Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008078.1 Hibiscus syriacus cultivar Beakdansim tig00110580_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: 1434613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:845993 original size:20 final size:20
Alignment explanation
Indices: 845968--846013 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
845958 TAGTTTACTT
845968 TCGCAACACGAAAAT-GACTA
1 TCGCAACACGAAAATAG-CTA
* *
845988 TCGCAACGCGGAAATAGCTA
1 TCGCAACACGAAAATAGCTA
846008 TCGCAA
1 TCGCAA
846014 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATAGCTA
Found at i:846029 original size:19 final size:19
Alignment explanation
Indices: 846007--846056 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
845997 GGAAATAGCT
846007 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
846026 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
846045 ATCGCAATGCGA
1 ATCGCAATGCGA
846057 TTTGTGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:846068 original size:19 final size:19
Alignment explanation
Indices: 846063--846186 Score: 71
Period size: 20 Copynumber: 6.7 Consensus size: 19
846053 GCGATTTGTG
*
846063 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
846082 TTTCGCATTGCGA---T--
1 TTTCGCATTGCGATTTTCA
*
846096 TTT-GCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
***
846114 TTTCGCATTGCGATAGCCA
1 TTTCGCATTGCGATTTTCA
* **
846133 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCATTGCGATTTTCA
* **
846153 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCATTGCGATTTTCA
*
846173 TTTTCGCGTTGCGA
1 -TTTCGCATTGCGA
846187 AAGTAAGTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 15
0.79 0.07 0.13
Matches are distributed among these distances:
13 8 0.09
14 3 0.03
16 2 0.02
18 3 0.03
19 26 0.29
20 44 0.49
21 3 0.03
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:846108 original size:32 final size:32
Alignment explanation
Indices: 846067--846127 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
846057 TTTGTGTTTC
846067 GCGTTGCGATTTTCATTTCGCATTGCGATTTT
1 GCGTTGCGATTTTCATTTCGCATTGCGATTTT
846099 GCGTTGCGATTTTCATTTCGCATTGCGAT
1 GCGTTGCGATTTTCATTTCGCATTGCGAT
846128 AGCCATTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.44
Consensus pattern (32 bp):
GCGTTGCGATTTTCATTTCGCATTGCGATTTT
Found at i:846146 original size:20 final size:20
Alignment explanation
Indices: 846099--846186 Score: 124
Period size: 20 Copynumber: 4.5 Consensus size: 20
846089 TTGCGATTTT
**
846099 GCGTTGCGATTTTCATTT-C
1 GCGTTGCGATAGTCATTTCC
* *
846118 GCATTGCGATAGCCATTTCC
1 GCGTTGCGATAGTCATTTCC
846138 GCGTTGCGATAGTCATTTCC
1 GCGTTGCGATAGTCATTTCC
*
846158 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCATTTCC
846178 GCGTTGCGA
1 GCGTTGCGA
846187 AAGTAAGTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
19 14 0.23
20 47 0.77
ACGTcount: A:0.15, C:0.24, G:0.25, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCATTTCC
Found at i:846181 original size:40 final size:39
Alignment explanation
Indices: 846063--846186 Score: 127
Period size: 40 Copynumber: 3.3 Consensus size: 39
846053 GCGATTTGTG
**
846063 TTTCGCGTTGCGATTTTCATTTCGCATTGC----G--AT
1 TTTCGCGTTGCGATAGTCATTTCGCATTGCGATAGCCAT
**
846096 TTT-GCGTTGCGATTTTCATTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGTCATTTCGCATTGCGATAGCCAT
* * *
846134 TTCCGCGTTGCGATAGTCATTTCCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCATTT-CGCATTGCGATAGCCAT
846174 TTTCGCGTTGCGA
1 TTTCGCGTTGCGA
846187 AAGTAAGTTT
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
32 26 0.34
33 3 0.04
36 1 0.01
38 4 0.05
39 16 0.21
40 27 0.35
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (39 bp):
TTTCGCGTTGCGATAGTCATTTCGCATTGCGATAGCCAT
Found at i:846197 original size:20 final size:19
Alignment explanation
Indices: 846113--846212 Score: 83
Period size: 20 Copynumber: 5.1 Consensus size: 19
846103 TGCGATTTTC
* * **
846113 ATTTCGCATTGCGATAGCC
1 ATTTCGCGTTGCGAAAGTA
* *
846132 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGAAAGTA
*
846152 ATTTCCGCGTTGCGATAGTCA
1 ATTT-CGCGTTGCGAAAGT-A
*
846173 TTTTCGCGTTGCGAAAGTA
1 ATTTCGCGTTGCGAAAGTA
*
846192 AGTTTCGTGTTGCGAAAGTA
1 A-TTTCGCGTTGCGAAAGTA
846212 A
1 A
846213 ACTATTCTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
19 5 0.07
20 63 0.89
21 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (19 bp):
ATTTCGCGTTGCGAAAGTA
Found at i:846204 original size:40 final size:40
Alignment explanation
Indices: 846113--846206 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
846103 TGCGATTTTC
* * *
846113 ATTT-CGCATTGCGATAGCCATTTCCGCGTTGCGATAGTC
1 ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
* *
846152 ATTTCCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTA
1 ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
*
846192 AGTTT-CGTGTTGCGA
1 A-TTTCCGCGTTGCGA
846207 AAGTAAACTA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 4 0.09
40 40 0.85
41 3 0.06
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (40 bp):
ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
Found at i:846606 original size:21 final size:20
Alignment explanation
Indices: 846554--846614 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
846544 GACTCACCTG
846554 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGTCCCCT
* ** *
846574 CCAATCGTTCAAGAGACCCCT
1 TC-ATCCCTCAAGAGTCCCCT
846595 ATCATCCCTCAAGAGTCCCC
1 -TCATCCCTCAAGAGTCCCC
846615 CCCACCATTC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.43, G:0.11, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGTCCCCT
Found at i:846641 original size:41 final size:42
Alignment explanation
Indices: 846551--846641 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 42
846541 TCCGACTCAC
* * *
846551 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGACCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGACCA
* * *
846593 CTATCATCCCTCAAGAGTCCCC-CCCACCATTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGACCA
846634 CTGTCATC
1 CTGTCATC
846642 GTTGAATAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 21 0.50
42 21 0.50
ACGTcount: A:0.24, C:0.42, G:0.13, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGACCA
Found at i:848082 original size:14 final size:14
Alignment explanation
Indices: 848048--848086 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
848038 TTGATTGTTT
848048 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
848062 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
848076 TGTTGATTTGT
1 AATTGATTTGT
848087 TTAATTGATG
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:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:848232 original size:14 final size:14
Alignment explanation
Indices: 848213--848266 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
848203 GAAACTGACT
*
848213 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
848227 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
848246 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
848260 ATCGCAA
1 ATCGCAA
848267 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:848250 original size:19 final size:17
Alignment explanation
Indices: 848226--848271 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 17
848216 GCAACGAGAG
848226 AATCGCAATGCGAAATGAA
1 AATCGCAATGCG-AA-GAA
848245 AATCGCAA--CG-AGAA
1 AATCGCAATGCGAAGAA
848259 AATCGCAATGCGA
1 AATCGCAATGCGA
848272 TTTTCATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
14 11 0.46
15 1 0.04
16 2 0.08
17 2 0.08
19 8 0.33
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (17 bp):
AATCGCAATGCGAAGAA
Found at i:848312 original size:20 final size:20
Alignment explanation
Indices: 848287--848325 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
848277 ATTTCGCATT
848287 GCCATTTTCGCGTTGCGATA
1 GCCATTTTCGCGTTGCGATA
848307 GCCATTTTCGCGTTGCGAT
1 GCCATTTTCGCGTTGCGAT
848326 TTCCCCGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.13, C:0.26, G:0.26, T:0.36
Consensus pattern (20 bp):
GCCATTTTCGCGTTGCGATA
Found at i:848997 original size:20 final size:20
Alignment explanation
Indices: 848871--849005 Score: 110
Period size: 20 Copynumber: 6.7 Consensus size: 20
848861 GATTCTGTAT
*
848871 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* ** * *
848891 AATCTTGTTGCGAAAGTCAC
1 TATCGCGTTGCGATAGTCAG
* *
848911 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * * *
848931 AATCGCATTGCGAAAGTTAG
1 TATCGCGTTGCGATAGTCAG
* *
848951 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
848972 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
848992 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
849006 TTTCCAAATT
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
19 3 0.03
20 76 0.80
21 14 0.15
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:849024 original size:41 final size:41
Alignment explanation
Indices: 848932--849026 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
848922 GAAAGTCAGA
* * * ** *
848932 ATCGCATTGCGAAAGTTAGTATCGCGTTGCGATTTTGTATT
1 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCAAAT
*
848973 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT-CAAAT
849015 -TCGCATTGCGAT
1 ATCGCATTGCGAT
849027 TTACTTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCAAAT
Found at i:849038 original size:20 final size:21
Alignment explanation
Indices: 848994--849045 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
848984 ATAGTCAGTA
*
848994 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
849015 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
