Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 62
Found at i:3875262 original size:21 final size:21
Alignment explanation
Indices: 3875230--3875351 Score: 107
Period size: 21 Copynumber: 6.1 Consensus size: 21
3875220 ACAGTAATAA
3875230 TAGATGAAGAGTCAAGAACAC
1 TAGATGAAGAGTCAAGAACAC
3875251 TAGAT-AAGGAGTCAAG-A-AC
1 TAGATGAA-GAGTCAAGAACAC
* ** *
3875270 -A-AT--TGA-TTGAGAACAG
1 TAGATGAAGAGTCAAGAACAC
* *
3875286 TAGATGAAGAGTCAATAACAA
1 TAGATGAAGAGTCAAGAACAC
* *
3875307 TAGATGAAGAGTCAATAACAA
1 TAGATGAAGAGTCAAGAACAC
3875328 TAGATGAAGAGTCAAGAACAC
1 TAGATGAAGAGTCAAGAACAC
3875349 TAG
1 TAG
3875352 GAGTAGATGA
Statistics
Matches: 82, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
14 3 0.04
15 3 0.04
16 1 0.01
17 3 0.04
18 3 0.04
19 2 0.02
20 5 0.06
21 62 0.76
ACGTcount: A:0.48, C:0.11, G:0.23, T:0.18
Consensus pattern (21 bp):
TAGATGAAGAGTCAAGAACAC
Found at i:3877791 original size:30 final size:30
Alignment explanation
Indices: 3877757--3878139 Score: 314
Period size: 30 Copynumber: 12.7 Consensus size: 30
3877747 ATGTATTAAA
* *
3877757 AGAAACTAAAAGGGCTAAAATAGCAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
*
3877787 AGAAACTTAAAGGAATAAAATAGCAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
3877817 AGAAACTTAAAGGACTAAAATAGCAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
* * *
3877847 AAAAACTT-AATGACTGAAATAGCAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
* * *
3877876 AGAAAGTTAAAGTACTAAAATAGAAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
* * *
3877906 AGAAACTTAAAGGACCAAAATAACAAAAAAC
1 AGAAACTTAAAGGACTAAAATAGC-AAAAAT
* * *
3877937 AGAAACTTAAAAGATCGAAAA-AGGACTAAAAT
1 AGAAACTTAAAGGA-CTAAAATA-G-CAAAAAT
* ** * * * *
3877969 AAAAAAATAGAAAG-TTAAAAGACCAAATAA-
1 AGAAACTTA-AAGGACTAAAATAGCAAA-AAT
* * *
3877999 A-AAAATATAAAAAGGACTAAAATATCAAAAAC
1 AGAAACT-T--AAAGGACTAAAATAGCAAAAAT
* * * *
3878031 ATAAAGTTAAAGGACTAAAATAACAAAAAA
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
*
3878061 AGAAACTTTAAGGACTAAAATA--AAAAA-
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
* * * **
3878088 AGACAGTTAAAGGACCAAAATAATAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
3878118 AGAAACTTAAAGGACTAAAATA
1 AGAAACTTAAAGGACTAAAATA
3878140 ATAATTACCA
Statistics
Matches: 287, Mismatches: 49, Indels: 34
0.78 0.13 0.09
Matches are distributed among these distances:
27 18 0.06
28 5 0.02
29 34 0.12
30 162 0.56
31 30 0.10
32 29 0.10
33 9 0.03
ACGTcount: A:0.63, C:0.09, G:0.12, T:0.16
Consensus pattern (30 bp):
AGAAACTTAAAGGACTAAAATAGCAAAAAT
Found at i:3878052 original size:155 final size:159
Alignment explanation
Indices: 3877795--3878093 Score: 376
Period size: 155 Copynumber: 1.9 Consensus size: 159
3877785 ATAGAAACTT
* * * *
3877795 AAAGGAATAAAATAGCAAAAATAGAAACTTAAAGGACTAAAATAGCAAAAATAAAAACTTAATGA
1 AAAGGAATAAAATAGAAAAAATAGAAACTTAAAAGACTAAAATAGAAAAAATAAAAA--TAAGGA
* * * *
3877860 CTGAAATAGCAAAAATAGAAAGTTAAAGTACTAAAATAGA-AAAAATAGAAACTTAAAGGACCAA
64 CTAAAATAGCAAAAACAGAAAGTTAAAGGACTAAAATA-ACAAAAAAAGAAACTTAAAGGACCAA
3877924 AATAACAAAAA-ACAGAAACTTAAAAGATCGAA
128 AATAA-AAAAAGACAGAAACTTAAAAGATCGAA
* * * *
3877956 AAAGGACTAAAATA-AAAAAATAGAAAGTTAAAAGAC-CAAATA-AAAAAATATAAA-AAGGACT
1 AAAGGAATAAAATAGAAAAAATAGAAACTTAAAAGACTAAAATAGAAAAAATAAAAATAAGGACT
* * * *
3878017 AAAATATCAAAAACATAAAGTTAAAGGACTAAAATAACAAAAAAAGAAACTTTAAGGACTAAAAT
66 AAAATAGCAAAAACAGAAAGTTAAAGGACTAAAATAACAAAAAAAGAAACTTAAAGGACCAAAAT
3878082 AAAAAAAGACAG
131 AAAAAAAGACAG
3878094 TTAAAGGACC
Statistics
Matches: 120, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
154 6 0.05
155 67 0.56
158 10 0.08
159 5 0.04
160 19 0.16
161 13 0.11
ACGTcount: A:0.64, C:0.09, G:0.12, T:0.16
Consensus pattern (159 bp):
AAAGGAATAAAATAGAAAAAATAGAAACTTAAAAGACTAAAATAGAAAAAATAAAAATAAGGACT
AAAATAGCAAAAACAGAAAGTTAAAGGACTAAAATAACAAAAAAAGAAACTTAAAGGACCAAAAT
AAAAAAAGACAGAAACTTAAAAGATCGAA
Found at i:3878086 original size:57 final size:54
Alignment explanation
Indices: 3877957--3878140 Score: 194
Period size: 57 Copynumber: 3.3 Consensus size: 54
3877947 AAGATCGAAA
* * *
3877957 AAGGACTAAAATAAAAAAATAGAAAGTTAAAAGACCAAATAAAAAAATATAAA---
1 AAGGACTAAAATAAAAAAAT--AAAGTTAAAGGACAAAATAAAAAAATAGAAACTT
*
3878010 AAGGACTAAAATATCAAAAACATAAAGTTAAAGGACTAAAATAACAAAAAAAGAAACTTT
1 AAGGACTAAAATA--AAAAA-ATAAAGTTAAAGGAC-AAAATAA-AAAAATAGAAAC-TT
* *
3878070 AAGGACTAAAATAAAAAAAGACAGTTAAAGGACCAAAATAATAAAAATAGAAACTT
1 AAGGACTAAAATAAAAAAATAAAGTTAAAGGA-CAAAATAA-AAAAATAGAAACTT
3878126 AAAGGACTAAAATAA
1 -AAGGACTAAAATAA
3878141 TAATTACCAA
Statistics
Matches: 112, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
53 13 0.12
54 12 0.11
55 11 0.10
56 13 0.12
57 44 0.39
58 6 0.05
60 13 0.12
ACGTcount: A:0.65, C:0.08, G:0.11, T:0.16
Consensus pattern (54 bp):
AAGGACTAAAATAAAAAAATAAAGTTAAAGGACAAAATAAAAAAATAGAAACTT
Found at i:3878108 original size:87 final size:83
Alignment explanation
Indices: 3877956--3878140 Score: 210
Period size: 87 Copynumber: 2.2 Consensus size: 83
3877946 AAAGATCGAA
* * * * * *
3877956 AAAGGACTAAAATAAAAAAATAGAAAGTTAAAAGACCAAATAAAAAAATATAAAAAGGACTAAAA
1 AAAGGACTAAAATAAAAAAAAAGAAACTTAAAAGACAAAATAAAAAAAGACAAAAAGGACCAAAA
* *
3878021 T-ATCAAAAACATAAAGTT
66 TAAT-AAAAACAGAAACTT
* * *
3878039 AAAGGACTAAAATAACAAAAAAAGAAACTTTAAGGACTAAAATAAAAAAAGACAGTTAAAGGACC
1 AAAGGACTAAAATAA-AAAAAAAGAAACTTAAAAGAC-AAAATAAAAAAAGACA--AAAAGGACC
*
3878104 AAAATAATAAAAATAGAAACTT
62 AAAATAATAAAAACAGAAACTT
3878126 AAAGGACTAAAATAA
1 AAAGGACTAAAATAA
3878141 TAATTACCAA
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
83 15 0.18
84 17 0.20
85 13 0.15
87 38 0.45
88 2 0.02
ACGTcount: A:0.65, C:0.08, G:0.11, T:0.16
Consensus pattern (83 bp):
AAAGGACTAAAATAAAAAAAAAGAAACTTAAAAGACAAAATAAAAAAAGACAAAAAGGACCAAAA
TAATAAAAACAGAAACTT
Found at i:3878712 original size:74 final size:75
Alignment explanation
Indices: 3878591--3878740 Score: 293
Period size: 74 Copynumber: 2.0 Consensus size: 75
3878581 CTGTTGAAAC
3878591 GACGTCATTTCGTTAGGGACATATAAGCCCAAAAATCGGGCTTCAACTATCATCTTCACTGA-TT
