Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold271
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: 492225
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
File 2 of 4
Found at i:150852 original size:56 final size:56
Alignment explanation
Indices: 150756--150861 Score: 142
Period size: 56 Copynumber: 1.9 Consensus size: 56
150746 AAATATAAAC
* *
150756 GCCACTAAATTTGAATATTTAGCGGCGTTTACTAAAAAAAACGCCACTAAAAAATT
1 GCCACTAAATTTGAATAGTTAGCGGCGTTTACCAAAAAAAACGCCACTAAAAAATT
* ***
150812 GCCACTAAATTT-AAGTAGTTAGCGGCGTTTTCCCTGAAAAACGCCACTAA
1 GCCACTAAATTTGAA-TAGTTAGCGGCGTTTACCAAAAAAAACGCCACTAA
150862 TTATTTTTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
55 2 0.05
56 41 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (56 bp):
GCCACTAAATTTGAATAGTTAGCGGCGTTTACCAAAAAAAACGCCACTAAAAAATT
Found at i:153757 original size:22 final size:21
Alignment explanation
Indices: 153732--153774 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
153722 TTATATTAAT
*
153732 TATG-TAAATATTATTAATTATA
1 TATGTTAAA-ATT-TTAAATATA
153754 TATGTTAAAATTTTAAATATA
1 TATGTTAAAATTTTAAATATA
153775 AATATGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 7 0.37
23 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
TATGTTAAAATTTTAAATATA
Found at i:153825 original size:31 final size:34
Alignment explanation
Indices: 153790--153858 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 34
153780 GATATACGTA
153790 TTAAATATATTAT-AT-TATATATTA-ATTATAT
1 TTAAATATATTATGATATATATATTATATTATAT
* * * *
153821 TTAAATGTATTGTGATATATTTATTATATTATTT
1 TTAAATATATTATGATATATATATTATATTATAT
153855 TTAA
1 TTAA
153859 TTTATTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 11 0.35
32 2 0.06
33 8 0.26
34 10 0.32
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (34 bp):
TTAAATATATTATGATATATATATTATATTATAT
Found at i:154996 original size:21 final size:21
Alignment explanation
Indices: 154972--155039 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
154962 TTTCAAATGA
154972 TAATATTTTAATA-TAAAATAT
1 TAATA-TTTAATATTAAAATAT
* *
154993 TAATATTAAATAATTAAAATAA
1 TAATATTTAAT-ATTAAAATAT
* *
155015 TATTATTTATTATTAAAATAT
1 TAATATTTAATATTAAAATAT
155036 TAAT
1 TAAT
155040 TATATAAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 5 0.13
21 18 0.47
22 15 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATATTTAATATTAAAATAT
Found at i:155008 original size:14 final size:13
Alignment explanation
Indices: 154979--155051 Score: 56
Period size: 15 Copynumber: 5.2 Consensus size: 13
154969 TGATAATATT
154979 TTAATATAAAATA
1 TTAATATAAAATA
*
154992 TTAATATTAAATAA
1 TTAATATAAAAT-A
* *
155006 TTAAAATAATATTA
1 TTAATATAA-AATA
*
155020 TTTATTATTAAAATA
1 -TTAATA-TAAAATA
155035 TTAATTATATAAATA
1 TTAA-TATA-AAATA
155050 TT
1 TT
155052 TTAAAATATT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
13 11 0.24
14 14 0.30
15 18 0.39
16 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TTAATATAAAATA
Found at i:155056 original size:25 final size:24
Alignment explanation
Indices: 154985--155061 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 24
154975 TATTTTAATA
*
154985 TAAAATATTAA-TATTAAATA-AT
1 TAAAATATTAATTATTAAATATTT
*
155007 TAAAATAAT-ATTATT---TATTAT
1 TAAAATATTAATTATTAAATATT-T
155028 TAAAATATTAATTATATAAATATTT
1 TAAAATATTAATTAT-TAAATATTT
155053 TAAAATATT
1 TAAAATATT
155062 TAAAATATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
19 2 0.05
21 10 0.23
22 17 0.39
23 1 0.02
25 10 0.23
26 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAAATATTAATTATTAAATATTT
Found at i:155102 original size:20 final size:21
Alignment explanation
Indices: 155036--155092 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 21
155026 ATTAAAATAT
* *
155036 TAATTATAT-AAATATTTTAA
1 TAATTATTTAAAATATTATAA
155056 -AA-TATTTAAAATATTATAA
1 TAATTATTTAAAATATTATAA
155075 TAATTATTT-AAATATTAT
1 TAATTATTTAAAATATTAT
155093 TTTTATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 4 0.12
19 12 0.38
20 11 0.34
21 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATTATTTAAAATATTATAA
Found at i:156811 original size:15 final size:16
Alignment explanation
Indices: 156785--156814 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
156775 AAATTAAAAA
156785 TTATTATATTTTTTAT
1 TTATTATATTTTTTAT
156801 TTATT-TATTTTTTA
1 TTATTATATTTTTTA
156815 AATATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTATATTTTTTAT
Found at i:156919 original size:20 final size:20
Alignment explanation
Indices: 156882--156920 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
156872 AATTTATTTG
* * *
156882 ATATATATATATATATGTGT
1 ATATATATACACACATGTGT
156902 ATATATATACACACATGTG
1 ATATATATACACACATGTG
156921 AAGATATAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (20 bp):
ATATATATACACACATGTGT
Found at i:158982 original size:21 final size:21
Alignment explanation
Indices: 158910--158985 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
158900 CTATAAAAAT
*
158910 TATATCTTTTCATCCAACAAA
1 TATATCATTTCATCCAACAAA
* * *
158931 TGTAT-ACTTTCATCTAACAAT
1 TATATCA-TTTCATCCAACAAA
* * *
158952 TACATTATTTCACCCAACAAA
1 TATATCATTTCATCCAACAAA
158973 TATATCATTTCAT
1 TATATCATTTCAT
158986 TAAAGATAGT
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
21 40 0.98
22 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.01, T:0.39
Consensus pattern (21 bp):
TATATCATTTCATCCAACAAA
Found at i:159545 original size:30 final size:31
Alignment explanation
Indices: 159511--159573 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
159501 ATTGCAAATA
* *
159511 AATTTTAAGTTAAATATTTACTC-TAAATTT
1 AATTTTAAATTAAATATTTAATCTTAAATTT
*
159541 AATTTTAAATTAAATGTTTAATCTTAAATTT
1 AATTTTAAATTAAATATTTAATCTTAAATTT
159572 AA
1 AA
159574 CATATTTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 20 0.69
31 9 0.31
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (31 bp):
AATTTTAAATTAAATATTTAATCTTAAATTT
Found at i:160543 original size:20 final size:20
Alignment explanation
Indices: 160515--160589 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
160505 TTTTACCTTG
160515 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
160535 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
160555 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
160575 ATGTATCGATACATT
1 ATGTATCGATACATT
160590 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:160582 original size:40 final size:39
Alignment explanation
Indices: 160515--160592 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
160505 TTTTACCTTG
* *
160515 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
160555 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
160593 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:161526 original size:22 final size:22
Alignment explanation
Indices: 161501--161556 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
161491 AGCCTTTGAC
161501 CATGCATTTTTTTATTATGTTA
1 CATGCATTTTTTTATTATGTTA
*
161523 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTA
161545 CATG--TTTTTTTA
1 CATGCATTTTTTTA
161557 ACATGTCCAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 8 0.24
22 25 0.76
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTA
Found at i:167198 original size:80 final size:78
Alignment explanation
Indices: 166915--167200 Score: 227
Period size: 79 Copynumber: 3.6 Consensus size: 78
166905 ATATTTCCTG
* * * * * *
166915 ATGAGAAATTTAATATTTTGGAGATAATAA-CGGGGTTGGAGTGTCTCCTTGAAAATAACGGGGC
1 ATGAGAAA-TCAATATTTTGGAAATAA-AATC-GGGTTGGAGTATCCCCTCGAAAATAACGGGGT
* **
166979 TGGAGTATCTCCGGTT
63 TGGAGTATCCCCAATT
* * * * *
166995 GTGAGAAATCGATGA-TTAGGAAAAAAAATCGGGCTTGGAGTATCCCATCGAAAATAACGGGGTT
1 ATGAGAAATCAAT-ATTTTGGAAATAAAATCGGG-TTGGAGTATCCCCTCGAAAATAACGGGGTT
167059 GGAGTATCCCCAATT
64 GGAGTATCCCCAATT
* ** * **
167074 ATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTG
1 ATGAGAAATCAATATTTTGGAAATAAAATC-GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTG
* *
167139 GAGTATCCTCGATT
65 GAGTATCCCCAATT
* *** *
167153 GTGA-AAATTTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
1 ATGAGAAA-TCAAT-ATTTTGGAAATAAAATCGG-GTTGGAGTATCCCC
167201 GATTATGGAA
Statistics
Matches: 163, Mismatches: 35, Indels: 16
0.76 0.16 0.07
Matches are distributed among these distances:
78 9 0.06
79 116 0.71
80 38 0.23
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.28
Consensus pattern (78 bp):
ATGAGAAATCAATATTTTGGAAATAAAATCGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGG
AGTATCCCCAATT
Found at i:167248 original size:51 final size:52
Alignment explanation
Indices: 167135--167265 Score: 185
Period size: 51 Copynumber: 2.5 Consensus size: 52
167125 AGGTAACGGG
* * * *
167135 GTTGGAGTATCCTCGATTGTGAAAATTTGGTGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAATTGGGTGTTTTTAGAAATAAAATCGGA
