAT-GTTGA-TTGTTGATTTTCAATCTGCTTTATGTTGAAGGC-AAACA
456 ATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACA
3806909 GACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCATTG
521 GACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCATTG
3806974 CG
586 CG
3806976 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCT-ATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
3807040 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTT-A
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
3807104 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATACTCCTTTTGGTTTG-AAAT
131 AAGTGCACACAT-AAATACACATAATGCAAGTTTTGTTAACATATACTCCTTTTGGTTTGAAAAT
*
3807168 ATTTGGTTAAGTACCTAGAATTCAATAAT
195 GTTTGGTTAAGTACCTAGAATTCAATAAT
3807197 AATTTTAAAA
Statistics
Matches: 3572, Mismatches: 25, Indels: 163
0.95 0.01 0.04
Matches are distributed among these distances:
564 5 0.00
566 11 0.00
567 166 0.05
568 102 0.03
569 121 0.03
570 82 0.02
571 127 0.04
572 224 0.06
573 89 0.02
574 224 0.06
575 284 0.08
576 363 0.10
577 216 0.06
578 425 0.12
579 290 0.08
580 159 0.04
581 123 0.03
582 63 0.02
583 133 0.04
584 261 0.07
585 81 0.02
586 23 0.01
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (587 bp):
ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
AAGTGCACACATAAATACACATAATGCAAGTTTTGTTAACATATACTCCTTTTGGTTTGAAAATG
TTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTG
TTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTACGGG
GTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTT
GATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATA
ATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACA
GACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCATTG
CG
Found at i:3808068 original size:24 final size:24
Alignment explanation
Indices: 3808012--3808070 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
3808002 AGTCAGTATT
* *
3808012 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
3808036 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
3808060 CGAATTTTGAT
1 CGAAATTTGAT
3808071 GATGTTCGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:3810537 original size:33 final size:33
Alignment explanation
Indices: 3810496--3810581 Score: 163
Period size: 33 Copynumber: 2.6 Consensus size: 33
3810486 TACTATCGCA
3810496 GCGAAATGAAAATCGCAACGAGAGAATCGCAAT
1 GCGAAATGAAAATCGCAACGAGAGAATCGCAAT
*
3810529 GCGAAATGAAAATCGCAACGAGGGAATCGCAAT
1 GCGAAATGAAAATCGCAACGAGAGAATCGCAAT
3810562 GCGAAATGAAAATCGCAACG
1 GCGAAATGAAAATCGCAACG
3810582 CGAATTTAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.44, C:0.19, G:0.26, T:0.12
Consensus pattern (33 bp):
GCGAAATGAAAATCGCAACGAGAGAATCGCAAT
Found at i:3810544 original size:19 final size:18
Alignment explanation
Indices: 3810490--3810585 Score: 75
Period size: 19 Copynumber: 5.7 Consensus size: 18
3810480 GGAAATTACT
3810490 ATCGC-AGCGAAATGAAA
1 ATCGCAAGCGAAATGAAA
*
3810507 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
3810521 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
3810540 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
3810554 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
3810573 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
3810586 TTTAATTTCG