849035 TCGCATTGCGA
1 TCGCATTGCGA
849046 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:849087 original size:21 final size:22
Alignment explanation
Indices: 849035--849087 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
849025 ATTTACTTAT
849035 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
849056 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
849077 TCGCATTGCGA
1 TCGCATTGCGA
849088 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:851589 original size:60 final size:60
Alignment explanation
Indices: 851501--851648 Score: 199
Period size: 60 Copynumber: 2.5 Consensus size: 60
851491 ATGTAATTGA
* * * * *
851501 AATATTCAAAGGTCTAGGGACCAATTTAGAAAGAGTGTCATAGTTTAGGG-ATGAAATTAG
1 AATATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAGTCATAGTTT-GGGTATAAAATTAG
* * * *
851561 AATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTGGGTTTAAAATTAG
1 AATATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAGTCATAGTTTGGGTATAAAATTAG
851621 AATATTCAAAAGTTTAAGGACCAATTTA
1 AATATTCAAAAGTTTAAGGACCAATTTA
851649 AAATGAGGGA
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
59 3 0.04
60 73 0.96
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (60 bp):
AATATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAGTCATAGTTTGGGTATAAAATTAG
Found at i:852112 original size:10 final size:10
Alignment explanation
Indices: 852099--852152 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
852089 AAAATAATAT
852099 TATATTATTA
1 TATATTATTA
852109 TATATATAATTA
1 TATAT-T-ATTA
*
852121 TA-A--ATAA
1 TATATTATTA
852128 TATATTATTA
1 TATATTATTA
852138 TATATTATTA
1 TATATTATTA
852148 TATAT
1 TATAT
852153 AAATGGTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 5 0.14
8 1 0.03
10 23 0.62
11 2 0.05
12 6 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TATATTATTA
Found at i:852114 original size:27 final size:29
Alignment explanation
Indices: 852080--852156 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
852070 TAGGAATTTA
*
852080 TATATATATAA-AAT-AATATTATATTAT
1 TATATATATAATAATAAATAATATATTAT
*
852107 TATATATATAATTATAAATAATATATTAT
1 TATATATATAATAATAAATAATATATTAT
*
852136 TATATATTATTATATATAAAT
1 TATATA-TATAATA-ATAAAT
852157 GGTTGACCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 11 0.26
28 2 0.05
29 18 0.43
30 5 0.12
31 6 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TATATATATAATAATAAATAATATATTAT
Found at i:852150 original size:37 final size:37
Alignment explanation
Indices: 852082--852154 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
852072 GGAATTTATA
*
852082 TATATATAAAATAATATTATATTATTATATATATAAT
1 TATAAATAAAATAATATTATATTATTATATATATAAT
* *
852119 TATAAATAATATATTATTATA-TATTATTATATATAA
1 TATAAATAAAATAATATTATATTATTA-TATATATAA
852155 ATGGTTGACC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 5 0.16
37 27 0.84
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
TATAAATAAAATAATATTATATTATTATATATATAAT
Found at i:854242 original size:22 final size:22
Alignment explanation
Indices: 854195--854283 Score: 112
Period size: 22 Copynumber: 4.1 Consensus size: 22
854185 GTACAGATTA
*
854195 CCCCTAGGGGGAACAGATT--C
1 CCCCCAGGGGGAACAGATTCCC
*
854215 CCCCCAGGAGGAACAGATTCCC
1 CCCCCAGGGGGAACAGATTCCC
854237 CCCCCAGGGGGAACAGATTCCC
1 CCCCCAGGGGGAACAGATTCCC
*
854259 CCCTCCAGGGGGTATC-GATTCCC
1 CCC-CCAGGGGG-AACAGATTCCC
854282 CC
1 CC
854284 TGTCTAACGG
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
20 17 0.28
22 25 0.41
23 17 0.28
24 2 0.03
ACGTcount: A:0.21, C:0.39, G:0.26, T:0.13
Consensus pattern (22 bp):
CCCCCAGGGGGAACAGATTCCC
Found at i:854284 original size:22 final size:22
Alignment explanation
Indices: 854180--854284 Score: 112
Period size: 20 Copynumber: 4.9 Consensus size: 22
854170 CAGATTGCCT
* *
854180 AGGGGGTACAGATTACCCCT--
1 AGGGGGAACAGATTCCCCCTCC
854200 AGGGGGAACAGATT-CCCC-CC
1 AGGGGGAACAGATTCCCCCTCC
* *
854220 AGGAGGAACAGATTCCCCCCCC
1 AGGGGGAACAGATTCCCCCTCC
854242 AGGGGGAACAGATTCCCCCCTCC
1 AGGGGGAACAGATT-CCCCCTCC
*
854265 AGGGGGTATC-GATTCCCCCT
1 AGGGGG-AACAGATTCCCCCT
854285 GTCTAACGGT
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.05
20 26 0.35
21 4 0.05
22 21 0.28
23 17 0.23
24 2 0.03
ACGTcount: A:0.23, C:0.34, G:0.28, T:0.15
Consensus pattern (22 bp):
AGGGGGAACAGATTCCCCCTCC
Found at i:857446 original size:21 final size:20
Alignment explanation
Indices: 857407--857515 Score: 119
Period size: 20 Copynumber: 5.1 Consensus size: 20
857397 AATCAGATTG
857407 CCCAGGGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
857427 CCCAGGGGGAACAGATTTCCCCCCCC
1 CCCAGGGGGTACAGA-TT-----CCC
*
857453 CCCAAGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATT-CCC
*
857474 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
857494 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
857514 CC
1 CC
857516 TGTCTAATGG
Statistics
Matches: 78, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
20 39 0.50
21 21 0.27
25 2 0.03
26 16 0.21
ACGTcount: A:0.18, C:0.41, G:0.27, T:0.14
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:857471 original size:25 final size:26
Alignment explanation
Indices: 857424--857476 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
857414 GGTACAGATT
*
857424 CCCCCCAGGGGGAACAGATTTCCCCC
1 CCCCCCAAGGGGAACAGATTTCCCCC
*
857450 CCCCCCAAGGGGTACAGA-TTCCCCC
1 CCCCCCAAGGGGAACAGATTTCCCCC
857475 CC
1 CC
857477 AGGGGGTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.19, C:0.49, G:0.21, T:0.11
Consensus pattern (26 bp):
CCCCCCAAGGGGAACAGATTTCCCCC
Found at i:857493 original size:46 final size:46
Alignment explanation
Indices: 857407--857496 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
857397 AATCAGATTG
*
857407 CCCAGGGGGTACAGATTCCCCCCAGGGGGAACAGATTTCCCCCCCC
1 CCCAAGGGGTACAGATTCCCCCCAGGGGGAACAGATTTCCCCCCCC
* *
857453 CCCAAGGGGTACAGATTCCCCCCCAGGGGGTACCGA-TTCCCCCC
1 CCCAAGGGGTACAGATT-CCCCCCAGGGGGAACAGATTTCCCCCC
857497 AGGGGGTACC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 24 0.60
47 16 0.40
ACGTcount: A:0.19, C:0.42, G:0.26, T:0.13
Consensus pattern (46 bp):
CCCAAGGGGTACAGATTCCCCCCAGGGGGAACAGATTTCCCCCCCC
Found at i:859543 original size:35 final size:35
Alignment explanation
Indices: 859496--859563 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
859486 CTAAATCCTA
*
859496 AATTGAAGTATTTTAGAATATGGGGTTTAAAATTT
1 AATTGAAGTATTTTAGAATATGGAGTTTAAAATTT
* *
859531 AATTGAATTATTTTAGAATTTGGAGTTTAAAAT
1 AATTGAAGTATTTTAGAATATGGAGTTTAAAAT
859564 GAAATTAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (35 bp):
AATTGAAGTATTTTAGAATATGGAGTTTAAAATTT
Found at i:878852 original size:45 final size:45
Alignment explanation
Indices: 878788--878881 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
878778 AGAAAATAAT
878788 AGACCAGATGAGAATAACAATATACAACCCAACGGAAAGATGCAG
1 AGACCAGATGAGAATAACAATATACAACCCAACGGAAAGATGCAG
878833 AGACCAGATGAGAATAACAATATACAACCCAACGGAAAGATGCAG
1 AGACCAGATGAGAATAACAATATACAACCCAACGGAAAGATGCAG
878878 AGAC
1 AGAC
878882 TATATAATCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (45 bp):
AGACCAGATGAGAATAACAATATACAACCCAACGGAAAGATGCAG
Found at i:881822 original size:20 final size:20
Alignment explanation
Indices: 881793--881866 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
881783 GCAGCCTTCG
* *
881793 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCATGA
* * *
881813 CGCATCGATGCACAACCTTGA
1 TGCATCGATGCAC-AGCATGA
*
881834 TGCATCGATGCACAGAATGA
1 TGCATCGATGCACAGCATGA
881854 TGCATCGATGCAC
1 TGCATCGATGCAC
881867 TAATTGCATT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAGCATGA
Found at i:881936 original size:21 final size:21
Alignment explanation
Indices: 881887--882028 Score: 207
Period size: 21 Copynumber: 6.7 Consensus size: 21
881877 CGGTGTTTGA
881887 ATGCATGGATGCACTAGTGCA-GG
1 ATGCATGGATGCAC---TGCAGGG
881910 -TGCATGGATGCACTGCAGGG
1 ATGCATGGATGCACTGCAGGG
881930 ATGCATGGATGCACTGCAGGG
1 ATGCATGGATGCACTGCAGGG
881951 ATGCATGGATGCACTGCAGGG
1 ATGCATGGATGCACTGCAGGG
*
881972 ATGCATGGATGCACTGCAGAG
1 ATGCATGGATGCACTGCAGGG
* *
881993 ATGCATGGATGCATTGTAGGG
1 ATGCATGGATGCACTGCAGGG
*
882014 GTGCATGGATGCACT
1 ATGCATGGATGCACT
882029 TTGACACCCT
Statistics
Matches: 111, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.04
20 2 0.02
21 92 0.83
22 13 0.12
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (21 bp):
ATGCATGGATGCACTGCAGGG
Found at i:881989 original size:13 final size:13
Alignment explanation
Indices: 881910--881976 Score: 55
Period size: 13 Copynumber: 5.9 Consensus size: 13
881900 CTAGTGCAGG
881910 TGCATGGATGCAC
1 TGCATGGATGCAC
881923 TGCA-GG--G-A-
1 TGCATGGATGCAC
881931 TGCATGGATGCAC
1 TGCATGGATGCAC
881944 TGCA-GG--G-A-
1 TGCATGGATGCAC
881952 TGCATGGATGCAC
1 TGCATGGATGCAC
*
881965 TGCAGGGATGCA
1 TGCATGGATGCA
881977 TGGATGCACT
Statistics
Matches: 43, Mismatches: 1, Indels: 20
0.67 0.02 0.31
Matches are distributed among these distances:
8 8 0.19
9 6 0.14
10 2 0.05
11 2 0.05
12 6 0.14
13 19 0.44
ACGTcount: A:0.24, C:0.19, G:0.37, T:0.19
Consensus pattern (13 bp):
TGCATGGATGCAC
Found at i:890475 original size:17 final size:17
Alignment explanation
Indices: 890453--890496 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
890443 TTCATAAATC
890453 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
890470 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
890487 -AAATATCCAA
1 CAAA-ATCCAA
890497 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:890488 original size:9 final size:8
Alignment explanation
Indices: 890448--890498 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
890438 CACTATTCAT