1 GACGTCATTTCGTTAGGGACATATAAGCCCAAAAATCGGGCTTCAACTATCATCTTCACTGATTT
3878655 TTTTCTCTTT
66 TTTTCTCTTT
3878665 GACGTCATTTCGTTAGGGACATATAAGCCCAAAAATCGGGCTTCAACTATCATCTTCACTGATTT
1 GACGTCATTTCGTTAGGGACATATAAGCCCAAAAATCGGGCTTCAACTATCATCTTCACTGATTT
3878730 TTTTCTCTTT
66 TTTTCTCTTT
3878740 G
1 G
3878741 CTTCAGAAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 62 0.83
75 13 0.17
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (75 bp):
GACGTCATTTCGTTAGGGACATATAAGCCCAAAAATCGGGCTTCAACTATCATCTTCACTGATTT
TTTTCTCTTT
Found at i:3879395 original size:21 final size:21
Alignment explanation
Indices: 3879371--3879414 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3879361 GGTTTGGGCT
3879371 GGGTCGAATCGACCATGGGTC
1 GGGTCGAATCGACCATGGGTC
* * *
3879392 GGGTCGGATCGGCCATGGTTC
1 GGGTCGAATCGACCATGGGTC
3879413 GG
1 GG
3879415 TTTGAGTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.43, T:0.20
Consensus pattern (21 bp):
GGGTCGAATCGACCATGGGTC
Found at i:3880281 original size:220 final size:223
Alignment explanation
Indices: 3879882--3880338 Score: 627
Period size: 220 Copynumber: 2.1 Consensus size: 223
3879872 CAGCTTATAT
3879882 GTGATGAAGAGGTATGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGCGATGAGGACGAC
1 GTGATGAAGAGGTATGGCCATCTTTAGGAAGGGCGATAACAC-GTTCCTACGCGATGAGGACGAC
* * *
3879947 TGGTTATATAGGGTGACATGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGCTAC
65 TGATTATATAGGGTGACATGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGCTAC
* * * * *
3880012 TACATGAAGAGGATAATATGCCATCTTTAGGGATGATAACACAGTTCCTACGTGATGAGGACGAC
130 TACATGAAGAGGATAATAGGCCATCTTTAGGGATGATAACACAGTTCCTACATGATAAAGACAAC
* *
3880077 TGGTTATC-AGGGGTGACACGGCTCCTAC
195 TGGTTATCTAAGGGTGACACGCCTCCTAC
* * *
3880105 GTGATGAAGAGTTCTGGCTATCTTTAGGAAGGGCGAT-A-A-GTTCCTACGCGATGAGGACGACT
1 GTGATGAAGAGGTATGGCCATCTTTAGGAAGGGCGATAACACGTTCCTACGCGATGAGGACGACT
* * * * *
3880167 GATTATCTAAGGGTGACACT-GCTCCTACGTGATTAGGAGGTCTGGTCGGGGGATGACTCAGTTC
66 GATTATAT-AGGGTGACA-TGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGCTA
* * ** * *
3880231 CTACGTGATGAGGATGGTAGGCCATCTTTAGGGATGGTAACACGGTTCCTACATGATAAAGACAA
129 CTACATGAAGAGGATAATAGGCCATCTTTAGGGATGATAACACAGTTCCTACATGATAAAGACAA
3880296 CTGGTTATCTAAGGGTGACACGCCTCCTAC
194 CTGGTTATCTAAGGGTGACACGCCTCCTAC
*
3880326 GTGATGAGGAGGT
1 GTGATGAAGAGGT
3880339 TTGGTCGGGG
Statistics
Matches: 205, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
219 29 0.14
220 110 0.54
221 31 0.15
222 1 0.00
223 34 0.17
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (223 bp):
GTGATGAAGAGGTATGGCCATCTTTAGGAAGGGCGATAACACGTTCCTACGCGATGAGGACGACT
GATTATATAGGGTGACATGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGCTACT
ACATGAAGAGGATAATAGGCCATCTTTAGGGATGATAACACAGTTCCTACATGATAAAGACAACT
GGTTATCTAAGGGTGACACGCCTCCTAC
Found at i:3880498 original size:31 final size:32
Alignment explanation
Indices: 3880463--3880522 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
3880453 GGAGACAAAA
* *
3880463 TTTGTTTCAAGGGAAAC-GACTCAAAGATGGT
1 TTTGTTTAAAGAGAAACAGACTCAAAGATGGT
3880494 TTTGTTTAAAGAGAAACAGACTCAAAGAT
1 TTTGTTTAAAGAGAAACAGACTCAAAGAT
3880523 TTTCCTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (32 bp):
TTTGTTTAAAGAGAAACAGACTCAAAGATGGT
Found at i:3880583 original size:66 final size:62
Alignment explanation
Indices: 3880505--3880665 Score: 216
Period size: 62 Copynumber: 2.5 Consensus size: 62
3880495 TTGTTTAAAG
* *
3880505 AGAAACAGACTCAAAGATTTTCCTTCAAAAGATATTGTCTCA-AGAGAGATAAAATTTCATTTCC
1 AGAAACAAACTCAAAGATTTTTCTTCAAAAGA-A---TCTCAGA-AGAGATAAAATTTCATTTCC
3880569 AA
61 AA
**
3880571 AGAAACAAACTCAAAGATTTTTCTTCAAAAGAATCTCAGAAGAGATAAAATTTTGTTTCCAA
1 AGAAACAAACTCAAAGATTTTTCTTCAAAAGAATCTCAGAAGAGATAAAATTTCATTTCCAA
* *
3880633 AAAAACATACTCAAAGATTTTTCTTCAAAAGAA
1 AGAAACAAACTCAAAGATTTTTCTTCAAAAGAA
3880666 ACTATCACAA
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
62 56 0.64
63 1 0.01
65 1 0.01
66 30 0.34
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.29
Consensus pattern (62 bp):
AGAAACAAACTCAAAGATTTTTCTTCAAAAGAATCTCAGAAGAGATAAAATTTCATTTCCAA
Found at i:3880601 original size:29 final size:29
Alignment explanation
Indices: 3880569--3880667 Score: 76
Period size: 29 Copynumber: 3.3 Consensus size: 29
3880559 TTTCATTTCC
3880569 AAAGAAACAAACTCAAAGATTTTTCTTCA
1 AAAGAAACAAACTCAAAGATTTTTCTTCA
* *** *
3880598 AAAGAATCTCAGAAGAGATAAAATTTTGT-TTCCA
1 AAAGAA--ACA-AACTCA-AAGATTTT-TCTT-CA
*
3880632 AAA-AAACATACTCAAAGATTTTTCTTCA
1 AAAGAAACAAACTCAAAGATTTTTCTTCA
3880660 AAAGAAAC
1 AAAGAAAC
3880668 TATCACAAGA
Statistics
Matches: 51, Mismatches: 11, Indels: 16
0.65 0.14 0.21
Matches are distributed among these distances:
28 6 0.12
29 19 0.37
30 2 0.04
31 4 0.08
32 3 0.06
33 11 0.22
34 6 0.12
ACGTcount: A:0.48, C:0.15, G:0.09, T:0.27
Consensus pattern (29 bp):
AAAGAAACAAACTCAAAGATTTTTCTTCA
Found at i:3880817 original size:37 final size:39
Alignment explanation
Indices: 3880744--3880823 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 39
3880734 TTTCTTAAGA
* * *
3880744 GAGACAAAAATTTTATTTTGAGTAAAAATTGTCTCAATC
1 GAGACAAAAATTTGATTTTAAGTAAAAATTGTCTCAAGC
* *
3880783 GAGAC-AAAATTTGCTTTTAAG-AAAACTTGTCTCAAGC
1 GAGACAAAAATTTGATTTTAAGTAAAAATTGTCTCAAGC
3880820 GAGA
1 GAGA
3880824 TGACACTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 18 0.50
38 13 0.36
39 5 0.14
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.31
Consensus pattern (39 bp):
GAGACAAAAATTTGATTTTAAGTAAAAATTGTCTCAAGC
Found at i:3881173 original size:16 final size:16
Alignment explanation
Indices: 3881152--3881192 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3881142 TTCATGTATC
*
3881152 ATGTATGTATA-TGTTG
1 ATGTATGT-TAGTATTG
3881168 ATGTATGTTAGTATTG
1 ATGTATGTTAGTATTG
3881184 ATGTATGTT
1 ATGTATGTT
3881193 TTCTCGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.09
16 21 0.91
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (16 bp):
ATGTATGTTAGTATTG