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.07
17 9 0.15
18 3 0.05
19 24 0.39
ACGTcount: A:0.44, C:0.20, G:0.25, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:3810655 original size:19 final size:18
Alignment explanation
Indices: 3810585--3810656 Score: 71
Period size: 19 Copynumber: 4.1 Consensus size: 18
3810575 CGCAACGCGA
*
3810585 ATTTAATTTCGCGTTGCG
1 ATTTCATTTCGCGTTGCG
3810603 ATTTCATTTTCGCGTTGCG
1 ATTTCA-TTTCGCGTTGCG
*
3810622 A-TTC---TCTCGTTGCG
1 ATTTCATTTCGCGTTGCG
*
3810636 ATTTTCATTTCGCATTGCG
1 A-TTTCATTTCGCGTTGCG
3810655 AT
1 AT
3810657 AGTACTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
14 10 0.23
16 3 0.07
18 9 0.20
19 22 0.50
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (18 bp):
ATTTCATTTCGCGTTGCG
Found at i:3812200 original size:41 final size:42
Alignment explanation
Indices: 3812155--3812242 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 42
3812145 CCTCTTCAAC
* * * *
3812155 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGA-G
1 GATGACAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
* * *
3812196 GATGATAGGGGCCTCTTCAACGATAGGAGTGGACTCTTGAGG
1 GATGACAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
3812238 GATGA
1 GATGA
3812243 GGCGAGTCGG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 33 0.85
42 6 0.15
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
Found at i:3814292 original size:33 final size:33
Alignment explanation
Indices: 3814239--3814335 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 33
3814229 ACGAGATAAT
* *
3814239 GAATTGCAACGCGGAAATGACTATCGCAATGAGA
1 GAATCGCAACGC-GAAATGACTATCGCAACGAGA
*
3814273 GAATCGCAACGCGAAATGACTATCGCGACGAGA
1 GAATCGCAACGCGAAATGACTATCGCAACGAGA
**
3814306 GAATCGCAACGCGAAATGAAAATCGCAACG
1 GAATCGCAACGCGAAATGACTATCGCAACG
3814336 CGAATGAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 46 0.81
34 11 0.19
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (33 bp):
GAATCGCAACGCGAAATGACTATCGCAACGAGA
Found at i:3814343 original size:18 final size:19
Alignment explanation
Indices: 3814307--3814374 Score: 113
Period size: 18 Copynumber: 3.7 Consensus size: 19
3814297 GCGACGAGAG
3814307 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
3814326 AATCGCAACGCG-AATGAA
1 AATCGCAACGCGAAATGAA
3814344 AATCGC-ACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
3814362 AATCGCAATGCGA
1 AATCGCAACGCGA
3814375 TTTTGGTTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
17 5 0.11
18 24 0.52
19 17 0.37
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:3814403 original size:19 final size:19
Alignment explanation
Indices: 3814370--3814436 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
3814360 AAAATCGCAA
**
3814370 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
3814389 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
** *
3814408 TGCGATAGTTATTTCCGCTT
1 TGCGATTTTTATTT-CGCGT
3814428 TGCGATTTT
1 TGCGATTTT
3814437 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:3815017 original size:21 final size:21
Alignment explanation
Indices: 3814984--3815063 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
3814974 TGCGAAAGTA
* * *
3814984 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
3815005 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