890448 AAATCC-A
1 AAATCCAA
890455 AAATCCAA
1 AAATCCAA
*
890463 CAATCCACA
1 AAATCCA-A
890472 AAAT-CAA
1 AAATCCAA
890479 ACAATCCAA
1 A-AATCCAA
890488 AATATCCAA
1 AA-ATCCAA
890497 AA
1 AA
890499 TGTTGAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATCCAA
Found at i:892461 original size:21 final size:21
Alignment explanation
Indices: 892435--892474 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
892425 CAGAACCCCA
*
892435 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
892456 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
892475 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:892509 original size:20 final size:21
Alignment explanation
Indices: 892455--892517 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
892445 GATTCCCCTG
892455 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
892479 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
892499 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
892518 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:895899 original size:21 final size:21
Alignment explanation
Indices: 895870--895947 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
895860 GGGCTTCATA
* *
895870 GGTCATTCGGGATAATACAAT
1 GGTCCTTCGGGACAATACAAT
895891 GGTCCTTCGGGACAATACAAT
1 GGTCCTTCGGGACAATACAAT
* * *
895912 GGTCTTTCAGGACAATACAGT
1 GGTCCTTCGGGACAATACAAT
895933 GGTCCTTCGGGACAA
1 GGTCCTTCGGGACAA
895948 ATTTCATATG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
GGTCCTTCGGGACAATACAAT
Found at i:920906 original size:9 final size:9
Alignment explanation
Indices: 920892--920925 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
920882 TAAGTAAAAT
920892 ATTAAATAA
1 ATTAAATAA
920901 ATTAAAT-A
1 ATTAAATAA
920909 ATTAAATAA
1 ATTAAATAA
920918 ATTAAATA
1 ATTAAATA
920926 CAAATATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:920924 original size:17 final size:17
Alignment explanation
Indices: 920888--920925 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
920878 TATATAAGTA
920888 AAAT-ATTAAATAAATT
1 AAATAATTAAATAAATT
920904 AAATAATTAAATAAATT
1 AAATAATTAAATAAATT
920921 AAATA
1 AAATA
920926 CAAATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATAATTAAATAAATT
Found at i:920989 original size:10 final size:10
Alignment explanation
Indices: 920971--921009 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
920961 AGATAATATA
*
920971 AGAGTATTTG
1 AGAGAATTTG
920981 AGAGAATTTG
1 AGAGAATTTG
*
920991 AGAGAAATTG
1 AGAGAATTTG
921001 AGAGAATTT
1 AGAGAATTT
921010 AGTGTGATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:924629 original size:2 final size:2
Alignment explanation
Indices: 924622--924655 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
924612 CAATTTAATC
924622 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
924656 TGGTTCGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:926874 original size:18 final size:18
Alignment explanation
Indices: 926847--926882 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
926837 ACGGCAGCCA
*
926847 CCGCAACCATTTATGATG
1 CCGCAACCATATATGATG
*
926865 CCGCAGCCATATATGATG
1 CCGCAACCATATATGATG
926883 TCGCCGCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:927442 original size:26 final size:24
Alignment explanation
Indices: 927371--927442 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
927361 ATATATTTGT
927371 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
927396 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
927418 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
927443 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:931169 original size:51 final size:51
Alignment explanation
Indices: 931093--931222 Score: 163
Period size: 51 Copynumber: 2.5 Consensus size: 51
931083 CCCCTACGTG
* * **
931093 GCGTATAGCGCGGAACAGGGGGCACGTTATA-CCCACGTGTAAGCCATGTCA
1 GCGTATAGCGCGGAACAGGGGGCACGCTATACCCCACGTGGAA-CCAAATCA
* *
931144 GCGTATAGCGCGGTACAGGGGGCACGCTATACCCCACGTGGCACCAAATCA
1 GCGTATAGCGCGGAACAGGGGGCACGCTATACCCCACGTGGAACCAAATCA
* * *
931195 GCATATAGCGCGGGACAGGGAGCACGCT
1 GCGTATAGCGCGGAACAGGGGGCACGCT
931223 TTACTACTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 60 0.87
52 9 0.13
ACGTcount: A:0.25, C:0.28, G:0.32, T:0.15
Consensus pattern (51 bp):
GCGTATAGCGCGGAACAGGGGGCACGCTATACCCCACGTGGAACCAAATCA
Found at i:939145 original size:22 final size:22
Alignment explanation
Indices: 939117--939166 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
939107 GATGTATCGA
939117 ATCGCGATTTTGAAACGATCCG
1 ATCGCGATTTTGAAACGATCCG
939139 ATCGCGATTTTGAAACGATCCG
1 ATCGCGATTTTGAAACGATCCG
*
939161 AACGCG
1 ATCGCG
939167 TTCGTACCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (22 bp):
ATCGCGATTTTGAAACGATCCG
Found at i:944135 original size:3 final size:3
Alignment explanation
Indices: 944127--944194 Score: 127
Period size: 3 Copynumber: 22.3 Consensus size: 3
944117 TTTTTTACCC
944127 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
944176 ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
944195 AAAATAAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 61 0.95
4 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:949754 original size:15 final size:15
Alignment explanation
Indices: 949734--949765 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
949724 ATCAATACCT
949734 TTTTGCATACATACA
1 TTTTGCATACATACA
*
949749 TTTTGCATACATTCA
1 TTTTGCATACATACA
949764 TT
1 TT
949766 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:957117 original size:7 final size:7
Alignment explanation
Indices: 957105--957202 Score: 83
Period size: 7 Copynumber: 13.4 Consensus size: 7
957095 ATGCGTGAAG
957105 AAAGAAA
1 AAAGAAA
957112 AAAGAAA
1 AAAGAAA
*
957119 AAAAAAGA
1 AAAGAA-A
*
957127 AAAAAAGA
1 AAAGAA-A
957135 GAAAGAAA
1 -AAAGAAA
957143 AAAGAAA
1 AAAGAAA
957150 AAAGAAGGA
1 AAAGAA--A
*
957159 AAA-AAG
1 AAAGAAA
*
957165 AGAGAAAA
1 AAAG-AAA
*
957173 AAAGAGA
1 AAAGAAA
957180 AAAGAAA
1 AAAGAAA
957187 AAAG-AA
1 AAAGAAA
957193 AAAGAAA
1 AAAGAAA
957200 AAA
1 AAA
957203 AGGGGTCAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
6 8 0.11
7 42 0.55
8 17 0.22
9 9 0.12
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:957124 original size:10 final size:10
Alignment explanation
Indices: 957102--957203 Score: 107
Period size: 10 Copynumber: 10.0 Consensus size: 10
957092 ATTATGCGTG
957102 AAGAAAGAAAA
1 AAGAAA-AAAA
957113 AAGAAAAAAA
1 AAGAAAAAAA
957123 AAGAAAAAAA
1 AAGAAAAAAA
*
957133 GAGAAAGAAAA
1 AAGAAA-AAAA
*
957144 AAGAAAAAAG
1 AAGAAAAAAA
*
957154 AAGGAAAAAA
1 AAGAAAAAAA
* *
957164 GAGAGAAAAA
1 AAGAAAAAAA
*
957174 AAGAGAAAAGA
1 AAGA-AAAAAA
*
957185 AA-AAAGAAA
1 AAGAAAAAAA
957194 AAGAAAAAAA
1 AAGAAAAAAA
957204 GGGGTCAAGA
Statistics
Matches: 74, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
9 6 0.08
10 47 0.64
11 21 0.28
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:957139 original size:31 final size:32
Alignment explanation
Indices: 957103--957195 Score: 127
Period size: 31 Copynumber: 2.9 Consensus size: 32
957093 TTATGCGTGA
957103 AGAAAGAAAAAAGAAAAAAAAAGAAAAAA-AG
1 AGAAAGAAAAAAGAAAAAAAAAGAAAAAAGAG
*
957134 AGAAAGAAAAAAGAAAAAAGAAGGAAAAAAGAG
1 AGAAAGAAAAAAGAAAAAA-AAAGAAAAAAGAG
*
957167 AGAAA-AAAAGAGAAAAGAAAAAAGAAAAA
1 AGAAAGAAAAAAG-AAA-AAAAAAGAAAAA
957196 GAAAAAAAGG
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
31 19 0.35
32 15 0.27
33 18 0.33
34 3 0.05
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (32 bp):
AGAAAGAAAAAAGAAAAAAAAAGAAAAAAGAG
Found at i:957198 original size:43 final size:42
Alignment explanation
Indices: 957102--957195 Score: 136
Period size: 44 Copynumber: 2.2 Consensus size: 42
957092 ATTATGCGTG
*
957102 AAGAAAGAAA-AAAGAAAAAAAAAGAAAAAAAGAGAAAGAAAA
1 AAGAAA-AAAGAAGGAAAAAAAAAGAAAAAAAGAGAAAGAAAA
*
957144 AAGAAAAAAGAAGGAAAAAAGAGAGAAAAAAAGAGAAAAGAAAA
1 AAGAAAAAAGAAGGAAAAAA-AAAGAAAAAAAGAG-AAAGAAAA
957188 AAGAAAAA
1 AAGAAAAA
957196 GAAAAAAAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 3 0.06
42 15 0.32
43 13 0.28
44 16 0.34
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (42 bp):
AAGAAAAAAGAAGGAAAAAAAAAGAAAAAAAGAGAAAGAAAA
Found at i:958366 original size:92 final size:92
Alignment explanation
Indices: 958209--958380 Score: 283
Period size: 92 Copynumber: 1.9 Consensus size: 92
958199 CCATATGCTC
* *
958209 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAATATGAACCCCGAAAACCAA
1 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTAATATGAACACCGAAAACCAA
958274 TCATTAGATTTGAAATAAAGAGACTCA
66 TCATTAGATTTGAAATAAAGAGACTCA
**
958301 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAA-ACCGAAAAACCA
1 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTAATATGAACACCG-AAAACCA
*
958365 ATCATTGGATTTGAAA
65 ATCATTAGATTTGAAA
958381 GATGAATGTG
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
91 3 0.04
92 71 0.96
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (92 bp):
ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTAATATGAACACCGAAAACCAA
TCATTAGATTTGAAATAAAGAGACTCA
Found at i:959401 original size:112 final size:109
Alignment explanation
Indices: 959191--959822 Score: 773
Period size: 112 Copynumber: 5.7 Consensus size: 109
959181 GCAAAGATTC
* * * * *
959191 AAATCCATCAATTGATGGATCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATTCATCATTTGATGGATCAGCATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
959256 AATGAAGAAGAATTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 AA-GAAG-A-AA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * *
959304 AAATTCATTATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTG
1 AAATTCATCATTTGATGGATCAGCATTACCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTG
*
959369 AAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTT
63 AAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* ** * * *
959416 GAATTCATCATTCAATGGATCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATTCATCATTTGATGGATCAGCATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
959481 AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGTTT
66 AA-GAAG-A-AA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * *
959529 AAATTCATTATTTGATGGATTAACATTACCAGTTAGAGTTCATAATGAGAAGAACTCGTCATCTG
1 AAATTCATCATTTGATGGATCAGCATTACCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTG
*
959594 AAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
63 AAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * * * * *
959641 AAATCCATCAATTAATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCCGAA
1 AAATTCATCATTTGATGGATCAGCATTACCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAA
*
959705 GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * * *
959750 AAATCCATCAATTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATTCATCATTTGATGGATCAGCATTACCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAA
959814 GAAGAAGAA
65 GAAGAAGAA
959823 GAAGAAGTTC
Statistics
Matches: 460, Mismatches: 48, Indels: 26
0.86 0.09 0.05
Matches are distributed among these distances:
109 136 0.30
110 6 0.01
111 1 0.00
112 154 0.33
113 127 0.28
114 2 0.00
115 10 0.02
116 24 0.05
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (109 bp):
AAATTCATCATTTGATGGATCAGCATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
Found at i:959596 original size:225 final size:223
Alignment explanation
Indices: 959189--959822 Score: 929
Period size: 225 Copynumber: 2.8 Consensus size: 223
959179 TAGCAAAGAT
*
959189 TCAAATCCATCAATTGATGGATCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGA
1 TCAAATCCATCAATTAATGGATCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGA
959254 AGAATGAAGAAGAATTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGA
66 AGAA-GAAGAAGAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGA
* *
959319 TGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAATTC
129 TGGATTAACATTACCAGATAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAATTC
*
959384 ATAATGAGAAGAATTTGTTCAACTTTTTGC
194 ATAATGAGAAGAATTTGTTCAACCTTTTGC
** *
959414 TTGAATTCATC-ATTCAATGGATCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTG
1 TCAAATCCATCAATT-AATGGATCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTG
*
959478 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTG
65 AAGAA-GAAGAAGAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTG
*
959543 ATGGATTAACATTACCAGTTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAATT
128 ATGGATTAACATTACCAGATAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAATT
959608 CATAATGAGAAGAATTTGTTCAACCTTTTGC
193 CATAATGAGAAGAATTTGTTCAACCTTTTGC
* * **** * *
959639 TCAAATCCATCAATTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCCGA
1 TCAAATCCATCAATTAATGGATCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGA
* * * * *
959704 AGAAGAAG-A-AATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCAATTGATG
66 AGAAGAAGAAGAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATG
* * * * * *
959767 GATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGAAGAA
131 GATTAACATTACCAGATAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAA
959823 GAAGAAGTTC
Statistics
Matches: 373, Mismatches: 34, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
218 18 0.05
219 1 0.00
221 76 0.20
222 2 0.01
223 1 0.00
224 7 0.02
225 265 0.71
226 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (223 bp):
TCAAATCCATCAATTAATGGATCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGA
AGAAGAAGAAGAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATG
GATTAACATTACCAGATAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAATTCAT
AATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:960092 original size:3 final size:3
Alignment explanation
Indices: 960084--960147 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
960074 TTTTTTACCC
960084 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
960132 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
960148 AAAATAAATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:963176 original size:16 final size:14
Alignment explanation
Indices: 963142--963178 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
963132 TCCAGCTCAT
963142 CCTCTCTCCGGGTA
1 CCTCTCTCCGGGTA
963156 CCTCTCTCCGGGTA
1 CCTCTCTCCGGGTA
963170 CCTCTCTCC
1 CCTCTCTCC
963179 AAACGGTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.05, C:0.49, G:0.16, T:0.30
Consensus pattern (14 bp):
CCTCTCTCCGGGTA
Found at i:963766 original size:20 final size:22
Alignment explanation
Indices: 963733--963777 Score: 76
Period size: 20 Copynumber: 2.1 Consensus size: 22
963723 CTGAAAATAT
963733 TAAAAAACATTAATGTTTTAGG
1 TAAAAAACATTAATGTTTTAGG
963755 TAAAAAA-A-TAATGTTTTAGG
1 TAAAAAACATTAATGTTTTAGG
963775 TAA
1 TAA
963778 TTTTTTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 15 0.65
21 1 0.04
22 7 0.30
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (22 bp):
TAAAAAACATTAATGTTTTAGG
Found at i:964809 original size:28 final size:29
Alignment explanation
Indices: 964764--964824 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
964754 ATTTTTAAGA
* * **
964764 TTTATAAATTTGTTTTTTTCCT-TAAAAT
1 TTTATAAATTTATCTTTTTAATATAAAAT
964792 TTTATAAATTTATCTTTTTAATATAAAAT
1 TTTATAAATTTATCTTTTTAATATAAAAT
964821 TTTA
1 TTTA
964825 AATCCGTCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTATAAATTTATCTTTTTAATATAAAAT
Found at i:965539 original size:3 final size:3
Alignment explanation
Indices: 965531--965555 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
965521 GACATGACAT
965531 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
965556 CATATATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:967280 original size:20 final size:20
Alignment explanation
Indices: 967257--967297 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
967247 TTGAAAATCG
*
967257 CATTGCGATAGTACTGTTTA
1 CATTGCGATAATACTGTTTA
967277 CATTGCGATAATACTGTTTA
1 CATTGCGATAATACTGTTTA
967297 C
1 C
967298 CTATATCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (20 bp):
CATTGCGATAATACTGTTTA
Found at i:967344 original size:20 final size:20
Alignment explanation
Indices: 967315--967353 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
967305 GGTAATTAGC
967315 GTTGCAAATTTGAAAATCGT
1 GTTGCAAATTTGAAAATCGT
*
967335 GTTGCGAATTTGAAAATCG
1 GTTGCAAATTTGAAAATCG
967354 CATTGCGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
GTTGCAAATTTGAAAATCGT
Found at i:967359 original size:20 final size:20
Alignment explanation
Indices: 967316--967361 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
967306 GTAATTAGCG
* **
967316 TTGCAAATTTGAAAATCGTG
1 TTGCGAATTTGAAAATCGCA
967336 TTGCGAATTTGAAAATCGCA
1 TTGCGAATTTGAAAATCGCA
967356 TTGCGA
1 TTGCGA
967362 TAGTATTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.33
Consensus pattern (20 bp):
TTGCGAATTTGAAAATCGCA
Found at i:967377 original size:20 final size:20
Alignment explanation
Indices: 967354--967394 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
967344 TTGAAAATCG
*
967354 CATTGCGATAGTATTGTTTA
1 CATTGCGATAGTACTGTTTA
967374 CATTGCGATAGTACTGTTTA
1 CATTGCGATAGTACTGTTTA
967394 C
1 C
967395 CTATATCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (20 bp):
CATTGCGATAGTACTGTTTA
Found at i:967404 original size:97 final size:97
Alignment explanation
Indices: 967238--967430 Score: 332
Period size: 97 Copynumber: 2.0 Consensus size: 97
967228 GGTAATTAGA
967238 GTTGCGAATTTGAAAATCGCATTGCGATAGTACTGTTTACATTGCGATAATACTGTTTACCTATA
1 GTTGCGAATTTGAAAATCGCATTGCGATAGTACTGTTTACATTGCGATAATACTGTTTACCTATA
* *
967303 TCGGTAATTAGCGTTGCAAATTTGAAAATCGT
66 TCGGTAATTAACGTTACAAATTTGAAAATCGT
* *
967335 GTTGCGAATTTGAAAATCGCATTGCGATAGTATTGTTTACATTGCGATAGTACTGTTTACCTATA
1 GTTGCGAATTTGAAAATCGCATTGCGATAGTACTGTTTACATTGCGATAATACTGTTTACCTATA
* *
967400 TCGGTAATTAACGTTACGAATTTTAAAATCG
66 TCGGTAATTAACGTTACAAATTTGAAAATCG
967431 CATTGCGATA
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 90 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (97 bp):
GTTGCGAATTTGAAAATCGCATTGCGATAGTACTGTTTACATTGCGATAATACTGTTTACCTATA
TCGGTAATTAACGTTACAAATTTGAAAATCGT
Found at i:967455 original size:97 final size:95
Alignment explanation
Indices: 967252--967470 Score: 260
Period size: 97 Copynumber: 2.3 Consensus size: 95
967242 CGAATTTGAA
* *
967252 AATCGCATTGCGATAGTACTGTTTACATTGCGATAATACTGTTTACCTATATCGGTAATTAGCGT
1 AATCACATTGCGATAGTACTGTTTACATTGCGATAATACTGTTTACCTATATCGGTAATTAACGT
* ** *
967317 TGCAAATTTGAAAATCGTGTTGCGAATTTG
66 TACAAATTTGAAAATCGCATTGCGAATCTG
* * *
967347 AAAATCGCATTGCGATAGTATTGTTTACATTGCGATAGTACTGTTTACCTATATCGGTAATTAAC
1 --AATCACATTGCGATAGTACTGTTTACATTGCGATAATACTGTTTACCTATATCGGTAATTAAC
* *
967412 GTTACGAATTTTAAAATCGCATTGCGATAGTACTG
64 GTTACAAATTTGAAAATCGCATTGCGA-A-T-CTG
* * *
967447 -TTTACATTGTGATAGTACTGTTTA
1 AATCACATTGCGATAGTACTGTTTA
967471 TTTTCAAATT
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
97 101 0.96
98 1 0.01
99 1 0.01
100 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (95 bp):
AATCACATTGCGATAGTACTGTTTACATTGCGATAATACTGTTTACCTATATCGGTAATTAACGT
TACAAATTTGAAAATCGCATTGCGAATCTG
Found at i:967460 original size:20 final size:20
Alignment explanation