Found at i:3886695 original size:30 final size:30
Alignment explanation
Indices: 3886661--3887102 Score: 401
Period size: 30 Copynumber: 14.7 Consensus size: 30
3886651 TTATATTAAA
* **
3886661 AGAAACTTGAAGGGGTAAAATAGCAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
* *
3886691 AGAAACTTAAAGGA-TGAAAATAGTAAAAAC
1 AGAAACTTAAAGGACT-AAAATAGCAAAAAT
* *
3886721 AAAAACTTAAAGGACTAAAATAGAAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
3886751 AGAAACTTAAA-GACTAAAATAGCAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
* * *
3886780 AGAAAGTTAAAGGTCTAAAATAGAAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
3886810 AGAAACTTAAAGGACTAAAATAGCAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
* ** *
3886840 AAAAACTTAAAGGACTAAAATAATAAAAAA
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
* * *
3886870 AGAAAGTTCAAA-GACCAAAATAACAAAAAT
1 AGAAACTT-AAAGGACTAAAATAGCAAAAAT
* *
3886900 A-AAACTTAAAAGACTAAAAT-GATAAAAAT
1 AGAAACTTAAAGGACTAAAATAG-CAAAAAT
* * * *
3886929 AAAAAGTTAAAGGACCAAAATAACAAAAAAAT
1 AGAAACTTAAAGGACTAAAATAGC--AAAAAT
* *
3886961 ATAAACTTAAAGGACTAAAATATCAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
* * * * * *
3886991 TGAAAGTTAAAGGACCAAAATAACAAACAC
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
* * *
3887021 AAAAACTTAAAGGACTAAAATAACAAAAAC
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
* * * * *
3887051 ATATAGTTAAAGGACCATAATAATA-AAAAAAC
1 AGAAACTTAAAGGA-C-TAA-AATAGCAAAAAT
* *
3887083 AGAAATTTAAAAGACTAAAA
1 AGAAACTTAAAGGACTAAAA
3887103 CAATAATTAC
Statistics
Matches: 342, Mismatches: 57, Indels: 27
0.80 0.13 0.06
Matches are distributed among these distances:
28 3 0.01
29 50 0.15
30 234 0.68
31 6 0.02
32 45 0.13
33 4 0.01
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.17
Consensus pattern (30 bp):
AGAAACTTAAAGGACTAAAATAGCAAAAAT
Found at i:3886790 original size:89 final size:90
Alignment explanation
Indices: 3886676--3887064 Score: 398
Period size: 89 Copynumber: 4.3 Consensus size: 90
3886666 CTTGAAGGGG
* * *
3886676 TAAAATAGCAAAAATAGAAACTTAAAGGATGAAAATAGTAAAAACAAAAACTTAAAGGACTAAAA
1 TAAAATAACAAAAATAGAAAGTTAAAGGAT-AAAATAGTAAAAATAAAAACTTAAAGGACTAAAA
*
3886741 TAGA-AAAAATAGAAACTTAAA-GAC
65 TAGACAAAAATAAAAACTTAAAGGAC
* * * *
3886765 TAAAATAGCAAAAATAGAAAGTTAAAGGTCTAAAATAGAAAAAATAGAAACTTAAAGGACTAAAA
1 TAAAATAACAAAAATAGAAAGTTAAAGG-ATAAAATAGTAAAAATAAAAACTTAAAGGACTAAAA
3886830 TAG-CAAAAATAAAAACTTAAAGGAC
65 TAGACAAAAATAAAAACTTAAAGGAC
* * * ** *
3886855 TAAAATAATAAAAAAAGAAAGTTCAAA-GACCAAAATAACAAAAAT-AAAACTTAAAAGACTAAA
1 TAAAATAACAAAAATAGAAAGTT-AAAGGA-TAAAATAGTAAAAATAAAAACTTAAAGGACTAAA
* *
3886918 AT-GATAAAAATAAAAAGTTAAAGGAC
64 ATAGACAAAAATAAAAACTTAAAGGAC
* * * ** * *
3886944 CAAAATAACAAAAAAATATAAACTTAAAGGACTAAAATA-TCAAAAATTGAAAGTTAAAGGACCA
1 TAAAATAAC--AAAAATAGAAAGTTAAAGGA-TAAAATAGT-AAAAATAAAAACTTAAAGGACTA
* *
3887008 AAATA-ACAAACACAAAAACTTAAAGGAC
62 AAATAGACAAAAATAAAAACTTAAAGGAC
* * *
3887036 TAAAATAACAAAAACATATAGTTAAAGGA
1 TAAAATAACAAAAATAGAAAGTTAAAGGA
3887065 CCATAATAAT
Statistics
Matches: 252, Mismatches: 36, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
88 1 0.00
89 122 0.48
90 57 0.23
91 29 0.12
92 43 0.17
ACGTcount: A:0.63, C:0.09, G:0.11, T:0.17
Consensus pattern (90 bp):
TAAAATAACAAAAATAGAAAGTTAAAGGATAAAATAGTAAAAATAAAAACTTAAAGGACTAAAAT
AGACAAAAATAAAAACTTAAAGGAC
Found at i:3888313 original size:21 final size:21
Alignment explanation
Indices: 3888289--3888328 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3888279 GGCCAGGTTG
3888289 GATCGACCATAGGTCGGGTCA
1 GATCGACCATAGGTCGGGTCA
* *
3888310 GATCGGCCATGGGTCGGGT
1 GATCGACCATAGGTCGGGT
3888329 TGAGTGTTGT
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:0.17, C:0.23, G:0.40, T:0.20
Consensus pattern (21 bp):
GATCGACCATAGGTCGGGTCA
Found at i:3888529 original size:3 final size:3
Alignment explanation
Indices: 3888523--3888590 Score: 122
Period size: 3 Copynumber: 23.3 Consensus size: 3
3888513 GTAGTAGTAG
3888523 TAA TAA TAA TAA 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 TAA TAA TAA TAA
3888571 TAA TAA T-A TAA TAA -AA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
3888591 TTTTTGGTAG
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.06
3 59 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3889601 original size:18 final size:20
Alignment explanation
Indices: 3889578--3889620 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
3889568 AATAAATGAA
3889578 CATCGAATGCA-A-GGAGTG
1 CATCGAATGCATAGGGAGTG
3889596 CATCG-ATGCATAGGGAGTG
1 CATCGAATGCATAGGGAGTG
3889615 CATCGA
1 CATCGA
3889621 TACACCCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.23
18 6 0.27
19 11 0.50
ACGTcount: A:0.30, C:0.19, G:0.33, T:0.19
Consensus pattern (20 bp):
CATCGAATGCATAGGGAGTG
Found at i:3891065 original size:93 final size:93
Alignment explanation
Indices: 3890968--3891152 Score: 352
Period size: 93 Copynumber: 2.0 Consensus size: 93
3890958 AAGTTATAAA
*
3890968 AGTATATGTTTATGAGAAAATATAAGAATAAGTTATAAGCCATGTGATATGTGATTTATATGGAA
1 AGTATATATTTATGAGAAAATATAAGAATAAGTTATAAGCCATGTGATATGTGATTTATATGGAA
3891033 TTGTTCTACGTGCAAGTGATTATATGCG
66 TTGTTCTACGTGCAAGTGATTATATGCG
*
3891061 AGTATATATTTATGAGAAAATATAAGAATAAGTTATAAGTCATGTGATATGTGATTTATATGGAA
1 AGTATATATTTATGAGAAAATATAAGAATAAGTTATAAGCCATGTGATATGTGATTTATATGGAA
3891126 TTGTTCTACGTGCAAGTGATTATATGC
66 TTGTTCTACGTGCAAGTGATTATATGC
3891153 ATAATTCATC
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.37
Consensus pattern (93 bp):
AGTATATATTTATGAGAAAATATAAGAATAAGTTATAAGCCATGTGATATGTGATTTATATGGAA
TTGTTCTACGTGCAAGTGATTATATGCG
Found at i:3891394 original size:18 final size:18
Alignment explanation
Indices: 3891371--3891405 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3891361 AGGGATTATC
3891371 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
3891389 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
3891406 AATATTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:3895014 original size:11 final size:11