3815025 AGTATCGCATTGCGATTTTCTC
1 AGTATCGCATTGCGATTTT-TC
* *
3815047 AAT-TCGCGTTGCGATTT
1 AGTATCGCATTGCGATTT
3815064 ACTTATTCGC
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 16 0.35
21 26 0.57
22 4 0.09
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:3815040 original size:20 final size:20
Alignment explanation
Indices: 3814947--3815040 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
3814937 CGCTAAGTAA
*
3814947 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
3814967 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
3814987 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
3815008 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
3815028 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
3815041 TTTCTCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:3815059 original size:41 final size:41
Alignment explanation
Indices: 3814968--3815102 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
3814958 AAAGTCAGTA
* * * * *
3814968 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* *
3815008 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* ** * *
3815050 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCTCAAT
3815091 TCGCGTTGCGAT
1 TCGCGTTGCGAT
3815103 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 72 0.92
42 3 0.04
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
Found at i:3815073 original size:20 final size:20
Alignment explanation
Indices: 3815029--3815121 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
3815019 ATAGTCAGTA
*
3815029 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
3815050 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
3815070 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
3815091 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
3815111 TCGCATTGCGA
1 TCGCATTGCGA
3815122 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:3815103 original size:41 final size:41
Alignment explanation
Indices: 3815029--3815124 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
3815019 ATAGTCAGTA
* *
3815029 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
3815070 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
3815111 TCGCATTGCGAATT
1 TCGCATTGCGAATT
3815125 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:3815684 original size:14 final size:14
Alignment explanation
Indices: 3815665--3815703 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3815655 TAATGTGGAG
3815665 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
3815679 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
3815693 GAATCTCTGCA
1 TAATCCCTGCA
3815704 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:3816479 original size:2 final size:2
Alignment explanation
Indices: 3816474--3816509 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3816464 TTTTATAATC
3816474 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3816510 TAAATTATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3823519 original size:31 final size:30
Alignment explanation
Indices: 3823470--3823634 Score: 117
Period size: 31 Copynumber: 5.6 Consensus size: 30
3823460 TTGATTTAGT
* * * *
3823470 GGTCAATTTGATATTTTATATAAAATTTAGG
1 GGTCAAATTAATAATTTATATAAAATTT-GA
*
3823501 GGTTAAATTAATAATTTATATAAAATTTGA