167187 GTTGGAGTATCCCCGATTATGGAAAA-TGGGTG-TTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAATTGGGTGTTTTTAGAAATAAAATCGGA
* *
167238 GTTGGAGTATCCCCGATTAAGAGAATTG
1 GTTGGAGTATCCCCGATTATGAAAATTG
167266 AGAAACTCAA
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
50 4 0.06
51 39 0.55
52 23 0.32
53 5 0.07
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.32
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAAAATTGGGTGTTTTTAGAAATAAAATCGGA
Found at i:169635 original size:34 final size:33
Alignment explanation
Indices: 169592--169658 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
169582 AACTTCTTAG
* *
169592 ATGTATCGATACAAAGAATAGATGTATTGATACA
1 ATGTATCGATACAAAGAA-AAATGTATCGATACA
*
169626 ATGTATCGATACACAGAAAAATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCGATACA
169659 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 13 0.43
34 17 0.57
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATACA
Found at i:169700 original size:13 final size:13
Alignment explanation
Indices: 169682--169797 Score: 70
Period size: 13 Copynumber: 7.5 Consensus size: 13
169672 AGCTTCCTAG
169682 CGATACATTGTAT
1 CGATACATTGTAT
169695 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
169714 CGATACATTGTAT
1 CGATACATTGTAT
169727 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
169746 CGATACATTGTAT
1 CGATACATTGTAT
169759 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
169778 CGATACATTGTAT
1 CGATACATTGTAT
169791 CGATACA
1 CGATACA
169798 ACATTTATGT
Statistics
Matches: 85, Mismatches: 0, Indels: 36
0.70 0.00 0.30
Matches are distributed among these distances:
13 35 0.41
14 2 0.02
15 2 0.02
16 14 0.16
17 2 0.02
18 2 0.02
19 28 0.33
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:169714 original size:19 final size:18
Alignment explanation
Indices: 169690--169843 Score: 106
Period size: 19 Copynumber: 9.1 Consensus size: 18
169680 AGCGATACAT
169690 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
169709 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
169722 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
169741 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
169754 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
169773 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
169786 TGTATCGATACAACATTTA
1 TGTATCGATACAA-ACTTA
* *
169805 TGTATCGATACATTTACTGAA
1 TGTATCGATACA--AACT-TA
169826 TGTATCGATACAAA-TTA
1 TGTATCGATACAAACTTA
169843 T
1 T
169844 TGGAATTCAA
Statistics
Matches: 109, Mismatches: 5, Indels: 44
0.69 0.03 0.28
Matches are distributed among these distances:
13 33 0.30
14 3 0.03
16 6 0.06
17 2 0.02
18 4 0.04
19 46 0.42
20 2 0.02
21 13 0.12
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:169723 original size:32 final size:32
Alignment explanation
Indices: 169682--169818 Score: 256
Period size: 32 Copynumber: 4.3 Consensus size: 32
169672 AGCTTCCTAG
*
169682 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
169714 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
169746 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
169778 CGATACATTGTATCGATACAACATTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
169810 CGATACATT
1 CGATACATT
169819 TACTGAATGT
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 103 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:173391 original size:28 final size:29
Alignment explanation
Indices: 173344--173406 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
173334 TGTGGTCAAA
*
173344 TTATTTTTTCATATCGTATTATATTTTAG
1 TTATTTTTTCATATCATATTATATTTTAG
* *
173373 TTATTTTTT-ATGTCATATTGTATTTTAG
1 TTATTTTTTCATATCATATTATATTTTAG
173401 TTATTT
1 TTATTT
173407 CCATATTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 22 0.71
29 9 0.29
ACGTcount: A:0.22, C:0.05, G:0.08, T:0.65
Consensus pattern (29 bp):
TTATTTTTTCATATCATATTATATTTTAG
Found at i:173421 original size:28 final size:28
Alignment explanation
Indices: 173360--173424 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
173350 TTTCATATCG
* **
173360 TATTATATTTTAGTTATTTTTTATGTCA
1 TATTGTATTTTAGTTATTTCATATGTCA
173388 TATTGTATTTTAGTTATTTCCATAT-T-A
1 TATTGTATTTTAGTTATTT-CATATGTCA
173415 TATTTGTATT
1 TA-TTGTATT
173425 CGTATATGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 3 0.09
28 26 0.81
29 3 0.09
ACGTcount: A:0.25, C:0.05, G:0.08, T:0.63
Consensus pattern (28 bp):
TATTGTATTTTAGTTATTTCATATGTCA
Found at i:173590 original size:30 final size:30
Alignment explanation
Indices: 173531--173590 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
173521 TTGTTTTTAT
** *
173531 ATTATTGAATAAAAATTATTATTTTAATAA
1 ATTATTGAATAAAAATTAAAATTTGAATAA
173561 ATTATT-AATAAAAATTAAAATATTGAATAA
1 ATTATTGAATAAAAATTAAAAT-TTGAATAA
173591 TATATGAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (30 bp):
ATTATTGAATAAAAATTAAAATTTGAATAA
Found at i:178223 original size:15 final size:15
Alignment explanation
Indices: 178203--178231 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
178193 AAATATTTAA
178203 AATATTAAATATATT
1 AATATTAAATATATT
178218 AATATTAAATATAT
1 AATATTAAATATAT
178232 ACTCTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATTAAATATATT
Found at i:179495 original size:48 final size:48
Alignment explanation
Indices: 179389--179498 Score: 143
Period size: 48 Copynumber: 2.3 Consensus size: 48
179379 CAGCGGAACT
*
179389 GTTCTAAGCCCACCCGAATTCTCGATCATCCCGAATCCGCCACAAATA
1 GTTCTAAGCCCACCCGAATTCTCGATCATCCCGAATCCACCACAAATA
* * *
179437 GTTTTGAGCCCACCCGAATTCTCTG-TCA-CACCGAATCCACCGCAAATA
1 GTTCTAAGCCCACCCGAATTCTC-GATCATC-CCGAATCCACCACAAATA
*
179485 GTTCCAAGCCCACC
1 GTTCTAAGCCCACC
179499 ACAAGCAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.02
48 51 0.96
49 1 0.02
ACGTcount: A:0.27, C:0.38, G:0.14, T:0.21
Consensus pattern (48 bp):
GTTCTAAGCCCACCCGAATTCTCGATCATCCCGAATCCACCACAAATA
Found at i:180562 original size:2 final size:2
Alignment explanation
Indices: 180555--180584 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
180545 TTTCTTTTCC
180555 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
180585 TGGATTATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:187055 original size:27 final size:26
Alignment explanation
Indices: 187006--187072 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
186996 AAATTATTAT
* * *
187006 ATTTTTATATATATTTAACAATTAAA
1 ATTTTTATATTTAATAAACAATTAAA
*
187032 ATTTTTTATATTTAATAAATAATTAAA
1 A-TTTTTATATTTAATAAACAATTAAA
*
187059 AATTTTATAATTTA
1 ATTTTTAT-ATTTA
187073 TTTTAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 7 0.21
27 27 0.79
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTTTTATATTTAATAAACAATTAAA
Found at i:187099 original size:19 final size:20
Alignment explanation
Indices: 187057--187102 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
187047 TAAATAATTA
*
187057 AAAATTTTATAATTTATTTT
1 AAAATTTTATAATTTATCTT
187077 AAAATTTTATAATTTA-CTT
1 AAAATTTTATAATTTATCTT
187096 AAAATTT
1 AAAATTT
187103 GATTTTACGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
AAAATTTTATAATTTATCTT
Found at i:187695 original size:21 final size:21
Alignment explanation
Indices: 187684--187732 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 21
187674 CGATGGCTCC
187684 GAGAAGAGCAACGCTGGCTAA
1 GAGAAGAGCAACGCTGGCTAA
*
187705 GAGAAGAGCAGCGCTGGCTTAA
1 GAGAAGAGCAACGCTGGC-TAA
187727 CGAGAA
1 -GAGAA
187733 AGAATCGCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 17 0.68
22 3 0.12
23 5 0.20
ACGTcount: A:0.37, C:0.18, G:0.35, T:0.10
Consensus pattern (21 bp):
GAGAAGAGCAACGCTGGCTAA
Found at i:190291 original size:17 final size:17
Alignment explanation
Indices: 190265--190333 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
190255 ATATCTTTTG
*
190265 AATATATAAATTTGTTA
1 AATATTTAAATTTGTTA
*
190282 AATATTTAAATTTATTACGTAA
1 AATATTTAAA--T-TT--GTTA
*
190304 AATATTTAAATTTATTA
1 AATATTTAAATTTGTTA
*
190321 AATATTTTAATTT
1 AATATTTAAATTT
190334 TTTTAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
17 23 0.55
19 3 0.07
20 3 0.07
22 13 0.31
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
AATATTTAAATTTGTTA
Found at i:190658 original size:16 final size:17
Alignment explanation
Indices: 190614--190658 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
190604 AATGATATCG
190614 TTTA-ATTAAATATATA
1 TTTATATTAAATATATA
*
190630 TTTTTATTAAATATATA
1 TTTATATTAAATATATA
*
190647 -TTATATTTAATA
1 TTTATATTAAATA
190659 ATAATTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTATATTAAATATATA
Found at i:190718 original size:56 final size:57
Alignment explanation
Indices: 190614--190720 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 57
190604 AATGATATCG
* *
190614 TTTAATTAAATATATATTTTTATTAAATATATATTATATTTAATAATAATTAAAAAT
1 TTTAATTAAATATATATTTTAATTAAATATATATTATATTAAATAATAATTAAAAAT
*
190671 TTTAATTAAAT-TATATGATTTAATTGAATA-A-ATTA-ATTAAATTAATAATT
1 TTTAATTAAATATATAT--TTTAATTAAATATATATTATATTAAA-TAATAATT