Alignment explanation
Indices: 3894998--3895032 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
3894988 ATAAGCTTGA
*
3894998 TTGAAATCTGT
1 TTGAAATCTGG
3895009 TTGAAATCTGG
1 TTGAAATCTGG
3895020 TTGAAATCTGG
1 TTGAAATCTGG
3895031 TT
1 TT
3895033 TATTGGTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.43
Consensus pattern (11 bp):
TTGAAATCTGG
Found at i:3896831 original size:27 final size:27
Alignment explanation
Indices: 3896750--3896819 Score: 140
Period size: 27 Copynumber: 2.6 Consensus size: 27
3896740 TAATATTGTT
3896750 GATTTATAACAAAATGGTCATTATATC
1 GATTTATAACAAAATGGTCATTATATC
3896777 GATTTATAACAAAATGGTCATTATATC
1 GATTTATAACAAAATGGTCATTATATC
3896804 GATTTATAACAAAATG
1 GATTTATAACAAAATG
3896820 ATCACTCTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (27 bp):
GATTTATAACAAAATGGTCATTATATC
Found at i:3897447 original size:9 final size:9
Alignment explanation
Indices: 3897433--3897463 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3897423 CAAAGAAAGG
3897433 AGAAGAAAA
1 AGAAGAAAA
*
3897442 AGAAGAAGA
1 AGAAGAAAA
3897451 AGAAGAAAA
1 AGAAGAAAA
3897460 AGAA
1 AGAA
3897464 TGGTTTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (9 bp):
AGAAGAAAA
Found at i:3903371 original size:22 final size:22
Alignment explanation
Indices: 3903327--3903371 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3903317 CACTGTTTAT
* *
3903327 TATATATGATGTTTATCATGAA
1 TATATAAGATGTTTATCACGAA
*
3903349 TATATAAGATGTTTATTACGAA
1 TATATAAGATGTTTATCACGAA
3903371 T
1 T
3903372 GTTATTTCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (22 bp):
TATATAAGATGTTTATCACGAA
Found at i:3903595 original size:59 final size:59
Alignment explanation
Indices: 3903526--3903649 Score: 167
Period size: 59 Copynumber: 2.1 Consensus size: 59
3903516 ATTCGGGATT
* * *
3903526 GCACTTAAGTATAACTAGTGCAAATGGTCGGCACGACCTTATGTATCATATTCAGGCTA
1 GCACTAAAGTATAACTAGTGCAAATGGTCGGCACGACCTCATCTATCATATTCAGGCTA
** * * * *
3903585 GCACTAAAGTATAACTAGTGCTGATGGTGGGCACGACCTCATCTGTCATATTCGGGTTA
1 GCACTAAAGTATAACTAGTGCAAATGGTCGGCACGACCTCATCTATCATATTCAGGCTA
3903644 GCACTA
1 GCACTA
3903650 CGGTGCATGC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (59 bp):
GCACTAAAGTATAACTAGTGCAAATGGTCGGCACGACCTCATCTATCATATTCAGGCTA
Found at i:3904689 original size:3 final size:3
Alignment explanation
Indices: 3904681--3904766 Score: 172
Period size: 3 Copynumber: 28.7 Consensus size: 3
3904671 TGATGTTTAA
3904681 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3904729 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3904767 CAACTAGATA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3909901 original size:22 final size:22
Alignment explanation
Indices: 3909857--3909901 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3909847 CATTGTTTAT
* *
3909857 TATATATGATGTTTATCATGAA
1 TATATAAGATGTTTATCACGAA
*
3909879 TATATAAGATGTTTATTACGAA
1 TATATAAGATGTTTATCACGAA
3909901 T
1 T
3909902 GTTATTTCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (22 bp):
TATATAAGATGTTTATCACGAA
Found at i:3917157 original size:21 final size:21
Alignment explanation
Indices: 3917083--3917162 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 21
3917073 CATTTTCCTG
**
3917083 AAGGGATCGATATTTTTGAGC
1 AAGGGATCGATCCTTTTGAGC
* *
3917104 AAGGGATCGATCC-TTTGCGTA
1 AAGGGATCGATCCTTTTGAG-C
3917125 AAGGGATCGATCCTTTTGAGC
1 AAGGGATCGATCCTTTTGAGC
* *
3917146 AATGGATCGATCATTTT
1 AAGGGATCGATCCTTTT
3917163 CCTAAAGAGA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 5 0.10
21 39 0.80
22 5 0.10
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (21 bp):
AAGGGATCGATCCTTTTGAGC
Found at i:3917169 original size:42 final size:42
Alignment explanation
Indices: 3917065--3917204 Score: 172
Period size: 42 Copynumber: 3.3 Consensus size: 42
3917055 AGTGAGTTTG
* * ** *
3917065 GGATTGATCATTTTCCTGAAGGGATCGATATTTTTGAGCAAG
1 GGATCGATCATTTTCCTAAAGGGATCGATCCTTTTGAGCAAT
* * *
3917107 GGATCGATCCTTTGCGTAAAGGGATCGATCCTTTTGAGCAAT
1 GGATCGATCATTTTCCTAAAGGGATCGATCCTTTTGAGCAAT
* * *
3917149 GGATCGATCATTTTCCTAAAGAGATCAATCCTTTTGAGAAAT
1 GGATCGATCATTTTCCTAAAGGGATCGATCCTTTTGAGCAAT
*
3917191 TGATCGATCATTTT
1 GGATCGATCATTTT
3917205 TATAAAGAAT
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 83 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (42 bp):
GGATCGATCATTTTCCTAAAGGGATCGATCCTTTTGAGCAAT
Found at i:3919865 original size:34 final size:34
Alignment explanation
Indices: 3919825--3919899 Score: 114
Period size: 34 Copynumber: 2.2 Consensus size: 34
3919815 GAGAAAAGGT
* * *
3919825 GAAGAAATAATCTTGATTGAATAGAGAAAATCTA
1 GAAGAAACAATCTTGATTGAAGAGAGAAAATCAA
3919859 GAAGAAACAATCTTGATTGAAGAGAGAAAATCAA
1 GAAGAAACAATCTTGATTGAAGAGAGAAAATCAA
*
3919893 TAAGAAA
1 GAAGAAA
3919900 GGAGTAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.53, C:0.07, G:0.19, T:0.21
Consensus pattern (34 bp):
GAAGAAACAATCTTGATTGAAGAGAGAAAATCAA
Found at i:3920045 original size:13 final size:13
Alignment explanation
Indices: 3920027--3920074 Score: 96
Period size: 13 Copynumber: 3.7 Consensus size: 13
3920017 AGGAACGATT
3920027 AATGAAAATTAGA
1 AATGAAAATTAGA
3920040 AATGAAAATTAGA
1 AATGAAAATTAGA
3920053 AATGAAAATTAGA
1 AATGAAAATTAGA
3920066 AATGAAAAT
1 AATGAAAAT
3920075 AAGGAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
AATGAAAATTAGA
Found at i:3926478 original size:22 final size:22
Alignment explanation
Indices: 3926436--3926478 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3926426 TTCAAGTTGT
**
3926436 AAGATGTTCCCAACCGTCATGG
1 AAGATGTTCCCAACCACCATGG
3926458 AAGATGTTCCCAACCACCATG
1 AAGATGTTCCCAACCACCATG
3926479 CAACCTTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (22 bp):
AAGATGTTCCCAACCACCATGG
Found at i:3933493 original size:13 final size:13
Alignment explanation
Indices: 3933475--3933499 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3933465 AAATAAAGAA
3933475 TTTATTATTTTTT
1 TTTATTATTTTTT
3933488 TTTATTATTTTT
1 TTTATTATTTTT