1 GGTCAAATTAATAATTTATATAAAATTTGA
**
3823531 GGTCAAATTAAT-ATTT-TATCTAA---GA
1 GGTCAAATTAATAATTTATATAAAATTTGA
* * *
3823556 GATCAAATTAATATTTTATCTAAAATTTAGA
1 GGTCAAATTAATAATTTATATAAAATTT-GA
* * * *
3823587 GATCAAATTAATATTTTGTCTAAAATTTAGA
1 GGTCAAATTAATAATTTATATAAAATTT-GA
* *
3823618 GATCAAGTTAA-AATTTA
1 GGTCAAATTAATAATTTA
3823635 ACTATTTTTA
Statistics
Matches: 111, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
25 13 0.12
26 3 0.03
27 4 0.04
28 5 0.05
29 4 0.04
30 16 0.14
31 66 0.59
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (30 bp):
GGTCAAATTAATAATTTATATAAAATTTGA
Found at i:3827851 original size:20 final size:20
Alignment explanation
Indices: 3827793--3827851 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 20
3827783 GAAAGTCTAA
3827793 AAAAATTAACTTAATTTAAGGTT
1 AAAAATTAACTTAA--T-AGGTT
*
3827816 AAAAA-TAACGTAAATAGGTT
1 AAAAATTAAC-TTAATAGGTT
3827836 AAAAATTAACTTAATA
1 AAAAATTAACTTAATA
3827852 TTATTCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 15 0.47
21 5 0.16
22 4 0.12
23 8 0.25
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (20 bp):
AAAAATTAACTTAATAGGTT
Found at i:3828063 original size:21 final size:20
Alignment explanation
Indices: 3828023--3828065 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3828013 GTGTTGGTTT
*
3828023 TATTGATATATAAATATAAA
1 TATTGATATATAAACATAAA
3828043 TATT-ATATATAAAACATTAAA
1 TATTGATATAT-AAACA-TAAA
3828064 TA
1 TA
3828066 AATATATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 6 0.30
20 8 0.40
21 6 0.30
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
TATTGATATATAAACATAAA
Found at i:3832036 original size:14 final size:15
Alignment explanation
Indices: 3832008--3832036 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3831998 AAAAGGATTG
3832008 TAAATGAATTAAATT
1 TAAATGAATTAAATT
3832023 TAAATGAA-TAAATT
1 TAAATGAATTAAATT
3832037 CATGTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (15 bp):
TAAATGAATTAAATT
Found at i:3832259 original size:6 final size:6
Alignment explanation
Indices: 3832248--3832282 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
3832238 TAATTTTTTT
3832248 TAAATA TAAATAA TTAAATA TAAATA TAAATA TAA
1 TAAATA TAAAT-A -TAAATA TAAATA TAAATA TAA
3832283 TATGATTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.74
7 2 0.07
8 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
TAAATA
Found at i:3832266 original size:14 final size:13
Alignment explanation
Indices: 3832247--3832282 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
3832237 TTAATTTTTT
3832247 TTAAATATAAATAA
1 TTAAATATAAAT-A
3832261 TTAAATATAAATA
1 TTAAATATAAATA
3832274 -TAAATATAA
1 TTAAATATAA
3832283 TATGATTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 9 0.41
13 1 0.05
14 12 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAATATAAATA
Found at i:3832901 original size:60 final size:59
Alignment explanation
Indices: 3832835--3832947 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 59
3832825 TCGGGTGACC
*
3832835 ATTTTATAAATTTTAATAGTTAGGGTACTCAACAAAATAACG-TCTTATAATCGATGGATT
1 ATTTTATAAATTTTAATAATTAGGG-ACTCAACAAAATAACGCTC-TATAATCGATGGATT
* * * *
3832895 ATTTTATAACTTTTAATAATTAGGGACTCAATAGAGTAACGCTCTATAATCGA
1 ATTTTATAAATTTTAATAATTAGGGACTCAACAAAATAACGCTCTATAATCGA