190721 TGATAATCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
55 5 0.11
56 17 0.39
57 12 0.27
58 10 0.23
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.50
Consensus pattern (57 bp):
TTTAATTAAATATATATTTTAATTAAATATATATTATATTAAATAATAATTAAAAAT
Found at i:191311 original size:93 final size:98
Alignment explanation
Indices: 191157--191391 Score: 243
Period size: 97 Copynumber: 2.4 Consensus size: 98
191147 TAAAAGTCGC
* * * *
191157 ATTCAATAATTTTAAAAAATTTATATATCAATCCTTATAATCTTTTTTTCCTTTTCGGATTATGA
1 ATTCAATAA-TTT--AAAATTCATATCTCAATCCTTATAATCTTTTTTTCATTTTCAGATTATGA
* * *
191222 -TATTTTTTATAAAAAATAATT-TTAAA-AAA-T-AA
63 CT-TTTTTCATAAAAAACAATTATAAAACAAAGTGAA
*
191254 CATTTAATAATTTAAAATTCATATCTCAA-CACTTATAAT-TTTTTTT-ATTTTCAGATTATGAC
1 -ATTCAATAATTTAAAATTCATATCTCAATC-CTTATAATCTTTTTTTCATTTTCAGATTATGAC
*
191316 TTTTTTCATTAAAAACAATTATAAAAGCAAAGTGAA
64 TTTTTTCATAAAAAACAATTATAAAA-CAAAGTGAA
* * *
191352 ATTCAATAATTTGAAATTCATATCTTAATGCTTATAATCT
1 ATTCAATAATTTAAAATTCATATCTCAATCCTTATAATCT
191392 GTATCTATAT
Statistics
Matches: 115, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
93 29 0.25
94 13 0.11
95 22 0.19
96 3 0.03
97 37 0.32
98 11 0.10
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.45
Consensus pattern (98 bp):
ATTCAATAATTTAAAATTCATATCTCAATCCTTATAATCTTTTTTTCATTTTCAGATTATGACTT
TTTTCATAAAAAACAATTATAAAACAAAGTGAA
Found at i:191597 original size:2 final size:2
Alignment explanation
Indices: 191590--191617 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
191580 ACATGTTTGC
191590 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
191618 GTATTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:192656 original size:2 final size:2
Alignment explanation
Indices: 192644--192673 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
192634 AGAAATTAAT
*
192644 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
192674 AAGAAAGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:192922 original size:14 final size:14
Alignment explanation
Indices: 192905--192934 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
192895 ATTTTTATTG
192905 AAATCTTATATCTT
1 AAATCTTATATCTT
*
192919 AAATCTTATATTTT
1 AAATCTTATATCTT
192933 AA
1 AA
192935 CTTTTACCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATCTTATATCTT
Found at i:200108 original size:62 final size:62
Alignment explanation
Indices: 199908--200122 Score: 207
Period size: 63 Copynumber: 3.4 Consensus size: 62
199898 GGGGAGCGCT
* * * *
199908 TAGGTGCTAGATCTGCTGGTTCATGAAGCCTGTCAAGCACTGTA-GCATTAGAAAAGGAGCACC
1 TAGGCGCTAGATCTGCTGGTTCATGAAGGCTGTC-GGCACT-AAGGCATTAGAAAAGGAGCACC
* * * ** * *** *
199971 TAGGTGCTAGATTTGCTGGTTCATGAAGGCTATCGAGCTTTGAGGTGCTAGAAAAGGAGCAAC
1 TAGGCGCTAGATCTGCTGGTTCATGAAGGCTGTCG-GCACTAAGGCATTAGAAAAGGAGCACC
* ** *
200034 TAGACGCTAGATCTATTGGTTCATGAAGGCTGTCGGCACTAAGGCATTGGAAAAGGAGCACC
1 TAGGCGCTAGATCTGCTGGTTCATGAAGGCTGTCGGCACTAAGGCATTAGAAAAGGAGCACC
* * *
200096 TAGGCACTAGATCTGTTAGTTCATGAA
1 TAGGCGCTAGATCTGCTGGTTCATGAA
200123 AGCCGAAGGG
Statistics
Matches: 121, Mismatches: 29, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
62 43 0.36
63 78 0.64
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (62 bp):
TAGGCGCTAGATCTGCTGGTTCATGAAGGCTGTCGGCACTAAGGCATTAGAAAAGGAGCACC
Found at i:204580 original size:41 final size:41
Alignment explanation
Indices: 204523--204605 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
204513 ACTATAGTGT
204523 GAAAACAAGAAACTAAAGTTCATAAATAATGATGTGAAAAC
1 GAAAACAAGAAACTAAAGTTCATAAATAATGATGTGAAAAC
204564 GAAAACAAGAAACTAAAGTTCATAAATAATGATGTGAAAAC
1 GAAAACAAGAAACTAAAGTTCATAAATAATGATGTGAAAAC
204605 G
1 G
204606 CTCTTTATTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.55, C:0.10, G:0.16, T:0.19
Consensus pattern (41 bp):
GAAAACAAGAAACTAAAGTTCATAAATAATGATGTGAAAAC
Found at i:208361 original size:3 final size:3
Alignment explanation
Indices: 208353--208388 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
208343 TCAATAATTG
208353 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
208389 ATCAAGGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:208608 original size:26 final size:26
Alignment explanation
Indices: 208553--208608 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
208543 CAAGCATATT
** *
208553 TTAAATAAAATAAAATTATACTCTTG
1 TTAAATAAAATAAAATTATACAATTA
*
208579 TTAAATAAAATACAATTATACAATTA
1 TTAAATAAAATAAAATTATACAATTA
208605 TTAA
1 TTAA
208609 TAATGTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.38
Consensus pattern (26 bp):
TTAAATAAAATAAAATTATACAATTA
Found at i:209052 original size:32 final size:29
Alignment explanation
Indices: 209004--209075 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 29
208994 TTATGATAAA
*
209004 AATATAATATAATATTAAAATTTTTTAAAATT
1 AATATAA-ATAATATTAAAA--TATTAAAATT
209036 AATATAAATAATTATTAAAATATTAAAATT
1 AATATAAATAA-TATTAAAATATTAAAATT
*
209066 TATATAAATA
1 AATATAAATA
209076 TAAAATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 18 0.49
31 4 0.11
32 15 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
AATATAAATAATATTAAAATATTAAAATT
Found at i:209361 original size:44 final size:44
Alignment explanation
Indices: 209301--209393 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 44
209291 AATATCATTT
* *
209301 TTTTAATAGTCATTGGATCTAACAATAAATGACTCACACTGTCA
1 TTTTCATAGTCATTGGATCTAACAATAAATGACACACACTGTCA
* * * *
209345 TTTTCATATTCATTGGATCTAACAATAAATGTCACACTCTGTCT
1 TTTTCATAGTCATTGGATCTAACAATAAATGACACACACTGTCA
209389 TTTTC
1 TTTTC
209394 TCATATTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (44 bp):
TTTTCATAGTCATTGGATCTAACAATAAATGACACACACTGTCA
Found at i:209574 original size:18 final size:18
Alignment explanation
Indices: 209553--209587 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
209543 AAAAAATAAA
209553 TATTAAAATTTAAATTTT
1 TATTAAAATTTAAATTTT
* *
209571 TATTAAATTTTGAATTT
1 TATTAAAATTTAAATTT
209588 AAATTTATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TATTAAAATTTAAATTTT
Found at i:221446 original size:2 final size:2
Alignment explanation
Indices: 221439--221515 Score: 136
Period size: 2 Copynumber: 38.5 Consensus size: 2
221429 GGAAGGGAAA
*
221439 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
221481 AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
221516 ATGAAGAGTG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:221733 original size:23 final size:23
Alignment explanation
Indices: 221694--221762 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
221684 CATTGTTTAT
* *
221694 TTATTTAT-TAAAATTTAATATCA
1 TTATTTATATAAATTTTAATA-AA
221717 -TATTTATATAAATTTTAATAAA
1 TTATTTATATAAATTTTAATAAA
*
221739 TTAATTAATATAAATTTTAA-AAA
1 TT-ATTTATATAAATTTTAATAAA
221762 T
1 T
221763 AAATCATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 8 0.20
23 16 0.40
24 16 0.40
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
TTATTTATATAAATTTTAATAAA
Found at i:221897 original size:22 final size:22
Alignment explanation
Indices: 221845--221897 Score: 54
Period size: 25 Copynumber: 2.3 Consensus size: 22
221835 ATCAAAATAT
*
221845 TTTATTATATATCATAATTTTA
1 TTTATTAAATATCATAATTTTA
221867 TTAAATATTAAATATCAT-ATTATTA
1 TT---TATTAAATATCATAATT-TTA
221892 TTTATT
1 TTTATT
221898 TAATGATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
22 6 0.23
24 3 0.12
25 17 0.65
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTATTAAATATCATAATTTTA
Found at i:223527 original size:23 final size:21
Alignment explanation
Indices: 223492--223566 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 21
223482 AGAAAATTAG
223492 TTTTCTTT-T-TTTTTTTCTC
1 TTTTCTTTCTCTTTTTTTCTC
223511 TCTTCTCTCTTC-CTTTTTCTTC-C
1 T-TT-TCT-TTCTCTTTTT-TTCTC
223534 TTTTCTTTCTCTTTTTTTCT-
1 TTTTCTTTCTCTTTTTTTCTC
223554 TTTTCCTTT-TCTT
1 TTTT-CTTTCTCTT
223567 CTTCTCCCCC
Statistics
Matches: 47, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
19 1 0.02
20 16 0.34
21 16 0.34
22 4 0.09
23 7 0.15
24 3 0.06
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTCTTTCTCTTTTTTTCTC
Found at i:223540 original size:26 final size:27
Alignment explanation
Indices: 223511--223568 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
223501 TTTTTTTCTC
223511 TCTTCTCTCTTCCTTT-TTCTTCCTTT
1 TCTTCTCTCTTCCTTTCTTCTTCCTTT
** *
223537 TCTT-TCTCTTTTTTTCTTTTTCCTTT
1 TCTTCTCTCTTCCTTTCTTCTTCCTTT
223563 TCTTCT
1 TCTTCT
223569 TCTCCCCCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 9 0.33
26 17 0.63
27 1 0.04
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (27 bp):
TCTTCTCTCTTCCTTTCTTCTTCCTTT
Found at i:223738 original size:12 final size:12
Alignment explanation
Indices: 223721--223751 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
223711 TTAATTATAA
223721 AAAATTTATTTT
1 AAAATTTATTTT
223733 AAAATTTATTTT
1 AAAATTTATTTT
223745 AAAATTT
1 AAAATTT