3933500 ATTATTCATA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTATTATTTTTT
Found at i:3941799 original size:15 final size:15
Alignment explanation
Indices: 3941765--3941824 Score: 84
Period size: 15 Copynumber: 3.9 Consensus size: 15
3941755 CTGACCCGCT
*
3941765 GACCCGTGTCTGACCC
1 GACCCG-GTCCGACCC
* *
3941781 GACCTGGTCCGATCC
1 GACCCGGTCCGACCC
3941796 GACCCGGTCCGACCC
1 GACCCGGTCCGACCC
3941811 GACCCGGTCCGACC
1 GACCCGGTCCGACC
3941825 GTTGATTGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
15 34 0.87
16 5 0.13
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
GACCCGGTCCGACCC
Found at i:3945572 original size:16 final size:16
Alignment explanation
Indices: 3945551--3945594 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
3945541 CGATTAAGCG
3945551 CTGAATGATTCAAATA
1 CTGAATGATTCAAATA
*
3945567 CTGAATAATTCAAATA
1 CTGAATGATTCAAATA
3945583 CTGAATGATTCA
1 CTGAATGATTCA
3945595 GAGGCTCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (16 bp):
CTGAATGATTCAAATA
Found at i:3951501 original size:25 final size:23
Alignment explanation
Indices: 3951441--3951496 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
3951431 ATAGCCTCTT
*
3951441 GAGAGAGAATGAGCGCGTAGGAA
1 GAGAGAGAATGAGCACGTAGGAA
3951464 GAGAGAGAATGAGCACGTAGGAA
1 GAGAGAGAATGAGCACGTAGGAA
3951487 GAGAGAGAAT
1 GAGAGAGAAT
3951497 TTGAGAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.43, C:0.07, G:0.41, T:0.09
Consensus pattern (23 bp):
GAGAGAGAATGAGCACGTAGGAA
Found at i:3963365 original size:24 final size:23
Alignment explanation
Indices: 3963324--3963387 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
3963314 GTTAGATTGT
3963324 AAAATAAAAAAATAAATATGAA-A
1 AAAATAAAAAAATAAATAT-AATA
*
3963347 AAAATAAAAAATATTAATATAATA
1 AAAATAAAAAA-ATAAATATAATA
*
3963371 ATAATAAAATAAATAAA
1 AAAATAAAA-AAATAAA
3963388 ATACATAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 13 0.37
24 20 0.57
25 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (23 bp):
AAAATAAAAAAATAAATATAATA
Found at i:3963370 original size:11 final size:11
Alignment explanation
Indices: 3963326--3963434 Score: 52
Period size: 10 Copynumber: 9.9 Consensus size: 11
3963316 TAGATTGTAA
*
3963326 AATAAAAAAAT
1 AATAATAAAAT
*
3963337 AA-ATATGAAAAA
1 AATA-AT-AAAAT
3963349 AATAA-AAAAT
1 AATAATAAAAT
* *
3963359 ATTAATATAAT
1 AATAATAAAAT
3963370 AATAATAAAAT
1 AATAATAAAAT
3963381 -A-AATAAAAT
1 AATAATAAAAT
3963390 ACATAGATAAAGAT
1 A-ATA-ATAAA-AT
3963404 -A-AATAAAATT
1 AATAATAAAA-T
* *
3963414 GAGTAAGAAAA-
1 -AATAATAAAAT
3963425 AATAATAAAA
1 AATAATAAAA
3963435 AAAAGGATTA
Statistics
Matches: 74, Mismatches: 11, Indels: 27
0.66 0.10 0.24
Matches are distributed among these distances:
9 9 0.12
10 24 0.32
11 18 0.24
12 9 0.12
13 12 0.16
14 2 0.03
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.23
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:3963409 original size:23 final size:20
Alignment explanation
Indices: 3963344--3963412 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 20
3963334 AATAAATATG
*
3963344 AAAAAAATAA-AAAATATTAAT
1 AAAATAATAATAAAATA--AAT
*
3963365 ATAATAATAATAAAATAAAT
1 AAAATAATAATAAAATAAAT
3963385 AAAATACATAGATAAAGATAAAT
1 AAAATA-ATA-ATAAA-ATAAAT
3963408 AAAAT
1 AAAAT
3963413 TGAGTAAGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 8 0.20
21 11 0.27
22 11 0.27
23 11 0.27
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (20 bp):
AAAATAATAATAAAATAAAT
Found at i:3964592 original size:17 final size:17
Alignment explanation
Indices: 3964570--3964610 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
3964560 GTAGGTTTTT
*
3964570 TAGTGGTGAGATGAGGG
1 TAGTGGTGAGATGAGGA
*
3964587 TAGTGGTGAGATGATGA
1 TAGTGGTGAGATGAGGA
3964604 TAGTGGT
1 TAGTGGT
3964611 TAGGTTTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.46, T:0.29
Consensus pattern (17 bp):
TAGTGGTGAGATGAGGA
Found at i:3965176 original size:60 final size:61
Alignment explanation
Indices: 3965102--3965267 Score: 226
Period size: 66 Copynumber: 2.7 Consensus size: 61
3965092 GAAGTTGAGT
*
3965102 TTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATC-ATTGTTTCAACAAATTGGC
1 TTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATCAATTGCTTCAACAAATTGGC
* * * *
3965162 TTTGAGTTGAATATCATTCGTTGTGAAATTGAAATCTAATCTTAAATATTGCTTCACCAAATTGG
1 TTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATC----A-ATTGCTTCAACAAATTGG
3965227 C
61 C
*
3965228 TTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAAT
1 TTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAAT
3965268 TTTGAGTAAG
Statistics
Matches: 91, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
60 38 0.42
66 53 0.58
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (61 bp):
TTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATCAATTGCTTCAACAAATTGGC
Found at i:3966169 original size:85 final size:85
Alignment explanation
Indices: 3966000--3966238 Score: 311
Period size: 85 Copynumber: 2.8 Consensus size: 85
3965990 ATGTGTTGTC
* * * ** *
3966000 GAGCTGAATGGAATCGGACTCGACAGTTTTTTGTTGACAGATAGCCC-T-TCGTATTGAGATATA
1 GAGCTGAATGGAATCGAACTCGA-AGATTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATA
3966063 CTGTAAATTTGACATGCCCTT
65 CTGTAAATTTGACATGCCCTT
* * * *
3966084 GAGTTGAATGGAATCGAACTCGAAGGTATTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGGAATCGAACTCGAAGATTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATAC
* *
3966149 TGTAAATTTGATATGTCCTT
66 TGTAAATTTGACATGCCCTT
* * * *
3966169 GAGCTAAATGTAATTGAACTCGAAGATTTTTATTGACAGATAACCCTTCTCGCCTTGAGTTATAC
1 GAGCTGAATGGAATCGAACTCGAAGATTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATAC
3966234 TGTAA
66 TGTAA
3966239 TACCCTAATT
Statistics
Matches: 134, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
83 20 0.15
84 22 0.16
85 92 0.69
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (85 bp):
GAGCTGAATGGAATCGAACTCGAAGATTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATAC
TGTAAATTTGACATGCCCTT