Indices: 967431--967470 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
967421 TTTAAAATCG
967431 CATTGCGATAGTACTGTTTA
1 CATTGCGATAGTACTGTTTA
*
967451 CATTGTGATAGTACTGTTTA
1 CATTGCGATAGTACTGTTTA
967471 TTTTCAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (20 bp):
CATTGCGATAGTACTGTTTA
Found at i:968948 original size:2 final size:2
Alignment explanation
Indices: 968941--968973 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
968931 AAGGCATAGG
968941 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
968974 TTTTTTGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:971720 original size:2 final size:2
Alignment explanation
Indices: 971715--971747 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
971705 ATTTAAAATG
971715 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
971748 TCAAGAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:975968 original size:13 final size:13
Alignment explanation
Indices: 975950--975975 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
975940 AAACCATTTA
975950 TCGATTATAGAAT
1 TCGATTATAGAAT
975963 TCGATTATAGAAT
1 TCGATTATAGAAT
975976 ACTACTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
TCGATTATAGAAT
Found at i:984536 original size:17 final size:17
Alignment explanation
Indices: 984514--984578 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
984504 ACAGATTACA
984514 TCCTTCGGGATGATAGG
1 TCCTTCGGGATGATAGG
* **
984531 TCCTTCGGGACACAGATGACA
1 TCCTTCGGG--A-TGAT-AGG
*
984552 TCCTTTGGGATGATAGG
1 TCCTTCGGGATGATAGG
984569 TCCTTCGGGA
1 TCCTTCGGGA
984579 CATAGTTTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
17 19 0.53
18 3 0.08
19 2 0.06
20 3 0.08
21 9 0.25
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.28
Consensus pattern (17 bp):
TCCTTCGGGATGATAGG
Found at i:984538 original size:38 final size:38
Alignment explanation
Indices: 984485--984580 Score: 156
Period size: 38 Copynumber: 2.5 Consensus size: 38
984475 TATGAGACAT
* * *
984485 ATGATAGGTCATTCGGTACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
984523 ATGATAGGTCCTTCGGGACACAGATGACATCCTTTGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
984561 ATGATAGGTCCTTCGGGACA
1 ATGATAGGTCCTTCGGGACA
984581 TAGTTTATAC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:986263 original size:99 final size:100
Alignment explanation
Indices: 985888--986345 Score: 459
Period size: 99 Copynumber: 4.5 Consensus size: 100
985878 TGATTGTCTC
* * * * *
985888 ATTTTTAATTTTTACTTTAAATATAAATTAATTAGATTAGTTATTTTGATTTTACATATTATAAT
1 ATTTTTTATTTTTATTTTAAATATAAATTAATTAGACTATTTA-TTTGATTTTACAGATTA-AAT
* * *
985953 -GTATTCGGGTGGTTTGGTAAGTTTAATTTAAATTTT
64 CGTATTTGAGTGGTTTGGTAAGTTTAGTTTAAATTTT
* * * * * * *
985989 ATTGTTTATTTTTTGTTTTATTTTAAATA-ATATTTATCAGACTATTTATTTTAATTTACATATT
1 A----TT-TTTTAT-TTTTATTTTAAATATAAATTAATTAGACTATTTATTTGATTTTACAGATT
* * * *
986053 AAATCATATTTGAGT--TGTGGTAAGTTTACTGTAAATTTT
60 AAATCGTATTTGAGTGGTTTGGTAAGTTTAGTTTAAATTTT
* * * *
986092 A----TTGTTTTTATTTTAAAAATAAATTAATTAGATTATTTATTTTTATTTT-CAAGATTAAAT
1 ATTTTTTATTTTTATTTTAAATATAAATTAATTAGACTATTTA-TTTGATTTTAC-AGATTAAAT
986152 CGTATTTGAGTGGTTTGGTAAGTTTAGTTTAAATTTT
64 CGTATTTGAGTGGTTTGGTAAGTTTAGTTTAAATTTT
* *
986189 ATTTTTTATTTTTATTTTAAATATAAATT-ATTGGACTATTTATTTGATTTTATAGATTAAATCG
1 ATTTTTTATTTTTATTTTAAATATAAATTAATTAGACTATTTATTTGATTTTACAGATTAAATCG
*
986253 TATTTAAGTGGTTTGGTAAGTTTAGTTTAAATTTT
66 TATTTGAGTGGTTTGGTAAGTTTAGTTTAAATTTT
986288 ATTGTTTATTTATTATTTTTATTTTAAATATAAATTAATTAGACTATTTATTTGATTT
1 A-----T-TTT-TTATTTTTATTTTAAATATAAATTAATTAGACTATTTATTTGATTT
986346 AACATTTTTT
Statistics
Matches: 296, Mismatches: 36, Indels: 44
0.79 0.10 0.12
Matches are distributed among these distances:
93 13 0.04
94 19 0.06
95 26 0.09
97 22 0.07
99 54 0.18
100 11 0.04
101 23 0.08
103 22 0.07
104 4 0.01
105 27 0.09
106 42 0.14
107 33 0.11
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.55
Consensus pattern (100 bp):
ATTTTTTATTTTTATTTTAAATATAAATTAATTAGACTATTTATTTGATTTTACAGATTAAATCG
TATTTGAGTGGTTTGGTAAGTTTAGTTTAAATTTT
Found at i:986864 original size:42 final size:42
Alignment explanation
Indices: 986805--986888 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
986795 CATATAGGAT
*
986805 GACAGTGGTGGGGAAAAATGATCATAATGTGTTTGAAATTTG
1 GACAGTGGTGGGGAAAAATGATCATAACGTGTTTGAAATTTG
986847 GACAGTGGTGGGGAAAAATGATCATAACGTGTTTGAAATTTG
1 GACAGTGGTGGGGAAAAATGATCATAACGTGTTTGAAATTTG
986889 CGAGGCGTAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.33, C:0.06, G:0.31, T:0.30
Consensus pattern (42 bp):
GACAGTGGTGGGGAAAAATGATCATAACGTGTTTGAAATTTG
Found at i:993753 original size:22 final size:23
Alignment explanation
Indices: 993716--993797 Score: 107
Period size: 23 Copynumber: 3.7 Consensus size: 23
993706 TTAGTGTAGA
*
993716 GGGAATCGATACCCCCCTTGAAG
1 GGGAACCGATACCCCCCTTGAAG
993739 GGGAACCGATACCCCCCTTGAAG
1 GGGAACCGATACCCCCCTTGAAG
*
993762 GGGAACCGAT-TCCCCC-TGTAA-
1 GGGAACCGATACCCCCCTTG-AAG
*
993783 GGGAATCGATACCCC
1 GGGAACCGATACCCC
993798 ATGGGGTTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
21 11 0.21
22 10 0.19
23 32 0.60
ACGTcount: A:0.26, C:0.33, G:0.26, T:0.16
Consensus pattern (23 bp):
GGGAACCGATACCCCCCTTGAAG
Found at i:996138 original size:8 final size:8
Alignment explanation
Indices: 996125--996150 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
996115 TGTTGAAAAC
996125 ATTTTGAT
1 ATTTTGAT
996133 ATTTTGAT
1 ATTTTGAT
996141 ATTTTGAT
1 ATTTTGAT
996149 AT
1 AT
996151 AACAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (8 bp):
ATTTTGAT
Found at i:996416 original size:23 final size:23
Alignment explanation
Indices: 996374--996430 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 23
996364 TCCAGAGGGA
996374 ACCGATT--CCCCCCAAGGGGGT
1 ACCGATTCCCCCCCCAAGGGGGT
996395 ACCGATTTCCCCCCCCAAGGGGGT
1 ACCGA-TTCCCCCCCCAAGGGGGT
996419 ACCGATTCCCCC
1 ACCGATTCCCCC
996431 TGAATGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 5 0.15
22 2 0.06
23 7 0.21
24 19 0.58
ACGTcount: A:0.18, C:0.44, G:0.23, T:0.16
Consensus pattern (23 bp):
ACCGATTCCCCCCCCAAGGGGGT
Found at i:998219 original size:119 final size:120
Alignment explanation
Indices: 998057--998415 Score: 603
Period size: 120 Copynumber: 3.0 Consensus size: 120
998047 TTTGACGTCT
* *
998057 TTGCGTTGTTACTATAAAATTCACCCAAGATGAGAAAATAATCCCCGAATTGGATTATTTGGGGA
1 TTGCGTTGTTACTATAAAATTCACCCTAGATGAGAAAATAATCCCCGAGTTGGATTATTTGGGGA
****
998122 ATTCTTTTTCCCAA-AAAAAAAATTCAGTCATTTTGTCTTTAATTCTTATTATTA
66 ATTCTTTTTCCCAATAAAATTTTTTCAGTCATTTTGTCTTTAATTCTTATTATTA
*
998176 TTGCGTTGTTACTATAAAATTCACCCTAGATGAGAAAATAATCCCCGAGTTGGATTATTTAGGGA
1 TTGCGTTGTTACTATAAAATTCACCCTAGATGAGAAAATAATCCCCGAGTTGGATTATTTGGGGA
* *
998241 ATTCTTTTTCCCAATAAAATTTTTTCAATCATTTTATCTTTAATTCTTATTATTA
66 ATTCTTTTTCCCAATAAAATTTTTTCAGTCATTTTGTCTTTAATTCTTATTATTA
* * *
998296 TTGCGTTGTTACTGTAAAATTCACCCTAGATGAGAAAATAATCCTCGAGTTGGATTATTTGAGGA
1 TTGCGTTGTTACTATAAAATTCACCCTAGATGAGAAAATAATCCCCGAGTTGGATTATTTGGGGA
998361 ATTCTTTTTCCCAATAAAATTTTTTCAGTCATTTTGTCTTTAATTCTTATTATTA
66 ATTCTTTTTCCCAATAAAATTTTTTCAGTCATTTTGTCTTTAATTCTTATTATTA
998416 GTATTAATGT
Statistics
Matches: 224, Mismatches: 15, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
119 76 0.34
120 148 0.66
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (120 bp):
TTGCGTTGTTACTATAAAATTCACCCTAGATGAGAAAATAATCCCCGAGTTGGATTATTTGGGGA
ATTCTTTTTCCCAATAAAATTTTTTCAGTCATTTTGTCTTTAATTCTTATTATTA
Found at i:999307 original size:31 final size:31
Alignment explanation
Indices: 999265--999342 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
999255 AGAAACTATA
* * * *
999265 AGGTGGTGTTTGGTTTGTTGGAATGTTTTTG
1 AGGTGGCGTTTGGTTCGCTGGAATGTTTCTG
999296 AGGTGGCGTTTGGTTCGCTGGAATGTTTCTG
1 AGGTGGCGTTTGGTTCGCTGGAATGTTTCTG
*
999327 AGGTGACGTTTGGTTC
1 AGGTGGCGTTTGGTTC
999343 ACATGAATCC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.10, C:0.08, G:0.38, T:0.44
Consensus pattern (31 bp):
AGGTGGCGTTTGGTTCGCTGGAATGTTTCTG
Found at i:999890 original size:41 final size:42
Alignment explanation
Indices: 999833--999915 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 42
999823 AAATAATTTT
*
999833 TTTATTATTTCGGGTCGGGTC-GATTTCTAATTCATATATTC
1 TTTATTATTTCGGGTCGAGTCGGATTTCTAATTCATATATTC
999874 TTTATTATTTCGGGTCGAGTCGGATTTCTAATTCATATATTC
1 TTTATTATTTCGGGTCGAGTCGGATTTCTAATTCATATATTC
999916 GGGTCGGGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 20 0.50
42 20 0.50
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.48
Consensus pattern (42 bp):
TTTATTATTTCGGGTCGAGTCGGATTTCTAATTCATATATTC
Found at i:1000560 original size:33 final size:33
Alignment explanation
Indices: 1000513--1000726 Score: 132
Period size: 33 Copynumber: 6.3 Consensus size: 33
1000503 TTTTCACCCT
* * *
1000513 AAACCCGAATCCGACTCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGAATATCAAACTTAAAA
*
1000547 AAACTCGACCCGACCCGAATATCAAACTTAAAA
1 AAACCCGACCCGACCCGAATATCAAACTTAAAA
* * ** **
1000580 AAACCCGACTCGACCTGAA-CCCGAATTTTTTTAAAAA
1 AAACCCGACCCGACCCGAATATC-AA---ACTT-AAAA
* * * ***
1000617 AAATCCGACCCG-CTCTCGATTTTTTTA--TAAAA
1 AAACCCGACCCGAC-C-CGAATATCAAACTTAAAA
*
1000649 AAACCCCGACCCGACCCGAATATCACACTTAAAA
1 AAA-CCCGACCCGACCCGAATATCAAACTTAAAA
*
1000683 AAA-CCGACCCGACCTGAATATCAAACTTAAAAA
1 AAACCCGACCCGACCCGAATATCAAACTT-AAAA
*
1000716 AAACCCCACCC
1 AAACCCGACCC
1000727 CAACCTGAAT
Statistics
Matches: 136, Mismatches: 30, Indels: 28
0.70 0.15 0.14
Matches are distributed among these distances:
32 37 0.27
33 58 0.43
34 21 0.15
36 3 0.02
37 15 0.11
38 2 0.01
ACGTcount: A:0.41, C:0.31, G:0.09, T:0.19
Consensus pattern (33 bp):
AAACCCGACCCGACCCGAATATCAAACTTAAAA