223752 TTCATGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AAAATTTATTTT
Found at i:223847 original size:13 final size:11
Alignment explanation
Indices: 223813--223856 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
223803 TATAACATAT
*
223813 TTTTTATTTTA
1 TTTTTATATTA
223824 TTTTTATATTA
1 TTTTTATATTA
223835 TTATTTATAATTA
1 TT-TTTAT-ATTA
223848 TTTTT-TATT
1 TTTTTATATT
223857 TCATCAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 3 0.10
11 13 0.43
12 8 0.27
13 6 0.20
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTTATATTA
Found at i:224256 original size:19 final size:19
Alignment explanation
Indices: 224219--224271 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
224209 ATAAAAAAAA
*
224219 TTAATTTTAAATTA-A-TT
1 TTAATTTTTAATTATATTT
*
224236 TT-ATTATTTTATTATATTT
1 TTAATT-TTTAATTATATTT
224255 TTAATTTTTAATTATAT
1 TTAATTTTTAATTATAT
224272 ATTAAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 3 0.10
17 8 0.28
18 1 0.03
19 14 0.48
20 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTAATTTTTAATTATATTT
Found at i:224715 original size:19 final size:18
Alignment explanation
Indices: 224691--224733 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
224681 ATAACAAATA
224691 AATTTTACTA-AATATGGAT
1 AATTTT-CTATAA-ATGGAT
*
224710 AATTTTTTATAAATGGAT
1 AATTTTCTATAAATGGAT
224728 AATTTT
1 AATTTT
224734 TTAAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (18 bp):
AATTTTCTATAAATGGAT
Found at i:224766 original size:8 final size:8
Alignment explanation
Indices: 224745--224776 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
224735 TAAATTTTAA
224745 AAAATATGT
1 AAAATAT-T
224754 AAAATATT
1 AAAATATT
224762 AAAATATT
1 AAAATATT
224770 AAAATAT
1 AAAATAT
224777 CTTTCATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (8 bp):
AAAATATT
Found at i:227296 original size:14 final size:14
Alignment explanation
Indices: 227259--227296 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
227249 TTTACAAAAA
227259 TAATAT-TTAATTT
1 TAATATATTAATTT
*
227272 TAAGA-ATTAATTT
1 TAATATATTAATTT
227285 TAATATATTAAT
1 TAATATATTAAT
227297 CGGTGAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
TAATATATTAATTT
Found at i:227698 original size:13 final size:13
Alignment explanation
Indices: 227682--227706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
227672 CTTAAAATAT
227682 AAAAAATTATTTA
1 AAAAAATTATTTA
227695 AAAAAATTATTT
1 AAAAAATTATTT
227707 GAATTTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAAATTATTTA
Found at i:227938 original size:16 final size:16
Alignment explanation
Indices: 227888--227946 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
227878 CAAAAACACT
*
227888 AAAT-TAAAAAAATTAA
1 AAATCTAAAATAA-TAA
* * *
227904 AAA-CTAAAACAACAT
1 AAATCTAAAATAATAA
227919 AAATCTAAAATAATAA
1 AAATCTAAAATAATAA
*
227935 AAATTTAAAATA
1 AAATCTAAAATA
227947 TTTAAATCTA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
15 4 0.12
16 30 0.88
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATCTAAAATAATAA
Found at i:228207 original size:3 final size:3
Alignment explanation
Indices: 228199--228254 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
228189 CCAAAGTATT
* *
228199 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
228246 TAA TAA TAA
1 TAA TAA TAA
228255 AATGTGAGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:235584 original size:19 final size:20
Alignment explanation
Indices: 235560--235608 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
235550 AATAAAAAAC
*
235560 TTATTAAAAATAAATT-GAA
1 TTATTAAAAATAAATTCAAA
*
235579 TTATTAAAATTAAATTCAAA
1 TTATTAAAAATAAATTCAAA
*
235599 TTTTTAAAAA
1 TTATTAAAAA
235609 ATAATAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
TTATTAAAAATAAATTCAAA
Found at i:236654 original size:26 final size:26
Alignment explanation
Indices: 236620--236671 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
236610 TATATTGATT
236620 GAATGTTTGGTACCGTATTTGATTGA
1 GAATGTTTGGTACCGTATTTGATTGA
236646 GAATGTTTGGTACCGTATTTGATTGA
1 GAATGTTTGGTACCGTATTTGATTGA
236672 TAGGGTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.42
Consensus pattern (26 bp):
GAATGTTTGGTACCGTATTTGATTGA
Found at i:239727 original size:20 final size:19
Alignment explanation
Indices: 239693--239733 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
239683 ACTTGAAATA
239693 TATGTTTTTATAAAATTTT
1 TATGTTTTTATAAAATTTT
*
239712 TATGTTTTTATAAAAATTT
1 TATGTTTTTATAAAATTTT
239731 TAT
1 TAT
239734 CTTAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TATGTTTTTATAAAATTTT
Found at i:239810 original size:22 final size:24
Alignment explanation
Indices: 239763--239810 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
239753 GTTTTTATAT
*
239763 TATTAAATTAATCACTCTAATTAA
1 TATTAAATTAATCAATCTAATTAA
*
239787 TATTAAA-TAA-CAATCTTATTAA
1 TATTAAATTAATCAATCTAATTAA
239809 TA
1 TA
239811 ATAATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 12 0.55
23 3 0.14
24 7 0.32
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (24 bp):
TATTAAATTAATCAATCTAATTAA
Found at i:240518 original size:22 final size:21
Alignment explanation
Indices: 240481--240532 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
240471 AATAATGAGA
*
240481 ATTTAATTAATCTTAAAACTAT
1 ATTTAATTAATATT-AAACTAT
* *
240503 ATTTAATTATTATTAAATTAT
1 ATTTAATTAATATTAAACTAT
240524 ATTATAATT
1 ATT-TAATT
240533 CAAATGCATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTTAATTAATATTAAACTAT
Found at i:241060 original size:24 final size:24
Alignment explanation
Indices: 241033--241083 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
241023 CTGAGATAAT
*
241033 ATGCACTATAACTACAATCAACAA
1 ATGCACGATAACTACAATCAACAA
241057 ATGCACGATAACTACAATCAACAA
1 ATGCACGATAACTACAATCAACAA
241081 ATG
1 ATG
241084 TTTTTGCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.49, C:0.24, G:0.08, T:0.20
Consensus pattern (24 bp):
ATGCACGATAACTACAATCAACAA
Found at i:241140 original size:105 final size:105
Alignment explanation
Indices: 240953--241164 Score: 352
Period size: 105 Copynumber: 2.0 Consensus size: 105
240943 CGAGATAATC
*
240953 TGCATGATAACTACAATCAACAAATGTTTCTGCATATTTCACATTACTACTATCAACAACTAATC
1 TGCACGATAACTACAATCAACAAATGTTTCTGCATATTTCACATTACTACTATCAACAACTAATC
* *
241018 CGAATCTGAGATAATATGCACTATAACTACAATCAACAAA
66 CGAATCCGAGATAATATGCACGATAACTACAATCAACAAA
* * *
241058 TGCACGATAACTACAATCAACAAATGTTTTTGCATATTTCACTTTACTACTATCAATAACTAATC
1 TGCACGATAACTACAATCAACAAATGTTTCTGCATATTTCACATTACTACTATCAACAACTAATC
* *
241123 TGAATCCGAGATAATATGCACGATAACTACAATTAACAAA
66 CGAATCCGAGATAATATGCACGATAACTACAATCAACAAA
241163 TG
1 TG
241165 TTTCTGCATA
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
105 99 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (105 bp):
TGCACGATAACTACAATCAACAAATGTTTCTGCATATTTCACATTACTACTATCAACAACTAATC
CGAATCCGAGATAATATGCACGATAACTACAATCAACAAA
Found at i:241227 original size:39 final size:39
Alignment explanation
Indices: 241184--241388 Score: 124
Period size: 39 Copynumber: 5.4 Consensus size: 39
241174 ATTTCACAGT
*
241184 ACTACTATCAACAACTAATCCGAGATAATCTGCACGATA
1 ACTACTATCAACAAATAATCCGAGATAATCTGCACGATA
* * * ** * *
241223 ACTACAATTAATAAAT-AT-TTATGCAT-AT-TTCAC-ATT
1 ACTACTATCAACAAATAATCCGA-G-ATAATCTGCACGATA
* * *
241259 ACTACTATCAACAACTAATCCGAGATACTCTGCATGATA
1 ACTACTATCAACAAATAATCCGAGATAATCTGCACGATA
* ** * * *
241298 ACTA-TAATCAACAAATATTTTTG-CAT-AT-TTCAC-ATT
1 ACTACT-ATCAACAAATA-ATCCGAGATAATCTGCACGATA
*
241334 ACTACTATCAACAATTAATCCGAGATAATCTGCACGATA
1 ACTACTATCAACAAATAATCCGAGATAATCTGCACGATA
* *
241373 ACTACAATTAACAAAT
1 ACTACTATCAACAAAT
241389 GTTTCTGCAT
Statistics
Matches: 115, Mismatches: 37, Indels: 28
0.64 0.21 0.16
Matches are distributed among these distances:
35 2 0.02
36 34 0.30
37 15 0.13
38 15 0.13
39 47 0.41
40 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (39 bp):
ACTACTATCAACAAATAATCCGAGATAATCTGCACGATA
Found at i:241248 original size:75 final size:75
Alignment explanation
Indices: 241058--241442 Score: 547
Period size: 75 Copynumber: 5.1 Consensus size: 75
241048 AATCAACAAA
* * *
241058 TGCACGATAACTACAATCAACAAATGTTTTTGCATATTTCACTTTACTACTATCAATAACTAATC
1 TGCACGATAACTACAATTAACAAATGTTTCTGCATATTTCACATTACTACTATC---AAC-AA-C
*
241123 TGAATCCGAGATAATA
61 T-AATCCGAGATAATC
*
241139 TGCACGATAACTACAATTAACAAATGTTTCTGCATATTTCACAGTACTACTATCAACAACTAATC
1 TGCACGATAACTACAATTAACAAATGTTTCTGCATATTTCACATTACTACTATCAACAACTAATC
241204 CGAGATAATC
66 CGAGATAATC
* * *
241214 TGCACGATAACTACAATTAATAAATATTTATGCATATTTCACATTACTACTATCAACAACTAATC
1 TGCACGATAACTACAATTAACAAATGTTTCTGCATATTTCACATTACTACTATCAACAACTAATC
*
241279 CGAGATACTC
66 CGAGATAATC
* * * * * *
241289 TGCATGATAACTATAATCAACAAATATTTTTGCATATTTCACATTACTACTATCAACAATTAATC
1 TGCACGATAACTACAATTAACAAATGTTTCTGCATATTTCACATTACTACTATCAACAACTAATC
241354 CGAGATAATC
66 CGAGATAATC
*