Found at i:3970497 original size:31 final size:30
Alignment explanation
Indices: 3970462--3970544 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
3970452 CCAATGAGTC
* *
3970462 ACATTCAGTTACCTAATTGAACCACAAAAAA
1 ACATT-AGGTACCAAATTGAACCACAAAAAA
**
3970493 ACATTAGGTGGCAAATTGAACCACAAAAAA
1 ACATTAGGTACCAAATTGAACCACAAAAAA
**
3970523 ACATTAGGTGGCAAATTGAACC
1 ACATTAGGTACCAAATTGAACC
3970545 TTAAACCGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
30 43 0.90
31 5 0.10
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.20
Consensus pattern (30 bp):
ACATTAGGTACCAAATTGAACCACAAAAAA
Found at i:3970512 original size:30 final size:30
Alignment explanation
Indices: 3970476--3970544 Score: 138
Period size: 30 Copynumber: 2.3 Consensus size: 30
3970466 TCAGTTACCT
3970476 AATTGAACCACAAAAAAACATTAGGTGGCA
1 AATTGAACCACAAAAAAACATTAGGTGGCA
3970506 AATTGAACCACAAAAAAACATTAGGTGGCA
1 AATTGAACCACAAAAAAACATTAGGTGGCA
3970536 AATTGAACC
1 AATTGAACC
3970545 TTAAACCGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.17
Consensus pattern (30 bp):
AATTGAACCACAAAAAAACATTAGGTGGCA
Found at i:3979732 original size:45 final size:45
Alignment explanation
Indices: 3979666--3979770 Score: 165
Period size: 45 Copynumber: 2.3 Consensus size: 45
3979656 CTTCTTACCT
* * *
3979666 TAGAGCCAAAACCCAGTATATAATAAACCTAGAACTTGAGTCTAGA
1 TAGAGCC-TAACCCAGCATATAATAAACCTAGAACTTGAGTCTAAA
3979712 TAGAGCCTAACCCAGCATATAATAAACCTAGAACTTGAGTCTAAA
1 TAGAGCCTAACCCAGCATATAATAAACCTAGAACTTGAGTCTAAA
*
3979757 TGGAGCCTAACCCA
1 TAGAGCCTAACCCA
3979771 AATAAGTCTC
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
45 48 0.87
46 7 0.13
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (45 bp):
TAGAGCCTAACCCAGCATATAATAAACCTAGAACTTGAGTCTAAA
Found at i:3990127 original size:15 final size:15
Alignment explanation
Indices: 3990108--3990163 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
3990098 TTCATGGGGT
* *
3990108 AAGAAGACAACGTCT
1 AAGAAGAAAACGTCA
3990123 AAGAAGAAAACGTCA
1 AAGAAGAAAACGTCA
3990138 AAGAAGAAAACGTCA
1 AAGAAGAAAACGTCA
3990153 AAGAAGGAAAA
1 AAGAA-GAAAA
3990164 AGAAAGCATC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 33 0.87
16 5 0.13
ACGTcount: A:0.59, C:0.12, G:0.21, T:0.07
Consensus pattern (15 bp):
AAGAAGAAAACGTCA
Found at i:3993480 original size:15 final size:15
Alignment explanation
Indices: 3993460--3993494 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
3993450 ACGATTGATA
3993460 TTGCCTCCAATATAG
1 TTGCCTCCAATATAG
3993475 TTGCCTCCAATATAG
1 TTGCCTCCAATATAG
3993490 TTGCC
1 TTGCC
3993495 AAAGGAACGA
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:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (15 bp):
TTGCCTCCAATATAG
Found at i:3994027 original size:39 final size:38
Alignment explanation
Indices: 3993962--3994038 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 38
3993952 GGAAAAAGAG
* *
3993962 AAAGAAAATGAAGAGGGTAAAGGAGAAGGGACACCGAA
1 AAAGAAAAGGAAGAGGGTAAAAGAGAAGGGACACCGAA
3994000 AAAGAAAAAGGAAGAGGAG-AAAAGAGAAGGGACACCGAA
1 AAAG-AAAAGGAAGAGG-GTAAAAGAGAAGGGACACCGAA
3994039 GAGGGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
38 4 0.11
39 30 0.86
40 1 0.03
ACGTcount: A:0.56, C:0.08, G:0.34, T:0.03
Consensus pattern (38 bp):
AAAGAAAAGGAAGAGGGTAAAAGAGAAGGGACACCGAA
Found at i:3994384 original size:173 final size:172
Alignment explanation
Indices: 3994095--3994439 Score: 681
Period size: 173 Copynumber: 2.0 Consensus size: 172
3994085 ACAAGGCTAA
3994095 GAGTTGAAAGCAACCGTGTTTTGAAAGTGTTTGCATGTATGGTTGATATACAACTTAAAAATGTG
1 GAGTTGAAAGCAACCGTGTTTTGAAAGTGTTTGCATGTATGGTTGATATACAACTTAAAAATGTG
3994160 GAGTCCGTGAAAGTGAAATGTGAGGACGATATGTTTGGGTATGAGGGTTTCACGTACATAACTTG
66 GAGTCCGTGAAAGTGAAATGTGAGGACGATATGTTTGGGTATGAGGGTTTCACGTACATAACTTG
3994225 GGAAGATTTTGAAGTGGTTTTTTACTGTGGATGAGATGACCGG
131 GGAAGATTTTGAAGTGG-TTTTTACTGTGGATGAGATGACCGG
3994268 GAGTTGAAAGCAACCGTGTTTTGAAAGTGTTTGCATGTATGGTTGATATACAACTTAAAAATGTG
1 GAGTTGAAAGCAACCGTGTTTTGAAAGTGTTTGCATGTATGGTTGATATACAACTTAAAAATGTG
3994333 GAGTCCGTGAAAGTGAAATGTGAGGACGATATGTTTGGGTATGAGGGTTTCACGTACATAACTTG
66 GAGTCCGTGAAAGTGAAATGTGAGGACGATATGTTTGGGTATGAGGGTTTCACGTACATAACTTG
3994398 GGAAGATTTTGAAGTGGTTTTTACTGTGGATGAGATGACCGG
131 GGAAGATTTTGAAGTGGTTTTTACTGTGGATGAGATGACCGG
3994440 TTCTGCGATT
Statistics
Matches: 172, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
172 25 0.15
173 147 0.85
ACGTcount: A:0.28, C:0.09, G:0.30, T:0.32
Consensus pattern (172 bp):
GAGTTGAAAGCAACCGTGTTTTGAAAGTGTTTGCATGTATGGTTGATATACAACTTAAAAATGTG
GAGTCCGTGAAAGTGAAATGTGAGGACGATATGTTTGGGTATGAGGGTTTCACGTACATAACTTG
GGAAGATTTTGAAGTGGTTTTTACTGTGGATGAGATGACCGG
Found at i:3996780 original size:85 final size:84
Alignment explanation
Indices: 3996637--3996850 Score: 265
Period size: 85 Copynumber: 2.5 Consensus size: 84
3996627 AATGATGTGT
*
3996637 GCTTCAATGACATACAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTATGT
1 GCTTCAATGACACACAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTATGT
3996702 CAAGC-AGATTTATGACGGGG
66 C-AGCTA-ATTTATGACGGGG
* * ** *
3996722 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGATGCACAAATGTGTGT
1 GCTTCAATGACACACAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTATGT
*
3996787 CATCTTAATTTATGACGGGG
66 CAGC-TAATTTATGACGGGG
* *
3996807 TCTTCAATGACA-ATCAATG-AACGTCATTA-ATGCGCGTCATAAAT
1 GCTTCAATGACACA-CAATGTAA-GTCA-TACATGCGTGTCATAAAT
3996851 ATGTGTCATA
Statistics
Matches: 113, Mismatches: 11, Indels: 10
0.84 0.08 0.07
Matches are distributed among these distances:
84 4 0.04
85 106 0.94
86 3 0.03
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (84 bp):
GCTTCAATGACACACAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTATGT
CAGCTAATTTATGACGGGG
Found at i:3996871 original size:13 final size:13
Alignment explanation
Indices: 3996828--3996873 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
3996818 AATCAATGAA
* *
3996828 CGTCATTAATGCG
1 CGTCATAAATACG
*
3996841 CGTCATAAATATG
1 CGTCATAAATACG
*
3996854 TGTCATAAATACG