3832948 GGGTCATTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
59 22 0.47
60 25 0.53
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (59 bp):
ATTTTATAAATTTTAATAATTAGGGACTCAACAAAATAACGCTCTATAATCGATGGATT
Found at i:3834594 original size:14 final size:14
Alignment explanation
Indices: 3834563--3834605 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
3834553 CGTGTTTATG
* * *
3834563 TGTATGTGTGTGTG
1 TGTATGTGTATATA
3834577 TGTATGTGTATATA
1 TGTATGTGTATATA
*
3834591 TGTATGTATATATA
1 TGTATGTGTATATA
3834605 T
1 T
3834606 ATATAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (14 bp):
TGTATGTGTATATA
Found at i:3842423 original size:15 final size:15
Alignment explanation
Indices: 3842403--3842444 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
3842393 CTCATGAGCC
3842403 TCGAGTTTTGATTGA
1 TCGAGTTTTGATTGA
3842418 TCGAGTTTTGATTGA
1 TCGAGTTTTGATTGA
3842433 TCGAGTTTTGAT
1 TCGAGTTTTGAT
3842445 GCTGATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.19, C:0.07, G:0.26, T:0.48
Consensus pattern (15 bp):
TCGAGTTTTGATTGA
Found at i:3845173 original size:3 final size:3
Alignment explanation
Indices: 3845159--3845191 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
3845149 TAAAATTTGA
3845159 TAT TAGT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TA
3845192 ATATGGGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3848692 original size:2 final size:2
Alignment explanation
Indices: 3848685--3848720 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3848675 CTTCAACCCA
3848685 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3848721 GAGTAGGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3852896 original size:305 final size:306
Alignment explanation
Indices: 3852328--3852931 Score: 1183
Period size: 305 Copynumber: 2.0 Consensus size: 306
3852318 CCCCAACACC
3852328 AGGTTGAGAGCAGTTTCCGTGGAAGACCTCCGAATTATTAATTGCCCACCATGGGACTTGATTTC
1 AGGTTGAGAGCAGTTTCCGTGGAAGACCTCCGAATTATTAATTGCCCACCATGGGACTTGATTTC
3852393 ACGACCCCAAGGTTAAGAGCCTTGTGCTCTACCAACTGAGCTGGACAGGCAATTCTAAAAAAAAG
66 ACGACCCCAAGGTTAAGAGCCTTGTGCTCTACCAACTGAGCTGGACAGGCAATTCTAAAAAAAAG
3852458 ATGAACAAATAGTTATTAAATAATTAAATTAAAATATAATTATTAAAAAATATCATTACCTAAAT
131 ATGAACAAATAGTTATTAAATAATTAAATTAAAATATAATTATTAAAAAATATCATTACCTAAAT
3852523 TTAATATGTGAGTTATGCAAATATAAAATAATAAAATTGATAACTAATTTAATAACACAAAAATT
196 TTAATATGTGAGTTATGCAAATATAAAATAATAAAATTGATAACTAATTTAATAACACAAAAATT
3852588 ATTTAGTTCAAAATTAGAATATAATGTTAATGCATATTAGGTTCTA
261 ATTTAGTTCAAAATTAGAATATAATGTTAATGCATATTAGGTTCTA
3852634 AGGTTGAGAGCAGTTT-CGTGGAAGACCTCCGAATTATTAATTGCCCACCATGGGACTTGATTTC
1 AGGTTGAGAGCAGTTTCCGTGGAAGACCTCCGAATTATTAATTGCCCACCATGGGACTTGATTTC
*
3852698 ACGACCCCAAGGTTAAGAGCCTTGTGCTCTACCAACTGAGCTGGACAGGCAATTCTAAAAAAAGG
66 ACGACCCCAAGGTTAAGAGCCTTGTGCTCTACCAACTGAGCTGGACAGGCAATTCTAAAAAAAAG
*
3852763 ATGAACAAATAGTTATTAAATATTTAAATTAAAATATAATTATTAAAAAATATCATTACCTAAAT
131 ATGAACAAATAGTTATTAAATAATTAAATTAAAATATAATTATTAAAAAATATCATTACCTAAAT
3852828 TTAATATGTGAGTTATGCAAATATAAAATAATAAAATTGATAACTAATTTAATAACACAAAAATT
196 TTAATATGTGAGTTATGCAAATATAAAATAATAAAATTGATAACTAATTTAATAACACAAAAATT
3852893 ATTTAGTTCAAAATTAGAATATAATGTTAATGCATATTA
261 ATTTAGTTCAAAATTAGAATATAATGTTAATGCATATTA
3852932 AACATCAATT
Statistics
Matches: 296, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