241364 TGCACGATAACTACAATTAACAAATGTTTCTGCATATTTCACATTACTACTATTAACAACTAATC
1 TGCACGATAACTACAATTAACAAATGTTTCTGCATATTTCACATTACTACTATCAACAACTAATC
*
241429 C-AGTATAATT
66 CGAG-ATAATC
241439 TGCA
1 TGCA
241443 TATTTCACAT
Statistics
Matches: 278, Mismatches: 25, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
74 2 0.01
75 219 0.79
76 2 0.01
77 2 0.01
78 3 0.01
81 50 0.18
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.33
Consensus pattern (75 bp):
TGCACGATAACTACAATTAACAAATGTTTCTGCATATTTCACATTACTACTATCAACAACTAATC
CGAGATAATC
Found at i:241420 original size:36 final size:35
Alignment explanation
Indices: 241148--241422 Score: 95
Period size: 36 Copynumber: 7.4 Consensus size: 35
241138 ATGCACGATA
* * *
241148 ACTACAATTAACAAATGTTTCTGCATATTTCACAGT
1 ACTACTATCAACAAAT-TTTCTGCATATTTCACATT
* ** * * * *
241184 ACTACTATCAACAACTAATCCGAGATAATCTGCACGATA
1 ACTACTATCAACAAATTTTCTG-CAT-AT-TTCAC-ATT
* * * *
241223 ACTACAATTAATAAATATTTATGCATATTTCACATT
1 ACTACTATCAACAAAT-TTTCTGCATATTTCACATT
* ** * * * * *
241259 ACTACTATCAACAACTAATCCGAGATACTCTGCATGATA
1 ACTACTATCAACAAATTTTCTG-CATA-T-TTCA-CATT
*
241298 ACTA-TAATCAACAAATATTTTTGCATATTTCACATT
1 ACTACT-ATCAACAAAT-TTTCTGCATATTTCACATT
* * * * *
241334 ACTACTATCAAC-AATTAATCCGAGATAATCTGCACGATA
1 ACTACTATCAACAAATT-TTCTG-CAT-AT-TTCAC-ATT
* *
241373 ACTACAATTAACAAATGTTTCTGCATATTTCACATT
1 ACTACTATCAACAAAT-TTTCTGCATATTTCACATT
*
241409 ACTACTATTAACAA
1 ACTACTATCAACAA
241423 CTAATCCAGT
Statistics
Matches: 164, Mismatches: 56, Indels: 38
0.64 0.22 0.15
Matches are distributed among these distances:
34 1 0.01
35 10 0.06
36 61 0.37
37 17 0.10
38 17 0.10
39 47 0.29
40 10 0.06
41 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.33
Consensus pattern (35 bp):
ACTACTATCAACAAATTTTCTGCATATTTCACATT
Found at i:241782 original size:27 final size:27
Alignment explanation
Indices: 241742--241799 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
241732 GGGTCATGGC
* *
241742 AGGATATGATGGGTATGGAGGTTAAGT
1 AGGATATGACGGGTATGGAGATTAAGT
*
241769 AGGATATGACGGGTATGGAGATTGAGT
1 AGGATATGACGGGTATGGAGATTAAGT
241796 AGGA
1 AGGA
241800 AAATATGGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.41, T:0.26
Consensus pattern (27 bp):
AGGATATGACGGGTATGGAGATTAAGT
Found at i:241939 original size:15 final size:15
Alignment explanation
Indices: 241899--241939 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
241889 TGGGTAAACA
241899 GGTGGTAGATGCACG
1 GGTGGTAGATGCACG
*
241914 GGTTGTAGATGCACG
1 GGTGGTAGATGCACG
*
241929 GGTGGTGGATG
1 GGTGGTAGATG
241940 GATAGGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.17, C:0.10, G:0.49, T:0.24
Consensus pattern (15 bp):
GGTGGTAGATGCACG
Found at i:242490 original size:20 final size:20
Alignment explanation
Indices: 242462--242536 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
242452 TCATACCCTG
242462 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
242482 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
242502 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
242522 ATGTATCGATACATT
1 ATGTATCGATACATT
242537 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:242529 original size:40 final size:39
Alignment explanation
Indices: 242462--242539 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
242452 TCATACCCTG
* *
242462 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
242502 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
242540 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:243475 original size:24 final size:24
Alignment explanation
Indices: 243448--243504 Score: 100
Period size: 22 Copynumber: 2.5 Consensus size: 24
243438 AGCCTTTGAC
243448 CATGCATTTTTTTTTATTATGTTT
1 CATGCATTTTTTTTTATTATGTTT
243472 CATGCA--TTTTTTTATTATGTTT
1 CATGCATTTTTTTTTATTATGTTT
243494 CATGCATTTTT
1 CATGCATTTTT
243505 AACATGTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 22 0.71
24 9 0.29
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.63
Consensus pattern (24 bp):
CATGCATTTTTTTTTATTATGTTT
Found at i:243511 original size:20 final size:21
Alignment explanation
Indices: 243457--243511 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
243447 CCATGCATTT
**
243457 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
243478 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
243500 -TTTTTAACATGT
1 TTTTTTAACATGT
243512 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:250731 original size:15 final size:15
Alignment explanation
Indices: 250711--250745 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
250701 TTATAGGCTT
250711 TAAACTAATTACCCA
1 TAAACTAATTACCCA
250726 TAAACTAATTACCCA
1 TAAACTAATTACCCA
250741 TAAAC
1 TAAAC
250746 AAGAACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAACTAATTACCCA
Found at i:251859 original size:15 final size:15
Alignment explanation
Indices: 251839--251873 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
251829 TTATAGGCTT
251839 TAAACTAATTACCCA
1 TAAACTAATTACCCA
251854 TAAACTAATTACCCA
1 TAAACTAATTACCCA
251869 TAAAC
1 TAAAC
251874 AAGAACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAACTAATTACCCA
Found at i:252987 original size:15 final size:15
Alignment explanation
Indices: 252967--253001 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
252957 TTATAGGCTT
252967 TAAACTAATTACCCA
1 TAAACTAATTACCCA
252982 TAAACTAATTACCCA
1 TAAACTAATTACCCA
252997 TAAAC
1 TAAAC
253002 AAGAACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAACTAATTACCCA
Found at i:254115 original size:15 final size:15
Alignment explanation
Indices: 254095--254129 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
254085 TTATAGGCTT
254095 TAAACTAATTACCCA
1 TAAACTAATTACCCA
254110 TAAACTAATTACCCA
1 TAAACTAATTACCCA
254125 TAAAC
1 TAAAC
254130 AAGAACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAACTAATTACCCA
Found at i:255243 original size:15 final size:15
Alignment explanation
Indices: 255223--255257 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
255213 TTATAGGCTT
255223 TAAACTAATTACCCA
1 TAAACTAATTACCCA
255238 TAAACTAATTACCCA
1 TAAACTAATTACCCA
255253 TAAAC
1 TAAAC
255258 AAGAACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAACTAATTACCCA
Found at i:256371 original size:15 final size:15
Alignment explanation
Indices: 256351--256405 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
256341 TTATAGGCTT
256351 TAAACTAATTACCCA
1 TAAACTAATTACCCA
256366 TAAACTAATTACCCA
1 TAAACTAATTACCCA
*
256381 TAAACTAATTACTC-
1 TAAACTAATTACCCA
256395 TAAACCTAATT
1 TAAA-CTAATT
256406 CCACATAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
14 4 0.11
15 34 0.89
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAACTAATTACCCA
Found at i:256385 original size:30 final size:30
Alignment explanation
Indices: 256351--256413 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
256341 TTATAGGCTT
256351 TAAACTAATTACCCATAAA-CTAATTACC-CA
1 TAAACTAATTACCC-TAAACCTAATT-CCACA
*
256381 TAAACTAATTACTCTAAACCTAATTCCACA
1 TAAACTAATTACCCTAAACCTAATTCCACA
256411 TAA
1 TAA
256414 TAAACAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (30 bp):
TAAACTAATTACCCTAAACCTAATTCCACA
Found at i:256682 original size:23 final size:21
Alignment explanation
Indices: 256638--256682 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
256628 AAGAATTTAT
**
256638 AAAATTTTAGAGAGAAGTGAG
1 AAAATTTTAGAGAGAAAAGAG
256659 AAAATTTTAGAGAGTAGAAAGAG
1 AAAATTTTAGAGAG-A-AAAGAG
256682 A
1 A
256683 GTGAAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 1 0.05
23 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (21 bp):
AAAATTTTAGAGAGAAAAGAG
Found at i:260715 original size:26 final size:26
Alignment explanation
Indices: 260652--260718 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
260642 ATTATTTAAC
**
260652 ATAAA-TATAATTTTAATAAATTCTG
1 ATAAATTATAATTTTAATAAATTCAA
* *
260677 ATTATTTATTAATTTT-ATAAATATCAA
1 ATAAATTA-TAATTTTAATAAAT-TCAA
260704 ATAAATTATAATTTT
1 ATAAATTATAATTTT
260719 CATCATATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
25 3 0.09
26 15 0.45
27 15 0.45
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (26 bp):
ATAAATTATAATTTTAATAAATTCAA
Found at i:261528 original size:20 final size:21
Alignment explanation
Indices: 261505--261563 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
261495 TTTAAAATTT
261505 TATATAATATAAAT-TATAAA
1 TATATAATATAAATATATAAA
***
261525 TATATAA-ATTTTTATATAAA
1 TATATAATATAAATATATAAA
261545 TATATAATATTTAAATATA
1 TATATAATA--TAAATATA
261564 ATTATATTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
19 3 0.10
20 20 0.69
21 1 0.03
23 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATATAATATAAATATATAAA
Found at i:261584 original size:52 final size:52
Alignment explanation
Indices: 261485--261584 Score: 114
Period size: 52 Copynumber: 1.9 Consensus size: 52
261475 AAAATATTAA
* * * *