1 CGTCATAAATACG
3996867 CGTCATA
1 CGTCATA
3996874 GATTTATGAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (13 bp):
CGTCATAAATACG
Found at i:4013829 original size:13 final size:12
Alignment explanation
Indices: 4013809--4013835 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4013799 GGGGAGTAAT
4013809 TTTCAAAAATTA
1 TTTCAAAAATTA
4013821 TTTCAAAAATTA
1 TTTCAAAAATTA
4013833 TTT
1 TTT
4013836 TTCAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (12 bp):
TTTCAAAAATTA
Found at i:4014271 original size:71 final size:72
Alignment explanation
Indices: 4014155--4014320 Score: 226
Period size: 71 Copynumber: 2.3 Consensus size: 72
4014145 ATACCTAAGT
* * * *
4014155 CATAGGTACCAATACCTTTATGTTGATTTTGGTTCCGAGTAAAATAGAATGCCAAACGGGTA-CG
1 CATAGGTACCAATACCCTTATGTTAATTTTGGCTCCGAGAAAAATAGAATGCCAAACGGGTACCG
4014219 ATACCCC
66 ATACCCC
* * * *
4014226 CATAGGTACCGATACCCTTGTGTTAATTTTGGCTCCGAGAAAAATAGAATGCCCAATGGGTACCG
1 CATAGGTACCAATACCCTTATGTTAATTTTGGCTCCGAGAAAAATAGAATGCCAAACGGGTACCG
4014291 ATACCCC
66 ATACCCC
*
4014298 CTAGAGGTACCAATACCCATTAT
1 C-ATAGGTACCAATACCC-TTAT
4014321 CATTTAACGG
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
71 54 0.67
72 10 0.12
73 14 0.17
74 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (72 bp):
CATAGGTACCAATACCCTTATGTTAATTTTGGCTCCGAGAAAAATAGAATGCCAAACGGGTACCG
ATACCCC
Found at i:4016312 original size:20 final size:20
Alignment explanation
Indices: 4016276--4016392 Score: 141
Period size: 20 Copynumber: 5.9 Consensus size: 20
4016266 CGGGTAATTC
4016276 GTAAAGCCTCA-GGTCATTT
1 GTAAAGCCTCAGGGTCATTT
4016295 GTAAAGCCTCAGGGTCATTT
1 GTAAAGCCTCAGGGTCATTT
** *
4016315 GTAAAGCCTTTGGGTAATTT
1 GTAAAGCCTCAGGGTCATTT
* *
4016335 TTAAAGCCTGAGGGTCATTT
1 GTAAAGCCTCAGGGTCATTT
*
4016355 GTAAAGCCTTC-GGGTAATTT
1 GTAAAGCC-TCAGGGTCATTT
4016375 GTAAAGCCTTC-GGGTCAT
1 GTAAAGCC-TCAGGGTCAT
4016393 CTGTTAGTCT
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
19 11 0.13
20 73 0.86
21 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (20 bp):
GTAAAGCCTCAGGGTCATTT
Found at i:4016349 original size:40 final size:40
Alignment explanation
Indices: 4016267--4016392 Score: 166
Period size: 40 Copynumber: 3.2 Consensus size: 40
4016257 TAAATCCTTC
* * * *
4016267 GGGTAATTCGTAAAGCC-TCAGGTCATTTGTAAAGCCTCA
1 GGGTCATTTGTAAAGCCTTCGGGTAATTTGTAAAGCCTCA
* * *
4016306 GGGTCATTTGTAAAGCCTTTGGGTAATTTTTAAAGCCTGA
1 GGGTCATTTGTAAAGCCTTCGGGTAATTTGTAAAGCCTCA
4016346 GGGTCATTTGTAAAGCCTTCGGGTAATTTGTAAAGCCTTC-
1 GGGTCATTTGTAAAGCCTTCGGGTAATTTGTAAAGCC-TCA
4016386 GGGTCAT
1 GGGTCAT
4016393 CTGTTAGTCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
39 15 0.20
40 59 0.79
41 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
GGGTCATTTGTAAAGCCTTCGGGTAATTTGTAAAGCCTCA
Found at i:4016362 original size:60 final size:59
Alignment explanation
Indices: 4016257--4016389 Score: 187
Period size: 60 Copynumber: 2.2 Consensus size: 59
4016247 CTAGAAAAAT
* *
4016257 TAAATCCTTCGGGTAATTCGTAAAGCCTCAGGTCATTTGTAAAGCC-TCAGGGTCATTTG
1 TAAAGCCTTCGGGTAATTCGTAAAGCCTCAGGTCATTTGTAAAGCCTTC-GGGTAATTTG
* ** *
4016316 TAAAGCCTTTGGGTAATTTTTAAAGCCTGAGGGTCATTTGTAAAGCCTTCGGGTAATTTG
1 TAAAGCCTTCGGGTAATTCGTAAAGCCTCA-GGTCATTTGTAAAGCCTTCGGGTAATTTG
4016376 TAAAGCCTTCGGGT
1 TAAAGCCTTCGGGT
4016390 CATCTGTTAG
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
59 25 0.38
60 38 0.58
61 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (59 bp):
TAAAGCCTTCGGGTAATTCGTAAAGCCTCAGGTCATTTGTAAAGCCTTCGGGTAATTTG
Found at i:4016588 original size:89 final size:88
Alignment explanation
Indices: 4016474--4016693 Score: 323
Period size: 89 Copynumber: 2.5 Consensus size: 88
4016464 TCAAATTAAT
*
4016474 ATCGAATCTGATCTTCACAAAAGAGTAGTGAAATTAGATTCTTATCAAGTCAATTCAACATTCAC
1 ATCGAATCTGATCTTCACAAAAGAGTAGTGAAATTAGATTCTTATCAAGTAAATTCAACATTCAC
* *
4016539 GGAAGGGTAGTGAAGTCATCCAAC
66 GGAAGAGTAGTGAAGTAAT-CAAC
* * * * *
4016563 CTCGAATCTAATCTTCATAAAAGAGTAGTGAAATTAGATTCTTCTCAAGTAAATTCAACATTCAT
1 ATCGAATCTGATCTTCACAAAAGAGTAGTGAAATTAGATTCTTATCAAGTAAATTCAACATTCAC
*
4016628 GGAAGAGTTGTGAAGTAATCAAC
66 GGAAGAGTAGTGAAGTAATCAAC
* **
4016651 ATCAAATCTGATCTTCACGGAAGAGTAGTGAAATTAGATTCTT
1 ATCGAATCTGATCTTCACAAAAGAGTAGTGAAATTAGATTCTT
4016694 CTTAGTGCAA
Statistics
Matches: 116, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
88 41 0.35
89 75 0.65
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (88 bp):
ATCGAATCTGATCTTCACAAAAGAGTAGTGAAATTAGATTCTTATCAAGTAAATTCAACATTCAC
GGAAGAGTAGTGAAGTAATCAAC
Found at i:4016829 original size:96 final size:94
Alignment explanation
Indices: 4016715--4017018 Score: 420
Period size: 96 Copynumber: 3.2 Consensus size: 94
4016705 TCATCTTCAG
* *
4016715 CCTTCACGGAAGAGTAGTGAAGCAAGAGAAAGAGCAAGATCAAAATTTGTTCTCCACGGAAGAAT
1 CCTTCACGGAAGAGTAGTGAAG-AAGAGAAAGAGCAAGATCAAAATTT-TTCTCCACGAAAGAGT
*
4016780 AGTGGAACGGATTTTTCAGAAAAGTATGAAA
64 AGTGGAACGGATTTTTCAGCAAAGTATGAAA
*
4016811 CCTTCACGGAAGAGTAGTGAAGTAAGAGCAAGAGCAAGATCAAAATTTATTCTCCACGAAAGAGT
1 CCTTCACGGAAGAGTAGTGAAG-AAGAGAAAGAGCAAGATCAAAATTT-TTCTCCACGAAAGAGT
*
4016876 AGTGGAACGGATTTTTCAGCAAAGTATGAAG
64 AGTGGAACGGATTTTTCAGCAAAGTATGAAA
* * * * *
4016907 TCTTCACGGAAGAGTAGT---G-A-AGTAAGAGCAAAATCAAAATTCTCTCTCCGCGAAAGAGTA
1 CCTTCACGGAAGAGTAGTGAAGAAGAGAAAGAGCAAGATCAAAATT-TTTCTCCACGAAAGAGTA
4016967 GTGGAACGGATTTTTCAGCAAAGTATGAAA
65 GTGGAACGGATTTTTCAGCAAAGTATGAAA
* *
4016997 CCTTCACTGAAGAGTAATGAAG
1 CCTTCACGGAAGAGTAGTGAAG
4017019 TAATCCAATT
Statistics
Matches: 188, Mismatches: 16, Indels: 11
0.87 0.07 0.05
Matches are distributed among these distances:
90 78 0.41
91 2 0.01
93 2 0.01
96 106 0.56
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (94 bp):
CCTTCACGGAAGAGTAGTGAAGAAGAGAAAGAGCAAGATCAAAATTTTTCTCCACGAAAGAGTAG
TGGAACGGATTTTTCAGCAAAGTATGAAA
Found at i:4016990 original size:90 final size:90
Alignment explanation
Indices: 4016744--4017021 Score: 387
Period size: 90 Copynumber: 3.0 Consensus size: 90
4016734 AAGCAAGAGA
* * * * *