Found at i:1000783 original size:32 final size:31
Alignment explanation
Indices: 1000602--1000792 Score: 147
Period size: 32 Copynumber: 5.9 Consensus size: 31
1000592 ACCTGAACCC
1000602 GAATTTTTTTAAAAAAAATCCGACCCG-CTCT
1 GAATTTTTTTAAAAAAAATCCGACCCGAC-CT
* *
1000633 CG-ATTTTTTTATAAAAAAACCCCGACCCGACCC
1 -GAATTTTTTTA-AAAAAAA-TCCGACCCGACCT
***
1000666 GAATATCACACTT-AAAAAAA-CCGACCCGACCT
1 GAAT-T--TTTTTAAAAAAAATCCGACCCGACCT
*** * * *
1000698 GAATATCAAACTTAAAAAAAACCCCACCCCAACCT
1 GAAT-T--TTTTTAAAAAAAATCCGA-CCCGACCT
1000733 GAATTTTTTTAAAAAAAATCCGACCCGATCCT
1 GAATTTTTTTAAAAAAAATCCGACCCGA-CCT
1000765 GAATTTTTTTAAAAAAAATCCGACCCGA
1 GAATTTTTTTAAAAAAAATCCGACCCGA
1000793 ATACCAAAAA
Statistics
Matches: 133, Mismatches: 15, Indels: 22
0.78 0.09 0.13
Matches are distributed among these distances:
31 13 0.10
32 76 0.57
33 18 0.14
34 13 0.10
35 11 0.08
36 2 0.02
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.24
Consensus pattern (31 bp):
GAATTTTTTTAAAAAAAATCCGACCCGACCT
Found at i:1003672 original size:22 final size:23
Alignment explanation
Indices: 1003636--1003698 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
1003626 TTTTATTTCA
* *
1003636 TTTGTTTTATTTATTGTTATTAT
1 TTTGTTTTATATATTATTATTAT
1003659 TTTGTTTTA-ATATTATTATTAT
1 TTTGTTTTATATATTATTATTAT
* * *
1003681 ATTATATTAT-TATTATTA
1 TTTGTTTTATATATTATTA
1003699 AATAAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 25 0.74
23 9 0.26
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (23 bp):
TTTGTTTTATATATTATTATTAT
Found at i:1003674 original size:19 final size:19
Alignment explanation
Indices: 1003652--1003698 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
1003642 TTATTTATTG
* * *
1003652 TTATTATTTTGTTTTAATA
1 TTATTATTATATTATAATA
*
1003671 TTATTATTATATTATATTA
1 TTATTATTATATTATAATA
1003690 TTATTATTA
1 TTATTATTA
1003699 AATAAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TTATTATTATATTATAATA
Found at i:1003675 original size:3 final size:3
Alignment explanation
Indices: 1003646--1003698 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
1003636 TTTGTTTTAT
* * *
1003646 TTA TTG TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA -TA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1003690 TTA TTA TTA
1 TTA TTA TTA
1003699 AATAAATAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 8 0.19
3 34 0.81
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1005192 original size:18 final size:17
Alignment explanation
Indices: 1005159--1005192 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1005149 GAATAATTAA
1005159 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
1005176 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
1005193 AAACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:1005512 original size:36 final size:37
Alignment explanation
Indices: 1005455--1005525 Score: 85
Period size: 36 Copynumber: 1.9 Consensus size: 37
1005445 CATCAGTCGA
1005455 AACAGATAAGCACACACAGTGC-TATCACATCAGAAAT
1 AACAGATAAGCACACACAGTGCAT-TCACATCAGAAAT
* *
1005492 AACA-ATATGCACAC-CAAGTGCATTCAGATCAGAA
1 AACAGATAAGCACACAC-AGTGCATTCACATCAGAA
1005526 TATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
35 1 0.03
36 24 0.80
37 5 0.17
ACGTcount: A:0.45, C:0.24, G:0.14, T:0.17
Consensus pattern (37 bp):
AACAGATAAGCACACACAGTGCATTCACATCAGAAAT
Found at i:1013178 original size:29 final size:29
Alignment explanation
Indices: 1013145--1013202 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1013135 TAAGTATAAC
1013145 TTAGTGAGACAGTAATACTAAAGGTGAAA
1 TTAGTGAGACAGTAATACTAAAGGTGAAA
1013174 TTAGTGAGACAGTAATACTAAAGGTGAAA
1 TTAGTGAGACAGTAATACTAAAGGTGAAA
1013203 ATAATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.24
Consensus pattern (29 bp):
TTAGTGAGACAGTAATACTAAAGGTGAAA
Found at i:1016484 original size:2 final size:2
Alignment explanation
Indices: 1016477--1016512 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1016467 TATATTAGTC
1016477 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
1016513 TGTTTAATTA
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:1030658 original size:26 final size:24
Alignment explanation
Indices: 1030629--1030676 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
1030619 ATTTAACATA
*
1030629 TAAAAATAAGTTAATAATATTTATAG
1 TAAAAATAAG-AAAT-ATATTTATAG
*
1030655 TAAATATAAGAAATATATTTAT
1 TAAAAATAAGAAATATATTTAT
1030677 TTCATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 3 0.15
26 9 0.45
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (24 bp):
TAAAAATAAGAAATATATTTATAG
Found at i:1037094 original size:73 final size:73
Alignment explanation
Indices: 1036975--1037121 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
1036965 GAAGATTCAG
1036975 GATCATGTATAAGACCTCTAGGCACACTACTTCCCCTCAATTACTAAACCAACTTCAAAGTTAAA
1 GATCATGTATAAGACCTCTAGGCACACTACTTCCCCTCAATTACTAAACCAACTTCAAAGTTAAA
1037040 ACTACCAA
66 ACTACCAA
1037048 GATCATGTATAAGACCTCTAGGCACACTACTTCCCCTCAATTACTAAACCAACTTCAAAGTTAAA
1 GATCATGTATAAGACCTCTAGGCACACTACTTCCCCTCAATTACTAAACCAACTTCAAAGTTAAA
1037113 ACTACCAA
66 ACTACCAA
1037121 G
1 G
1037122 GAAATTGTCC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.38, C:0.29, G:0.09, T:0.24
Consensus pattern (73 bp):
GATCATGTATAAGACCTCTAGGCACACTACTTCCCCTCAATTACTAAACCAACTTCAAAGTTAAA
ACTACCAA
Found at i:1040027 original size:16 final size:17
Alignment explanation
Indices: 1039987--1040032 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
1039977 TGTTTATAAG
* *
1039987 AGAATTGGAATCTATTA
1 AGAATTGAAATCTAGTA
1040004 AGGAATTGAAATCT-GTA
1 A-GAATTGAAATCTAGTA
1040021 AGAATTGAAATC
1 AGAATTGAAATC
1040033 CAATTCCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 11 0.42
17 4 0.15
18 11 0.42
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (17 bp):
AGAATTGAAATCTAGTA
Found at i:1040481 original size:22 final size:22
Alignment explanation
Indices: 1040453--1040507 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
1040443 CGACTCAAAA
1040453 TAATAAAAAAATTATTTTTATT
1 TAATAAAAAAATTATTTTTATT
1040475 TAATAAAAAAATTATTTTTATT
1 TAATAAAAAAATTATTTTTATT
1040497 TAATAAAAAAA
1 TAATAAAAAAA
1040508 ATTGACTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATAAAAAAATTATTTTTATT
Found at i:1040667 original size:37 final size:38
Alignment explanation
Indices: 1040625--1040706 Score: 132
Period size: 37 Copynumber: 2.2 Consensus size: 38
1040615 TTAAACCTGA
* *
1040625 ACCCGACCT-GACCCGAATATCATACTTAAAAAACTCG
1 ACCCGACCTCGACCCGAATATCACACTTAAAAAACCCG
1040662 ACCCGA-CTCGACCCGAATATCACACTTAAAAAACCCG
1 ACCCGACCTCGACCCGAATATCACACTTAAAAAACCCG
1040699 ACCCGACC
1 ACCCGACC
1040707 CGAACAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
36 2 0.05
37 38 0.93
38 1 0.02
ACGTcount: A:0.37, C:0.38, G:0.11, T:0.15
Consensus pattern (38 bp):
ACCCGACCTCGACCCGAATATCACACTTAAAAAACCCG
Found at i:1040935 original size:27 final size:28
Alignment explanation
Indices: 1040871--1040937 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
1040861 CCTAAACCCG
*
1040871 AACCCTACCCGAATATCACACTTAAAAA
1 AACCCAACCCGAATATCACACTTAAAAA
* *
1040899 AACCCGACCCGAATGTCACACTT-AAAA
1 AACCCAACCCGAATATCACACTTAAAAA
*
1040926 AATCCAACCCGA
1 AACCCAACCCGA
1040938 CCCGAACAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
27 14 0.40
28 21 0.60
ACGTcount: A:0.43, C:0.34, G:0.07, T:0.15
Consensus pattern (28 bp):
AACCCAACCCGAATATCACACTTAAAAA
Found at i:1040943 original size:32 final size:28
Alignment explanation
Indices: 1040871--1040927 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1040861 CCTAAACCCG
*
1040871 AACCCTACCCGAATATCACACTTAAAAA
1 AACCCGACCCGAATATCACACTTAAAAA
*
1040899 AACCCGACCCGAATGTCACACTTAAAAA
1 AACCCGACCCGAATATCACACTTAAAAA
1040927 A
1 A
1040928 TCCAACCCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.32, G:0.07, T:0.16
Consensus pattern (28 bp):
AACCCGACCCGAATATCACACTTAAAAA
Found at i:1041183 original size:37 final size:38
Alignment explanation
Indices: 1041105--1041184 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
1041095 TTCACCCTAA
*
1041105 ACCCGACCCGACCCGAATATCACAATTAAAAAAACCCG
1 ACCCGACCCGACCCAAATATCACAATTAAAAAAACCCG
* * *
1041143 ACCCGACTCGACCCAAATATTACACTT-AAAAAACCCG
1 ACCCGACCCGACCCAAATATCACAATTAAAAAAACCCG
1041180 ACCCG
1 ACCCG
1041185 GCCTGAACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 15 0.39
38 23 0.61
ACGTcount: A:0.40, C:0.38, G:0.10, T:0.12
Consensus pattern (38 bp):
ACCCGACCCGACCCAAATATCACAATTAAAAAAACCCG
Found at i:1041275 original size:248 final size:244
Alignment explanation
Indices: 1040624--1041391 Score: 1088
Period size: 248 Copynumber: 3.2 Consensus size: 244
1040614 CTTAAACCTG
* * *
1040624 AACCCGACCTGACCCGAATATCATACTT-AAAAAACTCGACCCGACTCGACCCGAATATCACACT
1 AACCCGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCC-AATATCACACT
*
1040688 TAAAAAACCCGACCCGACCCGAACAAAATAAAATTTCATCAGACCCGACCCGAATATATGAATTA
65 TAAAAAACCCGACCCGACCCGAACAAAATAAAATTTCATCCGACCCGACCCGAATATATGAATTA
*
1040753 GAAAT---CCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCAA
130 GAAATCACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGA
* *
1040815 CCCGACCCGAATTATATATATTTTCGAGTCGGTCCGGTTTTTTTACCCTA
195 CCCGACCCTAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTACCCTA
* *
1040865 AACCCGAACCCTACCCGAATATCACACTTAAAAAAACCCGA--C--C-CG----AATGTCACACT
1 AACCCG-ACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCAATATCACACT
* *
1040921 TAAAAAATCCAACCCGACCCGAACAAAATAAAATTTCATCCGACCCGACCCGAATATATGAATTA
65 TAAAAAACCCGACCCGACCCGAACAAAATAAAATTTCATCCGACCCGACCCGAATATATGAATTA
* *