261485 TATATAAATATTTAAAATTTTATATAATATAAATTATAAATATATAAATTTT
1 TATATAAATATATAAAATTTAATATAATATAAATTAGAAATAAATAAATTTT
* *
261537 TATATAAATATATAATATTTAAATATAAT-TATATTACGAAA-AAATAAA
1 TATATAAATATATAAAATTT-AATATAATATAAATTA-GAAATAAATAAA
261585 ATACAAATAC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
52 30 0.75
53 10 0.25
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (52 bp):
TATATAAATATATAAAATTTAATATAATATAAATTAGAAATAAATAAATTTT
Found at i:263962 original size:32 final size:33
Alignment explanation
Indices: 263896--263962 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
263886 CATTTAAAAA
263896 TACGGTAAATTTATATTTAGCCTCAAATTTTTT
1 TACGGTAAATTTATATTTAGCCTCAAATTTTTT
*
263929 TACGGTAAATTTATATTTAGCTTC-AATTTTTT
1 TACGGTAAATTTATATTTAGCCTCAAATTTTTT
263961 TA
1 TA
263963 AGAATTTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 10 0.30
33 23 0.70
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (33 bp):
TACGGTAAATTTATATTTAGCCTCAAATTTTTT
Found at i:264825 original size:21 final size:21
Alignment explanation
Indices: 264799--264839 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
264789 ATTTTAAAAA
*
264799 AATT-AATTATAATATATTTAT
1 AATTAAATGATAA-ATATTTAT
264820 AATTAAATGATAAATATTTA
1 AATTAAATGATAAATATTTA
264840 ATTAAGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
AATTAAATGATAAATATTTAT
Found at i:265012 original size:2 final size:2
Alignment explanation
Indices: 265007--265031 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
264997 TGAAAAAAAC
265007 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
265032 GGGAAATAAT
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:265542 original size:21 final size:22
Alignment explanation
Indices: 265508--265556 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
265498 TGATTTTTTT
265508 TAAAAAAAATAAATAATA-ATA
1 TAAAAAAAATAAATAATATATA
*
265529 TAAAAAATAA-AAATTATATATA
1 TAAAAAA-AATAAATAATATATA
*
265551 TTAAAA
1 TAAAAA
265557 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAAAAAATAAATAATATATA
Found at i:265550 original size:20 final size:19
Alignment explanation
Indices: 265511--265548 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
265501 TTTTTTTTAA
265511 AAAAAATAAATAATAATAT
1 AAAAAATAAATAATAATAT
*
265530 AAAAAATAAA-AATTATAT
1 AAAAAATAAATAATAATAT
265548 A
1 A
265549 TATTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAAATAAATAATAATAT
Found at i:265551 original size:22 final size:21
Alignment explanation
Indices: 265508--265565 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
265498 TGATTTTTTT
*
265508 TAAAAAA-AATAAATAATAATA
1 TAAAAAATAA-AAATTATAATA
265529 TAAAAAATAAAAATTATATATA
1 TAAAAAATAAAAATTATA-ATA
* * *
265551 TTAAAATTTAAAATT
1 TAAAAAATAAAAATT
265566 TAAATTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 14 0.45
22 17 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAAATAAAAATTATAATA
Found at i:266145 original size:32 final size:29
Alignment explanation
Indices: 266108--266209 Score: 93
Period size: 32 Copynumber: 3.3 Consensus size: 29
266098 TAATAACTGT
266108 TAAATTTACATATAATTATATTTAATATTTA
1 TAAATTTA-A-ATAATTATATTTAATATTTA
266139 TCAAATTTTAAAATAATT-TAGTTTAATATTTAA
1 T-AAA-TTT-AAATAATTATA-TTTAATATTT-A
266172 TAAATTTATAAGTAATTATATTT-A-ATTTA
1 TAAATTTA-AA-TAATTATATTTAATATTTA
266201 TTAAATTTA
1 -TAAATTTA
266210 TGATTAATGT
Statistics
Matches: 62, Mismatches: 0, Indels: 19
0.77 0.00 0.23
Matches are distributed among these distances:
29 1 0.02
30 13 0.21
31 9 0.15
32 30 0.48
33 8 0.13
34 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (29 bp):
TAAATTTAAATAATTATATTTAATATTTA
Found at i:266766 original size:16 final size:16
Alignment explanation
Indices: 266741--266791 Score: 84
Period size: 16 Copynumber: 3.1 Consensus size: 16
266731 ATTATTATAA
266741 AAATTAATTTTAAATTT
1 AAATT-ATTTTAAATTT
*
266758 AAATTATTTTATATTT
1 AAATTATTTTAAATTT
266774 AAATTATTTTAAATTT
1 AAATTATTTTAAATTT
266790 AA
1 AA
266792 TTTAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 27 0.84
17 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AAATTATTTTAAATTT
Found at i:266790 original size:22 final size:22
Alignment explanation
Indices: 266765--266806 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
266755 TTTAAATTAT
266765 TTTATATTT-AAATTATTTTAAA
1 TTTA-ATTTAAAATTATTTTAAA
*
266787 TTTAATTTAAAATTTTTTTA
1 TTTAATTTAAAATTATTTTA
266807 TTTAAGTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTAATTTAAAATTATTTTAAA
Found at i:266821 original size:36 final size:37
Alignment explanation
Indices: 266744--266827 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 37
266734 ATTATAAAAA
* * *
266744 TTAATTTTAAATTTAAATTATTTTATATTTAAATTATT
1 TTAAATTT-AATTTAAATTATTTTATATTTAAATGAAT
*
266782 TTAAATTTAATTTAAAATT-TTTT-TATTTAAGTGAAT
1 TTAAATTTAATTT-AAATTATTTTATATTTAAATGAAT
266818 TTAAATTTAA
1 TTAAATTTAA
266828 CCTTTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 20 0.49
37 9 0.22
38 12 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (37 bp):
TTAAATTTAATTTAAATTATTTTATATTTAAATGAAT
Found at i:270169 original size:30 final size:30
Alignment explanation
Indices: 270135--270215 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 30
270125 AGCCTTTTAT
* *
270135 TTTTAATTTATACATTAATAAATATTTAAC
1 TTTTAATTTATACATAAATAAAAATTTAAC
*
270165 TTTTAACTTATATC-TAAATAAAAATTTAAC
1 TTTTAATTTATA-CATAAATAAAAATTTAAC
270195 TTTTAATTTATA-ATAAATAAA
1 TTTTAATTTATACATAAATAAA
270216 CCCTAATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
29 8 0.18
30 36 0.80
31 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (30 bp):
TTTTAATTTATACATAAATAAAAATTTAAC
Found at i:270313 original size:30 final size:29
Alignment explanation
Indices: 270238--270309 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
270228 CCAACTTGAA
270238 ATAAAAATTTATTTAAACAAATAAAAAAT
1 ATAAAAATTTATTTAAACAAATAAAAAAT
*
270267 ATAAAAATTTATTTAAATATAAT-AAAAAT
1 ATAAAAATTTATTTAAACA-AATAAAAAAT
270296 ATAAAAATTTATTT
1 ATAAAAATTTATTT
270310 TAAAAAGTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 38 0.93
30 3 0.07
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (29 bp):
ATAAAAATTTATTTAAACAAATAAAAAAT
Found at i:270653 original size:28 final size:27
Alignment explanation
Indices: 270606--270658 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
270596 ATAATTAAAA
*
270606 TTAAAATAAATTACATATTTTAATTTT
1 TTAAAATAAATAACATATTTTAATTTT
*
270633 TTAAAATCAAATAATATATTTTAATT
1 TTAAAAT-AAATAACATATTTTAATT
270659 GTCATAGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (27 bp):
TTAAAATAAATAACATATTTTAATTTT
Found at i:272262 original size:34 final size:34
Alignment explanation
Indices: 272219--272440 Score: 242
Period size: 34 Copynumber: 6.6 Consensus size: 34
272209 TTGGTAAAAA
*
272219 CTACCATTTAATCAACAATGGCAACCTACCAAAT
1 CTACCATTTAATCAACAATGGTAACCTACCAAAT
*
272253 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 CTACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
272287 C-ACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CTA-CCATTTAATCAACAATGGTAACCTACCAAAT
* * *
272321 -TTCTCATTTAATCAACAATAGTAAGCTACCAAAT
1 CTAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
272355 CT-CCTATTTAGTCAACAATGGCAAACC-ACAAAAT
1 CTACC-ATTTAATCAACAATGG-TAACCTACCAAAT
*
272389 C-ACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CTA-CCATTTAATCAACAATGGTAACCTACCAAAT
272423 C-ACCATTTAATCAACAAT
1 CTACCATTTAATCAACAAT
272441 TCTCCCACTT
Statistics
Matches: 160, Mismatches: 17, Indels: 23
0.80 0.09 0.12
Matches are distributed among these distances:
33 23 0.14
34 129 0.81
35 8 0.05
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (34 bp):
CTACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:272336 original size:68 final size:67
Alignment explanation
Indices: 272222--272440 Score: 269
Period size: 68 Copynumber: 3.2 Consensus size: 67
272212 GTAAAAACTA
* * *
272222 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
272287 CAC
65 CAC
* * * * *
272290 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATAGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
272355 CTC
65 CAC
* * * * * *
272358 CTATTTAGTCAACAATGGCAAACCACAAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
272423 CA-
65 CAC
272425 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
272441 TCTCCCACTT
Statistics
Matches: 127, Mismatches: 22, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
67 16 0.13
68 110 0.87
69 1 0.01
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:272364 original size:102 final size:101
Alignment explanation
Indices: 272221--272440 Score: 325
Period size: 102 Copynumber: 2.2 Consensus size: 101
272211 GGTAAAAACT
* * * *
272221 ACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAA
1 ACCATTTAATCAACAATAGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACAAAA
* * *
272286 TCACCCATTTAATCAATAATGGTAAGCTACCAAATT