305 280 0.95
306 16 0.05
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (306 bp):
AGGTTGAGAGCAGTTTCCGTGGAAGACCTCCGAATTATTAATTGCCCACCATGGGACTTGATTTC
ACGACCCCAAGGTTAAGAGCCTTGTGCTCTACCAACTGAGCTGGACAGGCAATTCTAAAAAAAAG
ATGAACAAATAGTTATTAAATAATTAAATTAAAATATAATTATTAAAAAATATCATTACCTAAAT
TTAATATGTGAGTTATGCAAATATAAAATAATAAAATTGATAACTAATTTAATAACACAAAAATT
ATTTAGTTCAAAATTAGAATATAATGTTAATGCATATTAGGTTCTA
Found at i:3864466 original size:60 final size:60
Alignment explanation
Indices: 3864333--3864466 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 60
3864323 GTCGAATGAT
* * * * * *
3864333 CATTTTGTAACTTTTAATAGTTGATGGACTCAACAAAGCAACATTCTATAGTCAAGAGAT
1 CATTTTATAACTTTTAATAGTCGATGGACTCAACAAAACAACATTATATAATCAAGAGAC
* * * *
3864393 TATTTTGTAACTTTTAATAGTCGATGGACTCAACAAAACAATATTATATAATC-GGAGGAC
1 CATTTTATAACTTTTAATAGTCGATGGACTCAACAAAACAACATTATATAATCAAGA-GAC
3864453 CA-TTTATATACTTT
1 CATTTTATA-ACTTT
3864467 GCCCATTTAT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 7 0.11
60 55 0.89
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (60 bp):
CATTTTATAACTTTTAATAGTCGATGGACTCAACAAAACAACATTATATAATCAAGAGAC
Found at i:3869369 original size:12 final size:12
Alignment explanation
Indices: 3869339--3869363 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3869329 AAATAACATT
3869339 ATAATGTGAAAA
1 ATAATGTGAAAA
3869351 ATAATGTGAAAA
1 ATAATGTGAAAA
3869363 A
1 A
3869364 ATATGTATGC
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:0.16, T:0.24
Consensus pattern (12 bp):
ATAATGTGAAAA
Found at i:3872349 original size:5 final size:5
Alignment explanation
Indices: 3872341--3872378 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
3872331 TTTTTATTCT
*
3872341 TTTCG TTTCG TTTCG TTTCG TTTCG TTTCG TTTTG TTT
1 TTTCG TTTCG TTTCG TTTCG TTTCG TTTCG TTTCG TTT
3872379 ATTTTATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.00, C:0.16, G:0.18, T:0.66
Consensus pattern (5 bp):
TTTCG
Found at i:3872384 original size:5 final size:5
Alignment explanation
Indices: 3872376--3872529 Score: 62
Period size: 5 Copynumber: 31.0 Consensus size: 5
3872366 TTTCGTTTTG
* * *
3872376 TTTAT TTTAT TTT-T GTTTAT TCTA- TTTA- TTTAT TTTCT TTATTT TTTGAT
1 TTTAT TTTAT TTTAT -TTTAT TTTAT TTTAT TTTAT TTTAT TT-TAT TTT-AT
* *
3872426 TTTA- TTTAT GTTT-C TTTAT TTTCAT TTT-G TTTAT TTTA- TTTACT
1 TTTAT TTTAT -TTTAT TTTAT TTT-AT TTTAT TTTAT TTTAT TTTA-T
* *
3872470 TGTTAT CTTTAT TTTA- -TTAT TATTAT TTT-T CTTTAT CTT-T CTTACT
1 T-TTAT -TTTAT TTTAT TTTAT T-TTAT TTTAT -TTTAT TTTAT TTTA-T
3872516 TTT-T TTTAT TTTAT
1 TTTAT TTTAT TTTAT
3872530 CTTCTTTATT
Statistics
Matches: 116, Mismatches: 11, Indels: 44
0.68 0.06 0.26
Matches are distributed among these distances:
3 3 0.03
4 31 0.27
5 46 0.40
6 32 0.28
7 4 0.03
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:3872427 original size:17 final size:16
Alignment explanation
Indices: 3872398--3872540 Score: 67
Period size: 19 Copynumber: 8.3 Consensus size: 16
3872388 TTGTTTATTC
3872398 TATTTATTTATTTTCTT
1 TATTT-TTTATTTTCTT
*
3872415 TATTTTTTGATTTTATT
1 TATTTTTT-ATTTTCTT
*
3872432 TATGTTTCTTTATTTTCAT
1 TA--TTT-TTTATTTTCTT
* *
3872451 T-TTGTTTATTTTATT
1 TATTTTTTATTTTCTT
* * *
3872466 TACTTGTTATCTTTATTT
1 TATTTTTTAT-TTT-CTT
3872484 TATTATTATTATTTTTCTT