1040986 GAAATCCGACCCGACCCAAAATAATAAAAAATTATTTTTATTTAATAAAAACGGTGACTTAATCC
130 GAAAT-C-ACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCC
* * *
1041051 GACCCAACCCTAATTATATATATTTTCGGGTCAGTCCGATTTTTTTCACCCTA
193 GACCCGACCCTAATTATATATATTTTCGGGTCGGTCCGGTTTTTTT-ACCCTA
* *
1041104 AACCCGACCCGACCCGAATATCACAATTAAAAAAACCCGACCCGACTCGACCCAAATATTACACT
1 AACCCGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCC-AATATCACACT
* * * *
1041169 TAAAAAACCCGACCCGGCCTGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATAAATTA
65 TAAAAAACCCGACCCGACCCGAACAAAATAAAATTTCATCCGACCCGACCCGAATATATGAATTA
* *
1041234 GAAATCAAACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAATGACTTAATCC
130 GAAATC--ACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCC
1041299 GACCCGA-CCTGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTACCCT-
193 GACCCGACCCT-AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTACCCTA
* *
1041350 AA----ACCTGACCCGAATATCACACTTAAAAAAACCCGATCCGAC
1 AACCCGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGAC
1041392 CCCACCAAAA
Statistics
Matches: 470, Mismatches: 37, Indels: 39
0.86 0.07 0.07
Matches are distributed among these distances:
233 77 0.16
238 127 0.27
239 13 0.03
240 1 0.00
241 7 0.01
242 57 0.12
243 12 0.03
246 2 0.00
247 9 0.02
248 165 0.35
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.24
Consensus pattern (244 bp):
AACCCGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCAATATCACACTT
AAAAAACCCGACCCGACCCGAACAAAATAAAATTTCATCCGACCCGACCCGAATATATGAATTAG
AAATCACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGAC
CCGACCCTAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTACCCTA
Found at i:1044516 original size:24 final size:23
Alignment explanation
Indices: 1044468--1044512 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1044458 ATAAAGAACC
*
1044468 AAAATAAACTTAAATATACCATA
1 AAAATAAACTTAAACATACCATA
*
1044491 AAAATAAAGTCTAAACAT-CCAT
1 AAAATAAACT-TAAACATACCAT
1044513 TAAACCTACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.58, C:0.16, G:0.02, T:0.24
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATA
Found at i:1061526 original size:22 final size:24
Alignment explanation
Indices: 1061481--1061526 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
1061471 CTAATGCATT
1061481 CAAAATCTATACTTATTATATCATA
1 CAAAATCTATAC-TATTATATCATA
*
1061506 CAAAATC-ATAC-ATTATGTCAT
1 CAAAATCTATACTATTATATCAT
1061527 GCAACCACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
24 4 0.20
25 7 0.35
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.37
Consensus pattern (24 bp):
CAAAATCTATACTATTATATCATA
Found at i:1062006 original size:23 final size:23
Alignment explanation
Indices: 1061980--1062045 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
1061970 CACCACAGCT
*
1061980 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
1062003 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1062026 CATAGAATTGCACCGTAGTG
1 CGTAGAATTGCACCGAAGTG
1062046 TCATATAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1071369 original size:81 final size:81
Alignment explanation
Indices: 1071282--1071555 Score: 318
Period size: 82 Copynumber: 3.4 Consensus size: 81
1071272 CAAAATGGTA
* * * *
1071282 ACTTTAGCGGCGTTTATT-TACAAACGCCGTAATAGGGTTAATCTATAGTGGCTTTTTTTGACAA
1 ACTTTAGCGGCGTTT-TTATACAAACGCCGTAATAGGATT-ATCTATAGTGGCGTTTTTTAATAA
*
1071346 ACGCCGCAACAGATTAGT
64 ACGCCGCAACATATTAGT
* * * *
1071364 A-TTTAGCGTCGTTTTTATACAAATGCCGCAATAGGATTCTCTTATAGTGGCGTTTTTTAATAAA
1 ACTTTAGCGGCGTTTTTATACAAACGCCGTAATAGGATTATC-TATAGTGGCGTTTTTTAATAAA
* *
1071428 TGCCGCAACATATTAGA
65 CGCCGCAACATATTAGT
* * * * *
1071445 ACTTTAGCGGCGTTTTTAAACAAACACCGTAATAGTATTTACCTATAGTGGCGTTTTTCAATAAA
1 ACTTTAGCGGCGTTTTTATACAAACGCCGTAATAGGA-TTATCTATAGTGGCGTTTTTTAATAAA
** *
1071510 CGCCATAACATAATAGT
65 CGCCGCAACATATTAGT
*
1071527 ACTTTAGCGGCGTTTCTATACAAACGCCG
1 ACTTTAGCGGCGTTTTTATACAAACGCCG
1071556 CTAAAGACTC
Statistics
Matches: 160, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
80 4 0.03
81 64 0.40
82 89 0.56
83 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (81 bp):
ACTTTAGCGGCGTTTTTATACAAACGCCGTAATAGGATTATCTATAGTGGCGTTTTTTAATAAAC
GCCGCAACATATTAGT
Found at i:1071392 original size:40 final size:40
Alignment explanation
Indices: 1071342--1071468 Score: 114
Period size: 41 Copynumber: 3.1 Consensus size: 40
1071332 GCTTTTTTTG
* *
1071342 ACAAACGCCGCAACAGATTAGTATTTAGCGTCGTTTTTAT
1 ACAAATGCCGCAACAGATTAGTATTTAGCGGCGTTTTTAT
* * * *
1071382 ACAAATGCCGCAATAGGATT-CTCTTATAGTGGCGTTTTT-T
1 ACAAATGCCGCAACA-GATTAGTATT-TAGCGGCGTTTTTAT
* * * *
1071422 AATAAATGCCGCAACATATTAGAACTTTAGCGGCGTTTTTAA
1 -ACAAATGCCGCAACAGATTAGTA-TTTAGCGGCGTTTTTAT
1071464 ACAAA
1 ACAAA
1071469 CACCGTAATA
Statistics
Matches: 66, Mismatches: 15, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
40 20 0.30
41 44 0.67
42 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (40 bp):
ACAAATGCCGCAACAGATTAGTATTTAGCGGCGTTTTTAT
Found at i:1071457 original size:41 final size:41
Alignment explanation
Indices: 1071412--1071555 Score: 119
Period size: 41 Copynumber: 3.5 Consensus size: 41
1071402 CTCTTATAGT
* * *
1071412 GGCGTTTTTTAATAAATGCCGCAACATATTAGAACTTTAGC
1 GGCGTTTTTAAATAAACGCCGTAACATATTAGAACTTTAGC
* * * * * * *
1071453 GGCGTTTTTAAACAAACACCGTAATAGTATT-TACCTATAGT
1 GGCGTTTTTAAATAAACGCCGTAACA-TATTAGAACTTTAGC
* * * *
1071494 GGCGTTTTTCAATAAACGCCATAACATAATAGTACTTTAGC
1 GGCGTTTTTAAATAAACGCCGTAACATATTAGAACTTTAGC
* * *
1071535 GGCGTTTCTATACAAACGCCG
1 GGCGTTTTTAAATAAACGCCG
1071556 CTAAAGACTC
Statistics
Matches: 75, Mismatches: 26, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
40 3 0.04
41 68 0.91
42 4 0.05
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (41 bp):
GGCGTTTTTAAATAAACGCCGTAACATATTAGAACTTTAGC
Found at i:1073532 original size:23 final size:23
Alignment explanation
Indices: 1073506--1073630 Score: 101
Period size: 23 Copynumber: 5.3 Consensus size: 23
1073496 CACCACAGCT
1073506 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
1073529 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * * *
1073552 CGTAGAATTGCATCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
1073575 TATAATAATTGCACC-AGAGTGCCG
1 CAT-ATAATTGCACCGA-AGTGCCA
* *
1073599 CGTAGAATTGCACC-ATAGTGCCA
1 CATATAATTGCACCGA-AGTGCCA
*
1073622 TATAATAAT
1 CAT-ATAAT
1073631 GTCCATAAGG
Statistics
Matches: 78, Mismatches: 21, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
23 58 0.74
24 20 0.26
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:1073595 original size:47 final size:47
Alignment explanation
Indices: 1073511--1073630 Score: 188
Period size: 47 Copynumber: 2.6 Consensus size: 47
1073501 CAGCTCATAT
* * *
1073511 AATTGCACCGAAGTGCCACAT-ATAATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCATATAATAATTGCACCAGAGTGCCGCGTAG
*
1073557 AATTGCATCGTAGTGCCATATAATAATTGCACCAGAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCATATAATAATTGCACCAGAGTGCCGCGTAG
*
1073604 AATTGCACCATAGTGCCATATAATAAT
1 AATTGCACCGTAGTGCCATATAATAAT
1073631 GTCCATAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
46 18 0.27
47 49 0.73
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.24
Consensus pattern (47 bp):
AATTGCACCGTAGTGCCATATAATAATTGCACCAGAGTGCCGCGTAG
Found at i:1073808 original size:103 final size:103
Alignment explanation
Indices: 1073637--1073957 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
1073627 TAATGTCCAT
* * *
1073637 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1073702 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1073740 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1073805 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1073843 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTATCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1073908 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1073946 AAAGACCACATA
1 AAGGACCACATA
1073958 GACCCTCGAC
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1076556 original size:42 final size:43
Alignment explanation
Indices: 1076482--1076911 Score: 444
Period size: 42 Copynumber: 10.1 Consensus size: 43
1076472 AAGGTAATTA
* * * *
1076482 GCGGCGTTTGTATCAAAAAATGTCGTTATAGAT-TTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTTGACCTTTT
*
1076525 GCGGTGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTTTT
* *
1076567 GCGGCATTTGTATCAAAAAACGCCGCTATAGAT-TTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTTGACCTTTT
* * * * * * *
1076610 ACGGCGTTTATT-CTAAAACGTCGTTATAGATCTCGATCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTTTT
* * *
1076652 GCGACGTTTGTTCCAAAAACGCTGCGATAGATC-TGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTTTT
* *
1076694 GCGGGGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTTCT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTTTT
* * ** * **
1076736 GCGGCGTTTGTTCCAAAAACACCACTGCAGATGTCAACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTTTT
** * * **
1076779 ATGGCGTTTGTTCTC-AAAACGTCGCTATAGATGTCAACCTTTT
1 GCGGCGTTTGTTC-CAAAAACGCCGCTATAGATCTTGACCTTTT
*
1076822 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTTTT
* * * *
1076865 GTGGCGTTTGTTCC-AAAACGTCGCTATAGATCTTGATCTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTTTT
1076907 GCGGC
1 GCGGC
1076912 ATTTTTTGTT
Statistics
Matches: 320, Mismatches: 59, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
41 15 0.05
42 153 0.48
43 151 0.47
44 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (43 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTTTT
Found at i:1076651 original size:85 final size:83