66 TCACCCATTTAATCAACAATGGTAAACTACCAAATC
* * *
272322 TCTCATTTAATCAACAATAGTAAGCTACCAAATCT-CCTATTTAGTCAACAATGGCAAACCACAA
1 AC-CATTTAATCAACAATAGCAACCTACCAAATCTACC-ATTTAGTCAACAATGGCAAACCACAA
272386 AATCACCCATTTAATCAACAATGGTAAACTACCAAATC
64 AATCACCCATTTAATCAACAATGGTAAACTACCAAATC
272424 ACCATTTAATCAACAAT
1 ACCATTTAATCAACAAT
272441 TCTCCCACTT
Statistics
Matches: 106, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
101 18 0.17
102 88 0.83
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.25
Consensus pattern (101 bp):
ACCATTTAATCAACAATAGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACAAAA
TCACCCATTTAATCAACAATGGTAAACTACCAAATC
Found at i:276884 original size:34 final size:33
Alignment explanation
Indices: 276836--277056 Score: 248
Period size: 34 Copynumber: 6.5 Consensus size: 33
276826 TGGTAAAAAC
*
276836 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
* *
276869 CTACCATTTAGTCAACAATAGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
276903 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** * *
276937 TTCTCATTTAATCAATAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
276971 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
277005 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
277039 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
277057 AAGGACTTTA
Statistics
Matches: 160, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 23 0.14
34 131 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:276961 original size:68 final size:67
Alignment explanation
Indices: 276838--277056 Score: 278
Period size: 68 Copynumber: 3.2 Consensus size: 67
276828 GTAAAAACCA
* * * *
276838 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
276903 CAC
65 CAC
* * * * *
276906 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAATAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
276971 CTC
65 CAC
* * * *
276974 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
277039 CA-
65 CAC
277041 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
277057 AAGGACTTTA
Statistics
Matches: 129, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
67 17 0.13
68 111 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:276980 original size:102 final size:101
Alignment explanation
Indices: 276836--277056 Score: 334
Period size: 102 Copynumber: 2.2 Consensus size: 101
276826 TGGTAAAAAC
* *
276836 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCACCAA
* *
276901 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * * * *
276937 TTCTCATTTAATCAATAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCACCA
277002 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
277039 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
277057 AAGGACTTTA
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
101 15 0.14
102 90 0.86
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:278042 original size:16 final size:16
Alignment explanation
Indices: 278007--278052 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
277997 GCACGGTCTA
* *
278007 AATTCAAAATAA-TCG
1 AATTTAAAATAATTTG
*
278022 AATTTAAAATTATTTG
1 AATTTAAAATAATTTG
278038 AATTTAAAATAATTT
1 AATTTAAAATAATTT
278053 AAAAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 10 0.38
16 16 0.62
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (16 bp):
AATTTAAAATAATTTG
Found at i:278068 original size:26 final size:26
Alignment explanation
Indices: 278022--278071 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
278012 AAAATAATCG
* *
278022 AATTTAAAATTATTTGAATTTAAAAT
1 AATTTAAAAATATTTAAATTTAAAAT
278048 AATTTAAAAAT-TTTAATATTTAAA
1 AATTTAAAAATATTTAA-ATTTAAA
278072 CTGATCAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AATTTAAAAATATTTAAATTTAAAAT
Found at i:280255 original size:21 final size:21
Alignment explanation
Indices: 280231--280277 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
280221 GTTACCAAGT
*
280231 TTATACAAAGGGTTATCAAAA
1 TTATACAAAGAGTTATCAAAA
* *
280252 TTATACTAATAGTTATCAAAA
1 TTATACAAAGAGTTATCAAAA
280273 TTATA
1 TTATA
280278 ATAAATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (21 bp):
TTATACAAAGAGTTATCAAAA
Found at i:280288 original size:21 final size:21
Alignment explanation
Indices: 280242--280294 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
280232 TATACAAAGG
*
280242 GTTATCAAAATTATACTAATA
1 GTTATCAAAATTATAATAATA
280263 GTTATCAAAATTATAATAAATA
1 GTTATCAAAATTATAAT-AATA
*
280285 -TTATAAAAAT
1 GTTATCAAAAT
280295 GTTTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.38
Consensus pattern (21 bp):
GTTATCAAAATTATAATAATA
Found at i:280334 original size:12 final size:11
Alignment explanation
Indices: 280319--281001 Score: 92
Period size: 11 Copynumber: 64.9 Consensus size: 11
280309 AAAGATTACT
*
280319 AAAAGTTATATA
1 AAAA-TTATATC
*
280331 AAAAAT-TATC
1 AAAATTATATC
280341 AAAATTATATC
1 AAAATTATATC
*
280352 AAAAGT-TATC
1 AAAATTATATC
280362 AAAAATTATATC
1 -AAAATTATATC
280374 AAAAGTTA-ATC
1 AAAA-TTATATC
*
280385 --AATCATATC
1 AAAATTATATC
*
280394 AAAGATTA-CT-
1 AAA-ATTATATC
280404 AAAATTATATC
1 AAAATTATATC
* *
280415 -AAA-GA-ACC
1 AAAATTATATC
*
280423 AATATTATATC
1 AAAATTATATC
*
280434 AAAGGTTAT-TC
1 AAA-ATTATATC
*
280445 AAAATCATAT-
1 AAAATTATATC
*
280455 AAAAATA-ATC
1 AAAATTATATC
* *
280465 ATAATTAAATC
1 AAAATTATATC
*
280476 AAAGA-T-TACC
1 AAA-ATTATATC
*
280486 AAACTTATATCC
1 AAAATTATAT-C
**
280498 AAGGTTAT-T-
1 AAAATTATATC
280507 AAAATGT-TATC
1 AAAAT-TATATC
*
280518 AAAGAGT-TA-C
1 AAA-ATTATATC
*
280528 TAAAATTATATA
1 -AAAATTATATC
280540 AACAATTAT-T-
1 AA-AATTATATC
280550 AAAATTAT-T-
1 AAAATTATATC
280559 ACAAATGT-TATC
1 A-AAAT-TATATC
*
280571 AAAATTATACC
1 AAAATTATATC
*
280582 AAAAGT-TA-C
1 AAAATTATATC
**
280591 AAAACGATATC
1 AAAATTATATC
* *
280602 AAAGATTACA-A
1 AAA-ATTATATC
** *
280613 AAAAGAATACTT
1 AAAATTATA-TC
*
280625 AAATTATATATC
1 AAAAT-TATATC
280637 AAAGAGGTTAT-T-
1 AAA-A--TTATATC
*
280649 AAAATTATATA
1 AAAATTATATC
*
280660 AAAATT-TATT
1 AAAATTATATC
*
280670 AAAACTAT-T-
1 AAAATTATATC
280679 ATAAATGT-TATC
1 A-AAAT-TATATC
280691 AAAATTATATC
1 AAAATTATATC
*
280702 AAAAGT-TAT-
1 AAAATTATATC
280711 AAAATTATATC
1 AAAATTATATC
*
280722 AAAGATTACA--
1 AAA-ATTATATC
**
280732 AAAAGAATA-C
1 AAAATTATATC
*
280742 TTAAATTATATC
1 -AAAATTATATC
*
280754 AAAATT-TACC
1 AAAATTATATC
*
280764 AAAATCATATC
1 AAAATTATATC
280775 AAAGA-T-TA-C
1 AAA-ATTATATC
*
280784 -CAATTATAT-
1 AAAATTATATC
* **
280793 ATGAGGT-TATC
1 A-AAATTATATC
*
280804 TAAATTATA-C
1 AAAATTATATC
*
280814 GAAAAGT-TATC
1 -AAAATTATATC
*
280825 AAAATTAATAGC
1 AAAATT-ATATC
* *
280837 AAAAGT-TACC
1 AAAATTATATC
*
280847 AAAATTATTTC
1 AAAATTATATC
280858 AAAGA-T-TA-C
1 AAA-ATTATATC
* *
280867 CAAATTGTATC
1 AAAATTATATC
280878 TAAAA-T-TATC
1 -AAAATTATATC
*
280888 AAAATTGT-TAC
1 AAAATTATAT-C
280899 AAAGATTAT-T-
1 AAA-ATTATATC
*
280909 AAAATTATATT
1 AAAATTATATC
*
280920 AAAAAT-TATC
1 AAAATTATATC
280930 AAAAATTATA--
1 -AAAATTATATC
280940 AACAATTAT-T-
1 AA-AATTATATC
*
280950 AAAATTATATT
1 AAAATTATATC
280961 AAAA--ATGATC
1 AAAATTAT-ATC
*
280971 AAAATCATATC
1 AAAATTATATC
280982 AAAATT-TATC
1 AAAATTATATC
*
280992 AAAATCATAT
1 AAAATTATAT
281002 TTAGGGTTAT
Statistics
Matches: 484, Mismatches: 95, Indels: 185
0.63 0.12 0.24
Matches are distributed among these distances:
7 1 0.00
8 7 0.01
9 70 0.14
10 154 0.32
11 168 0.35
12 76 0.16
13 4 0.01
14 3 0.01
15 1 0.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.33
Consensus pattern (11 bp):
AAAATTATATC
Found at i:280350 original size:21 final size:21
Alignment explanation
Indices: 280319--281001 Score: 213
Period size: 21 Copynumber: 32.5 Consensus size: 21
280309 AAAGATTACT
*
280319 AAAAGTTATATAAAAAATTATC
1 AAAA-TTATATCAAAAATTATC
*
280341 AAAATTATATCAAAAGTTATC
1 AAAATTATATCAAAAATTATC
*
280362 AAAAATTATATCAAAAGTTAATC
1 -AAAATTATATCAAAAATT-ATC
* *
280385 --AATCATATCAAAGATTA-C
1 AAAATTATATCAAAAATTATC
* *
280403 TAAAATTATATCAAAGA--ACC
1 -AAAATTATATCAAAAATTATC
* **
280423 AATATTATATCAAAGGTTATTC
1 AAAATTATATCAAAAATTA-TC
* *
280445 AAAATCATAT-AAAAATAATC
1 AAAATTATATCAAAAATTATC
* * * *
280465 ATAATTAAATCAAAGATTACC
1 AAAATTATATCAAAAATTATC
* * ** *
280486 AAACTTATATCCAAGGTTATT
1 AAAATTATATCAAAAATTATC
*
280507 AAAATGT-TATCAAAGAGTTA-C
1 AAAAT-TATATCAAA-AATTATC
*
280528 TAAAATTATAT-AAACAATTATT
1 -AAAATTATATCAAA-AATTATC
**
280550 AAAATTAT-TACAAATGTTATC
1 AAAATTATAT-CAAAAATTATC
* *
280571 AAAATTATACCAAAAGTTA-C
1 AAAATTATATCAAAAATTATC
** *
280591 AAAACGATATCAAAGATTA-C
1 AAAATTATATCAAAAATTATC
** * *
280611 AAAAAAGAATACTTAAATTATATATC
1 --AAAATTATA-TCAAA-AAT-TATC
* *
280637 AAAGAGGTTAT-T-AAAATTATATA
1 AAA-A--TTATATCAAAAAT-TATC
*
280660 AAAATT-TATTAAAACTATTAT-
1 AAAATTATATCAAAA--ATTATC
*
280681 -AAATGT-TATCAAAATTATATC
1 AAAAT-TATATCAAAAAT-TATC
* *
280702 AAAAGT-TAT-AAAATTATATC
1 AAAATTATATCAAAAAT-TATC