1 TATT-TT-TTA-TTTTCTT
3872503 TATCTTTCTTACTTTT-TT
1 TAT-TTT-TTA-TTTTCTT
* *
3872521 T-TATTTTATCTTCTT
1 TATTTTTTATTTTCTT
3872536 TATTT
1 TATTT
3872541 CATTTGTTTT
Statistics
Matches: 95, Mismatches: 18, Indels: 27
0.68 0.13 0.19
Matches are distributed among these distances:
14 3 0.03
15 16 0.17
16 14 0.15
17 18 0.19
18 8 0.08
19 25 0.26
20 10 0.11
21 1 0.01
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (16 bp):
TATTTTTTATTTTCTT
Found at i:3872447 original size:64 final size:65
Alignment explanation
Indices: 3872376--3872497 Score: 169
Period size: 64 Copynumber: 1.9 Consensus size: 65
3872366 TTTCGTTTTG
* *
3872376 TTTATTTT-ATTTTTGTTTATTCTATTTATTTATTTTCTTTATTTT-TTGATT-TTATTTATGTT
1 TTTATTTTCA-TTTTGTTTATTCTATTTACTTATTATCTTTATTTTATT-ATTATTATTTATGTT
3872438 TC
64 TC
* *
3872440 TTTATTTTCATTTTGTTTATTTTATTTACTTGTTATCTTTATTTTATTATTATTATTT
1 TTTATTTTCATTTTGTTTATTCTATTTACTTATTATCTTTATTTTATTATTATTATTT
3872498 TTCTTTATCT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
64 42 0.82
65 9 0.18
ACGTcount: A:0.17, C:0.05, G:0.04, T:0.74
Consensus pattern (65 bp):
TTTATTTTCATTTTGTTTATTCTATTTACTTATTATCTTTATTTTATTATTATTATTTATGTTTC
Found at i:3872461 original size:9 final size:9
Alignment explanation
Indices: 3872371--3872497 Score: 77
Period size: 9 Copynumber: 13.9 Consensus size: 9
3872361 TTTCGTTTCG
*
3872371 TTTTGTTTA
1 TTTTATTTA
*
3872380 TTTTATTTT
1 TTTTATTTA
3872389 TGTTTATTCTA
1 T-TTTATT-TA
3872400 -TTTATTTA
1 TTTTATTTA
*
3872408 TTTTCTTTA
1 TTTTATTTA
*
3872417 TTTT-TTGA
1 TTTTATTTA
3872425 TTTTATTTA
1 TTTTATTTA
*
3872434 TGTTTCTTTA
1 T-TTTATTTA
*
3872444 --TT-TTCA
1 TTTTATTTA
*
3872450 TTTTGTTTA
1 TTTTATTTA
3872459 TTTTATTTA
1 TTTTATTTA
3872468 CTTGTTATCTTTA
1 -TT-TTA--TTTA
3872481 TTTTA-TTA
1 TTTTATTTA
3872489 TTATTATTT
1 TT-TTATTT
3872498 TTCTTTATCT
Statistics
Matches: 94, Mismatches: 10, Indels: 27
0.72 0.08 0.21
Matches are distributed among these distances:
6 3 0.03
7 2 0.02
8 16 0.17
9 43 0.46
10 17 0.18
11 7 0.07
12 2 0.02
13 4 0.04
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (9 bp):
TTTTATTTA
Found at i:3873903 original size:13 final size:13
Alignment explanation
Indices: 3873885--3873917 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
3873875 CAAAGTAGAT
3873885 GAGCCTTTAATCA
1 GAGCCTTTAATCA
3873898 GAGCCTTTAATCA
1 GAGCCTTTAATCA
3873911 GAGCCTT
1 GAGCCTT
3873918 GATTCAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (13 bp):
GAGCCTTTAATCA
Found at i:3877413 original size:11 final size:11
Alignment explanation
Indices: 3877397--3877435 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
3877387 GGTGTTGTAT
3877397 AAGCTTAAAGA
1 AAGCTTAAAGA
* *
3877408 AAGCTTATA-T
1 AAGCTTAAAGA
3877418 AAGCTTAAAGA
1 AAGCTTAAAGA
3877429 AAGCTTA
1 AAGCTTA
3877436 TATAAGCTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (11 bp):
AAGCTTAAAGA
Found at i:3877418 original size:21 final size:21
Alignment explanation
Indices: 3877394--3877447 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
3877384 TTAGGTGTTG
3877394 TATAAGCTTAAAGAAAGCTTA
1 TATAAGCTTAAAGAAAGCTTA
3877415 TATAAGCTTAAAGAAAGCTTA
1 TATAAGCTTAAAGAAAGCTTA
3877436 TATAAGCTTAAA
1 TATAAGCTTAAA
3877448 ACACCAAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (21 bp):
TATAAGCTTAAAGAAAGCTTA
Done.