Alignment explanation
Indices: 1076482--1076911 Score: 446
Period size: 85 Copynumber: 5.1 Consensus size: 83
1076472 AAGGTAATTA
* * * * * *
1076482 GCGGCGTTTGTATCAAAAAATGTCGTTATAGATTTGACCTTTTGCGGTGTTTGTTCCAAAAACGC
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATTTGACCTTTTGCGGCGTTTGTT-CAAAAACGT
1076547 CGCTATAGATCTGACCTTTT
64 CGCTATAGATCTGACCTTTT
* * * * *
1076567 GCGGCATTTGTATCAAAAAACGCCGCTATAGATTTGACCTTTTACGGCGTTTATTCTAAAACGTC
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATTTGACCTTTTGCGGCGTTTGTTCAAAAACGTC
* *
1076632 GTTATAGATCTCGATCTTTT
65 GCTATAGATCT-GACCTTTT
* * * * * *
1076652 GCGACGTTTGTTCCAAAAACGCTGCGATAGATCTGACCTTTTGCGGGGTTTGTTCCAAAAACGCC
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATTTGACCTTTTGCGGCGTTTGTT-CAAAAACGTC
*
1076717 GCTATAGATCTGACCTTCT
65 GCTATAGATCTGACCTTTT
* * ** ** ** *
1076736 GCGGCGTTTGTTCCAAAAACACCACTGCAGATGTCAACCTTTTATGGCGTTTGTTCTCAAAACGT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGAT-TTGACCTTTTGCGGCGTTTGTTC-AAAAACGT
* *
1076801 CGCTATAGATGTCAACCTTTT
64 CGCTATAGATCT-GACCTTTT
* * *
1076822 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTGTGGCGTTTGTTCCAAAACGTC
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGAT-TTGACCTTTTGCGGCGTTTGTTCAAAAACGTC
* *
1076887 GCTATAGATCTTGATCTATT
65 GCTATAGATC-TGACCTTTT
1076907 GCGGC
1 GCGGC
1076912 ATTTTTTGTT
Statistics
Matches: 285, Mismatches: 54, Indels: 12
0.81 0.15 0.03
Matches are distributed among these distances:
84 86 0.30
85 143 0.50
86 56 0.20
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (83 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATTTGACCTTTTGCGGCGTTTGTTCAAAAACGTCG
CTATAGATCTGACCTTTT
Found at i:1076790 original size:43 final size:43
Alignment explanation
Indices: 1076518--1076895 Score: 329
Period size: 43 Copynumber: 8.9 Consensus size: 43
1076508 TATAGATTTG
* * * *
1076518 ACCTTTTGCGGTGTTTGTTCCAAAAACGCCGCTATAGATCT-G
1 ACCTTTTGTGGCGTTTGTTCCAAAAACGCCGCTATAGATGTCA
* * * **
1076560 ACCTTTTGCGGCATTTGTATCAAAAAACGCCGCTATAGAT-TTG
1 ACCTTTTGTGGCGTTTGT-TCCAAAAACGCCGCTATAGATGTCA
** * * * * * *
1076603 ACCTTTTACGGCGTTTATT-CTAAAACGTCGTTATAGATCTCG
1 ACCTTTTGTGGCGTTTGTTCCAAAAACGCCGCTATAGATGTCA
* * * * * * *
1076645 ATCTTTTGCGACGTTTGTTCCAAAAACGCTGCGATAGATCT-G
1 ACCTTTTGTGGCGTTTGTTCCAAAAACGCCGCTATAGATGTCA
* * * *
1076687 ACCTTTTGCGGGGTTTGTTCCAAAAACGCCGCTATAGATCT-G
1 ACCTTTTGTGGCGTTTGTTCCAAAAACGCCGCTATAGATGTCA
* * * * **
1076729 ACCTTCTGCGGCGTTTGTTCCAAAAACACCACTGCAGATGTCA
1 ACCTTTTGTGGCGTTTGTTCCAAAAACGCCGCTATAGATGTCA
* *
1076772 ACCTTTTATGGCGTTTGTTCTC-AAAACGTCGCTATAGATGTCA
1 ACCTTTTGTGGCGTTTGTTC-CAAAAACGCCGCTATAGATGTCA
* * *
1076815 ACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCG
1 ACCTTTTGTGGCGTTTGTTCCAAAAACGCCGCTATAGATGTCA
*
1076858 ACCTTTTGTGGCGTTTGTTCC-AAAACGTCGCTATAGAT
1 ACCTTTTGTGGCGTTTGTTCCAAAAACGCCGCTATAGAT
1076896 CTTGATCTAT
Statistics
Matches: 281, Mismatches: 48, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
41 15 0.05
42 124 0.44
43 141 0.50
44 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (43 bp):
ACCTTTTGTGGCGTTTGTTCCAAAAACGCCGCTATAGATGTCA
Found at i:1078525 original size:23 final size:23
Alignment explanation
Indices: 1078499--1078567 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1078489 CATCAGAGCT
* * *
1078499 CGTATAATTGCACCGAAGTGTCA
1 CGTAGAATTGCACCGTAGTGCCA
*
1078522 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAATTGCACCGTAGTGCCA
*
1078545 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAATTGCACCGTAGTGCCA
1078568 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGTAGTGCCA
Found at i:1081911 original size:76 final size:76
Alignment explanation
Indices: 1081820--1081971 Score: 277
Period size: 76 Copynumber: 2.0 Consensus size: 76
1081810 TAACACCACA
* *
1081820 GAACTATTGACATGATAGCGTTGCAGAAAGCTCTTTGGAGTAACTATTATCATAAATCAAGAGTT
1 GAACTATTAACATGATAGCATTGCAGAAAGCTCTTTGGAGTAACTATTATCATAAATCAAGAGTT
1081885 TAACATAAACT
66 TAACATAAACT
*
1081896 GAACTATTAACATGATAGCATTGCAGAAAGCTCTTTGGAGTAATTATTATCATAAATCAAGAGTT
1 GAACTATTAACATGATAGCATTGCAGAAAGCTCTTTGGAGTAACTATTATCATAAATCAAGAGTT
1081961 TAACATAAACT
66 TAACATAAACT
1081972 TAAAAGGGCT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (76 bp):
GAACTATTAACATGATAGCATTGCAGAAAGCTCTTTGGAGTAACTATTATCATAAATCAAGAGTT
TAACATAAACT
Found at i:1087202 original size:26 final size:26
Alignment explanation
Indices: 1087166--1087215 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1087156 TCAATTCTCA
*
1087166 TTAAACCACCAAAGTTAAAATCAATT
1 TTAAACCACCAAAATTAAAATCAATT
*
1087192 TTAAATCACCAAAATTAAAATCAA
1 TTAAACCACCAAAATTAAAATCAA
1087216 ATTGATGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.54, C:0.18, G:0.02, T:0.26
Consensus pattern (26 bp):
TTAAACCACCAAAATTAAAATCAATT
Found at i:1092129 original size:165 final size:164
Alignment explanation
Indices: 1091847--1092177 Score: 573
Period size: 165 Copynumber: 2.0 Consensus size: 164
1091837 ATCAAAAGAG
1091847 AGGTTAGCCATTAGTTTCATAAACATATTCATAAACATGTAATGGATAATTGGACATAATGTAAA
1 AGGTTAGCCATTAGTTTCATAAACATATTCATAAACATGTAATGGATAATTGGACATAATGTAAA
1091912 GATGCAAAATAAACACGAAATCCAAATCAAAATGTATTAAACATAATTCGAACATCCAAAAATAA
66 GATGCAAAATAAACACGAAATCCAAATCAAAATGTATTAAACATAATTCGAACATCCAAAAATAA
1091977 ACAATCC-AAAGCATTC-AAATGTTTTTAACAATA
131 ACAATCCAAAAGCATTCAAAATG-TTTTAACAATA
1092010 AGGTTAGCC-TTAGTTTCATAAACAATATTCATAAACATGTAATGGAT-ATTGGACATATATGTC
1 AGGTTAGCCATTAGTTTCATAAAC-ATATTCATAAACATGTAATGGATAATTGGACATA-ATG--
1092073 TAAAGATGCAAAATAAACACGAAATCCAAATC-AAATGTATTAAACATAAGTTCGAACATCCAAA
62 TAAAGATGCAAAATAAACACGAAATCCAAATCAAAATGTATTAAACATAA-TTCGAACATCCAAA
1092137 AATAAACAATCCAAAAGCATTCAAAATGTTTTAACAATA
126 AATAAACAATCCAAAAGCATTCAAAATGTTTTAACAATA
1092176 AG
1 AG
1092178 TTCAATTATC
Statistics
Matches: 161, Mismatches: 0, Indels: 11
0.94 0.00 0.06
Matches are distributed among these distances:
162 24 0.15
163 35 0.22
164 17 0.11
165 58 0.36
166 22 0.14
167 5 0.03
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (164 bp):
AGGTTAGCCATTAGTTTCATAAACATATTCATAAACATGTAATGGATAATTGGACATAATGTAAA
GATGCAAAATAAACACGAAATCCAAATCAAAATGTATTAAACATAATTCGAACATCCAAAAATAA
ACAATCCAAAAGCATTCAAAATGTTTTAACAATA
Found at i:1094160 original size:22 final size:22
Alignment explanation
Indices: 1094095--1094196 Score: 129
Period size: 22 Copynumber: 4.7 Consensus size: 22
1094085 AGAACCCCAG
*
1094095 GGGGGTATCGATTCCCC-T--A
1 GGGGGAATCGATTCCCCTTCAA
*
1094114 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTTC-AA
*
1094137 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
1094159 GGGGGTATCGATTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
1094181 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
1094197 TCTGCCCTAT
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
19 15 0.20
20 1 0.01
22 38 0.51
23 21 0.28
ACGTcount: A:0.18, C:0.26, G:0.31, T:0.25
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:1098050 original size:22 final size:21
Alignment explanation
Indices: 1098008--1098047 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1097998 GAGTTTATTT
*
1098008 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
1098029 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1098048 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:1107505 original size:18 final size:17
Alignment explanation
Indices: 1107484--1107531 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
1107474 AAATACCCAG
1107484 TCAGAAAAACAAACAAAA
1 TCAGAAAAACAAAC-AAA
1107502 TCAGATAAAAC-AACAAA
1 TCAGA-AAAACAAACAAA
*
1107519 TTAGAAAAACAAA
1 TCAGAAAAACAAA
1107532 ATCAGAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 5 0.19
17 9 0.33
18 8 0.30
19 5 0.19
ACGTcount: A:0.69, C:0.15, G:0.06, T:0.10
Consensus pattern (17 bp):
TCAGAAAAACAAACAAA
Found at i:1107541 original size:13 final size:14
Alignment explanation
Indices: 1107494--1107540 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 14
1107484 TCAGAAAAAC
1107494 AAACAAAATCAGATA
1 AAACAAAATCAGA-A
*
1107509 AAACAACAAATTAGAA
1 AAAC-A-AAATCAGAA
1107525 AAACAAAATCAGAA
1 AAACAAAATCAGAA
1107539 AA
1 AA
1107541 CCCCAACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.36
15 5 0.18
16 6 0.21
17 7 0.25
ACGTcount: A:0.70, C:0.13, G:0.06, T:0.11
Consensus pattern (14 bp):
AAACAAAATCAGAA
Found at i:1107553 original size:32 final size:31
Alignment explanation
Indices: 1107494--1107557 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 31
1107484 TCAGAAAAAC
1107494 AAACAAAATCAGATAAAACAACAAATTAGAA
1 AAACAAAATCAGATAAAACAACAAATTAGAA
*
1107525 AAACAAAATCAGA-AAACCCCAACAAATTAGAA
1 AAACAAAATCAGATAAA--ACAACAAATTAGAA
1107557 A
1 A
1107558 CAGATCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 3 0.10
31 13 0.43
32 14 0.47
ACGTcount: A:0.66, C:0.17, G:0.06, T:0.11
Consensus pattern (31 bp):
AAACAAAATCAGATAAAACAACAAATTAGAA
Found at i:1120928 original size:21 final size:20
Alignment explanation
Indices: 1120902--1120941 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1120892 AATTTAAACT
1120902 TTTATAATATTATTTAAATAA
1 TTTAT-ATATTATTTAAATAA
*
1120923 TTTATATCTTATTTAAATA
1 TTTATATATTATTTAAATA
1120942 TTAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTATATATTATTTAAATAA
Found at i:1122186 original size:17 final size:18
Alignment explanation
Indices: 1122152--1122184 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1122142 TTTTGTTAGT
1122152 AATTTATTTAACTATTTA
1 AATTTATTTAACTATTTA
1122170 AATTT-TTTAA-TATTT
1 AATTTATTTAACTATTT
1122185 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTATTTAACTATTTA
Done.