**
280722 AAAGA-T-TA-CAAAAAGAATAC
1 AAA-ATTATATCAAAAATTAT-C
* * *
280742 TTAAATTATATCAAAATTTACC
1 -AAAATTATATCAAAAATTATC
* *
280764 AAAATCATATCAAAGATTA-C
1 AAAATTATATCAAAAATTATC
* * **
280784 -CAATTATAT-ATGAGGTTATC
1 AAAATTATATCA-AAAATTATC
* *
280804 TAAATTATA-CGAAAAGTTATC
1 AAAATTATATC-AAAAATTATC
* * *
280825 AAAATTAATAGCAAAAGTTACC
1 AAAATT-ATATCAAAAATTATC
* *
280847 AAAATTATTTCAAAGATTA-C
1 AAAATTATATCAAAAATTATC
* * *
280867 CAAATTGTATCTAAAATTATC
1 AAAATTATATCAAAAATTATC
* * *
280888 AAAATTGT-TACAAAGATTATT
1 AAAATTATAT-CAAAAATTATC
*
280909 AAAATTATATTAAAAATTATC
1 AAAATTATATCAAAAATTATC
* *
280930 AAAAATTATA--AACAATTATT
1 -AAAATTATATCAAAAATTATC
* *
280950 AAAATTATATTAAAAATGATC
1 AAAATTATATCAAAAATTATC
* *
280971 AAAATCATATCAAAATTTATC
1 AAAATTATATCAAAAATTATC
*
280992 AAAATCATAT
1 AAAATTATAT
281002 TTAGGGTTAT
Statistics
Matches: 502, Mismatches: 104, Indels: 111
0.70 0.15 0.15
Matches are distributed among these distances:
18 2 0.00
19 41 0.08
20 99 0.20
21 229 0.46
22 93 0.19
23 23 0.05
24 8 0.02
25 4 0.01
26 1 0.00
27 2 0.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.33
Consensus pattern (21 bp):
AAAATTATATCAAAAATTATC
Found at i:280433 original size:82 final size:82
Alignment explanation
Indices: 280309--280496 Score: 202
Period size: 82 Copynumber: 2.3 Consensus size: 82
280299 AAAATTACAA
* * *
280309 AAAGATTACTAAAAGTTATATAAAAAATTATCAAAATTATATCAAAAGTTA-TCAAAAATTATAT
1 AAAGATTACTAAAA-TTATATCAAAAA-TACCAAAATTATATCAAAAGTTATTC-AAAATCATAT
* *
280373 CAAAAGTTAATC-AATCATATC
63 -AAAA-ATAATCAAATCAAATC
* * *
280394 AAAGATTACTAAAATTATATCAAAGA-ACCAATATTATATCAAAGGTTATTCAAAATCATATAAA
1 AAAGATTACTAAAATTATATCAAAAATACCAAAATTATATCAAAAGTTATTCAAAATCATATAAA
*
280458 AATAATCATAATTAAATC
66 AATAATCA-AATCAAATC
* *
280476 AAAGATTACCAAACTTATATC
1 AAAGATTACTAAAATTATATC
280497 CAAGGTTATT
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
80 5 0.06
81 4 0.04
82 54 0.61
83 2 0.02
84 10 0.11
85 14 0.16
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (82 bp):
AAAGATTACTAAAATTATATCAAAAATACCAAAATTATATCAAAAGTTATTCAAAATCATATAAA
AATAATCAAATCAAATC
Found at i:280669 original size:120 final size:118
Alignment explanation
Indices: 280514--280752 Score: 381
Period size: 120 Copynumber: 2.0 Consensus size: 118
280504 ATTAAAATGT
*
280514 TATCAAAGAGTTACTAAAATTATATAAACAATTATTAAAATTATTACAAATGTTATCAAAATTAT
1 TATCAAAGAGTTACTAAAATTATATAAACAATTATTAAAACTATTACAAATGTTATCAAAATTAT
280579 ACCAAAAGTTACAAAACGATATCAAAGATTACAAAAAAGAATACTTAAATTATA
66 ACCAAAAGTTACAAAACGATATCAAAGATTAC-AAAAAGAATACTTAAATTATA
* *
280633 TATCAAAGAGGTTATTAAAATTATATAAA-AATTTATTAAAACTATTATAAATGTTATCAAAATT
1 TATCAAAGA-GTTACTAAAATTATATAAACAA-TTATTAAAACTATTACAAATGTTATCAAAATT
* * **
280697 ATATCAAAAGTTATAAAATTATATCAAAGATTACAAAAAGAATACTTAAATTATA
64 ATACCAAAAGTTACAAAACGATATCAAAGATTACAAAAAGAATACTTAAATTATA
280752 T
1 T
280753 CAAAATTTAC
Statistics
Matches: 111, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
119 33 0.30
120 78 0.70
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (118 bp):
TATCAAAGAGTTACTAAAATTATATAAACAATTATTAAAACTATTACAAATGTTATCAAAATTAT
ACCAAAAGTTACAAAACGATATCAAAGATTACAAAAAGAATACTTAAATTATA
Found at i:280887 original size:10 final size:9
Alignment explanation
Indices: 280878--280957 Score: 52
Period size: 10 Copynumber: 8.0 Consensus size: 9
280868 AAATTGTATC
280878 TAAAATTAT
1 TAAAATTAT
* *
280887 CAAAATTGT
1 TAAAATTAT
280896 TACAAAGATTAT
1 T--AAA-ATTAT
280908 TAAAATTATAT
1 TAAAA-T-TAT
280919 TAAAAATTAT
1 T-AAAATTAT
*
280929 CAAAAATTAT
1 -TAAAATTAT
*
280939 AAACAATTAT
1 TAA-AATTAT
280949 TAAAATTAT
1 TAAAATTAT
280958 ATTAAAAATG
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
9 17 0.30
10 23 0.40
11 8 0.14
12 9 0.16
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (9 bp):
TAAAATTAT
Found at i:280893 original size:41 final size:42
Alignment explanation
Indices: 280799--281002 Score: 147
Period size: 41 Copynumber: 4.9 Consensus size: 42
280789 ATATATGAGG
* ** *
280799 TTATCTAAATTA-TACGAAA-AGTTATCAAAATTAATAGCAAAAG
1 TTATCAAAATTATTAC-AAAGA-TTATCAAAATT-ATATTAAAAA
* * * *
280842 TTACCAAAATTATTTCAAAGATTA-CCAAATTGTATCT-AAAA
1 TTATCAAAATTATTACAAAGATTATCAAAATTATAT-TAAAAA
* *
280883 TTATCAAAATTGTTACAAAGATTATTAAAATTATATTAAAAA
1 TTATCAAAATTATTACAAAGATTATCAAAATTATATTAAAAA
*
280925 TTATCAAAAATTA-TA-AACA-ATTATTAAAATTATATTAAAAA
1 TTATC-AAAATTATTACAA-AGATTATCAAAATTATATTAAAAA
* * *
280966 TGATCAAAATCA-TATCAAA-ATTTATCAAAATCATATT
1 TTATCAAAATTATTA-CAAAGA-TTATCAAAATTATATT
281003 TAGGGTTATT
Statistics
Matches: 132, Mismatches: 19, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
40 8 0.06
41 57 0.43
42 42 0.32
43 22 0.17
44 3 0.02
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.35
Consensus pattern (42 bp):
TTATCAAAATTATTACAAAGATTATCAAAATTATATTAAAAA
Found at i:280933 original size:83 final size:82
Alignment explanation
Indices: 280744--281001 Score: 202
Period size: 83 Copynumber: 3.1 Consensus size: 82
280734 AAGAATACTT
* * * ** *
280744 AAATTATATCAAAATTTACCAAAATCATATCAAAGATTACCAATTATATATGAGGTTATCTAAAT
1 AAATTATATCAAAAATTACCAAAATTATATCAAAGATTACCAATTATATATAAAATTATCAAAAT
280809 TATACGAAAAGTTATCA
66 TATACGAAAAGTTATCA
* * * * *
280826 AAATTAATAGCAAAAGTTACCAAAATTATTTCAAAGATTACCAAATTGTATCTAAAATTATCAAA
1 AAATT-ATATCAAAAATTACCAAAATTATATCAAAGATTACC-AATTATATATAAAATTATCAAA
* *
280891 ATTGTTAC--AAAGATTATTA
64 ATT-ATACGAAAAG-TTATCA
* * * ** * *
280910 AAATTATATTAAAAATTATCAAAAATTATAAACAATTATTA-AAATTATAT-TAAAAATGATCAA
1 AAATTATATCAAAAATTA-CCAAAATTAT-ATCAAAGATTACCAATTATATAT-AAAATTATCAA
* *
280973 AATCATATC-AAAATTTATCA
63 AATTATA-CGAAAAGTTATCA
*
280993 AAATCATAT
1 AAATTATAT
281002 TTAGGGTTAT
Statistics
Matches: 139, Mismatches: 28, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
82 8 0.06
83 80 0.58
84 41 0.29
85 10 0.07
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (82 bp):
AAATTATATCAAAAATTACCAAAATTATATCAAAGATTACCAATTATATATAAAATTATCAAAAT
TATACGAAAAGTTATCA
Found at i:281340 original size:3 final size:3
Alignment explanation
Indices: 281332--281415 Score: 100
Period size: 3 Copynumber: 27.7 Consensus size: 3
281322 CCTTAAAACA
* **
281332 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TAC AATAAA TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC --T-TC TTC TTC
281378 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
281416 AACAATAAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
2 3 0.04
3 67 0.92
4 1 0.01
5 1 0.01
6 1 0.01
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:281564 original size:32 final size:31
Alignment explanation
Indices: 281528--281616 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 31
281518 AAGTTTCCTT
281528 TAATAAAGACTTTAATGTTTAA-AAGTAAAAAA
1 TAATAAAGACTTTAATGTTTAATAAG--AAAAA
* * *
281560 TAATAAATATTTTATTAGTTTAATAAGAAAAA
1 TAATAAAGACTTTAAT-GTTTAATAAGAAAAA
* * *
281592 TTATGAGGACTTTAATGTTTAATAA
1 TAATAAAGACTTTAATGTTTAATAA
281617 ATTATTAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
31 9 0.20
32 28 0.61
33 6 0.13
34 3 0.07
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.38
Consensus pattern (31 bp):
TAATAAAGACTTTAATGTTTAATAAGAAAAA
Found at i:282721 original size:18 final size:19
Alignment explanation
Indices: 282688--282723 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
282678 ATTCTCATTT
282688 TATTTTTTATATTATATTA
1 TATTTTTTATATTATATTA
282707 TATTTTTTATA-TATATT
1 TATTTTTTATATTATATT
282724 TTATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTTTTATATTATATTA
Found at i:282725 original size:11 final size:10
Alignment explanation
Indices: 282688--282728 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
282678 ATTCTCATTT
282688 TATT-TTTTA
1 TATTATTTTA
*
282697 TATTATATTA
1 TATTATTTTA
282707 TATT-TTTTA
1 TATTATTTTA
282716 TATATATTTTA
1 TAT-TATTTTA
282727 TA
1 TA
282729 ATAATAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 11 0.41
10 9 0.33
11 7 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATTATTTTA
Found at i:284466 original size:20 final size:19
Alignment explanation
Indices: 284444--284508 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
284434 TAAATAAAAA
*
284444 ATTTAAATATTAAATATAT
1 ATTTAAATAATAAATATAT
*
284463 AATTATAATAATAAAT-TAGT
1 ATTTA-AATAATAAATATA-T
*
284483 ATTGTATATAATAAATATAT
1 ATT-TAAATAATAAATATAT
284503 ATTTAA
1 ATTTAA
284509 TTAGATGATA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
19 8 0.22
20 25 0.68
21 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
ATTTAAATAATAAATATAT
Found at i:286990 original size:20 final size:20
Alignment explanation
Indices: 286967--287008 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
286957 ATATTTTATC
*
286967 ATATTTTA-ATTATATTTAAA
1 ATATTTTATATT-TATATAAA
286987 ATATTTTATATTTATATAAA
1 ATATTTTATATTTATATAAA
287007 AT
1 AT
287009 TTAATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTTTATATTTATATAAA
Done.