4016744 AAGAGCAAGATCAAAATTTGTTCTCCACGGAAGAATAGTGGAACGGATTTTTCAGAAAAGTATGA
1 AAGAGCAAAATCAAAATTTATTCTCCACGAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGA
4016809 AACCTTCACGGAAGAGTAGTGAAGT
66 AACCTTCACGGAAGAGTAGTGAAGT
4016834 AAGAGCAAGAGCAAGATCAAAATTTATTCTCCACGAAAGAGTAGTGGAACGGATTTTTCAGCAAA
1 AAGAGC---A--AA-ATCAAAATTTATTCTCCACGAAAGAGTAGTGGAACGGATTTTTCAGCAAA
**
4016899 GTATGAAGTCTTCACGGAAGAGTAGTGAAGT
60 GTATGAAACCTTCACGGAAGAGTAGTGAAGT
* *
4016930 AAGAGCAAAATCAAAATTCT-CTCTCCGCGAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATG
1 AAGAGCAAAATCAAAATT-TATTCTCCACGAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATG
* *
4016994 AAACCTTCACTGAAGAGTAATGAAGT
65 AAACCTTCACGGAAGAGTAGTGAAGT
4017020 AA
1 AA
4017022 TCCAATTTCG
Statistics
Matches: 168, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
90 81 0.48
91 3 0.02
93 2 0.01
95 1 0.01
96 81 0.48
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.23
Consensus pattern (90 bp):
AAGAGCAAAATCAAAATTTATTCTCCACGAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGA
AACCTTCACGGAAGAGTAGTGAAGT
Found at i:4017146 original size:47 final size:47
Alignment explanation
Indices: 4017085--4017206 Score: 172
Period size: 47 Copynumber: 2.6 Consensus size: 47
4017075 GTCATGCAAA
* * **
4017085 TTCAGCCTTCACAAAAGAGTAGTGAAGCAAATCATTTGCGAGTCATT
1 TTCAGCCTTCACAAAAGAGTAGTGAAGCAAATCATTTGCAAATCACC
*
4017132 TTCAGCCTTCACAAAAGAGTAATGAAGCAAATCATTTGCAAATCACC
1 TTCAGCCTTCACAAAAGAGTAGTGAAGCAAATCATTTGCAAATCACC
* * *
4017179 ATCATCCTTCACGAAAGAGTAGTGAAGC
1 TTCAGCCTTCACAAAAGAGTAGTGAAGC
4017207 CAGAGCAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (47 bp):
TTCAGCCTTCACAAAAGAGTAGTGAAGCAAATCATTTGCAAATCACC
Found at i:4018450 original size:2 final size:2
Alignment explanation
Indices: 4018438--4018467 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4018428 ATTTTAGTCC
*
4018438 AT AT AT GT 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
4018468 GTTTTAGGAA
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4019979 original size:13 final size:13
Alignment explanation
Indices: 4019961--4020018 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
4019951 AATACAAAAC
*
4019961 TTTCATA-TCTCAT
1 TTTCATATTC-CAA
*
4019974 TTTCATCTTCCAA
1 TTTCATATTCCAA
4019987 TTTCATATT-CAA
1 TTTCATATTCCAA
* *
4019999 TTTCACATTCCAT
1 TTTCATATTCCAA
4020012 TTTCATA
1 TTTCATA
4020019 ATATGTACTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
12 11 0.30
13 24 0.65
14 2 0.05
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTCATATTCCAA
Found at i:4020009 original size:25 final size:26
Alignment explanation
Indices: 4019961--4020018 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
4019951 AATACAAAAC
*
4019961 TTTCATATCTCATTTTCATCTTCCAA
1 TTTCATATCTCAATTTCATCTTCCAA
*
4019987 TTTCATAT-TCAATTTCA-CATTCCAT
1 TTTCATATCTCAATTTCATC-TTCCAA
4020012 TTTCATA
1 TTTCATA
4020019 ATATGTACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 1 0.03
25 20 0.69
26 8 0.28
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTCATATCTCAATTTCATCTTCCAA
Found at i:4020112 original size:19 final size:18
Alignment explanation
Indices: 4020074--4020134 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 18
4020064 GTTTTCGGAC
*
4020074 TCATAACTTATTTCAAAT
1 TCATAACTTATTTTAAAT
*
4020092 TCATAACTTAATTTTAGAT
1 TCATAACTT-ATTTTAAAT
* *
4020111 TCATAGCTTATTTTCAAGT
1 TCATAACTTATTTT-AAAT
4020130 TCATA
1 TCATA
4020135 GCCCAATGCA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 14 0.39
19 22 0.61
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (18 bp):
TCATAACTTATTTTAAAT
Found at i:4023003 original size:30 final size:30
Alignment explanation
Indices: 4022962--4023031 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
4022952 GGTTAAAACA
4022962 CCTAAA-TTTTGAAAATTAAAC-TTTTAGTC
1 CCTAAACTTTTGAAAATT-AACTTTTTAGTC
* *
4022991 CCTAAACTTTTGAAAATTACCTTTTTGGTC
1 CCTAAACTTTTGAAAATTAACTTTTTAGTC
4023021 CCTAAACTTTT
1 CCTAAACTTTT
4023032 TCAAACTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 8 0.22
30 29 0.78
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (30 bp):
CCTAAACTTTTGAAAATTAACTTTTTAGTC
Found at i:4025474 original size:21 final size:22
Alignment explanation
Indices: 4025433--4025485 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
4025423 AAACAAAAGC
*
4025433 ATATA-TTATAAATGTTAACTAA
1 ATATACTTA-AAATATTAACTAA
4025455 ATATACTTAAAATATT-ACTAA
1 ATATACTTAAAATATTAACTAA
*
4025476 AGATACTTAA
1 ATATACTTAA
4025486 TTTTTTACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 14 0.50
22 11 0.39
23 3 0.11
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.38
Consensus pattern (22 bp):
ATATACTTAAAATATTAACTAA
Found at i:4032209 original size:14 final size:14
Alignment explanation
Indices: 4032192--4032312 Score: 74
Period size: 14 Copynumber: 8.7 Consensus size: 14
4032182 ATGTTTAAGT
*
4032192 TTTAAGGTTTGGGA
1 TTTAGGGTTTGGGA
4032206 TTTAGGGTTT-GGA
1 TTTAGGGTTTGGGA
* *
4032219 GTTTGGGGTTTGGGG
1 -TTTAGGGTTTGGGA
4032234 TTTAGGGTTTAGGG-
1 TTTAGGGTTT-GGGA
*
4032248 TTTAGGGTTT-AGA
1 TTTAGGGTTTGGGA
* *
4032261 GTTTA-AGTTT-GAA
1 -TTTAGGGTTTGGGA
* *
4032274 GTTTAGGG-TAGGGG
1 -TTTAGGGTTTGGGA
4032288 TTCTAGGGTTTGGGA
1 TT-TAGGGTTTGGGA
*
4032303 TTTTGGGTTT
1 TTTAGGGTTT
4032313 AAGACTTGGG
Statistics
Matches: 83, Mismatches: 15, Indels: 18
0.72 0.13 0.16
Matches are distributed among these distances:
12 1 0.01
13 16 0.19
14 55 0.66
15 11 0.13
ACGTcount: A:0.15, C:0.01, G:0.40, T:0.44
Consensus pattern (14 bp):
TTTAGGGTTTGGGA
Found at i:4032215 original size:28 final size:27
Alignment explanation
Indices: 4032184--4032244 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
4032174 AGGATTCAAT
4032184 GTTTAAGTTTTAAGGTTTGGGATTTAGG
1 GTTTAAG-TTTAAGGTTTGGGATTTAGG
* ** *
4032212 GTTTGGAGTTTGGGGTTTGGGGTTTAGG
1 GTTT-AAGTTTAAGGTTTGGGATTTAGG
4032240 GTTTA
1 GTTTA
4032245 GGGTTTAGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.15, C:0.00, G:0.39, T:0.46
Consensus pattern (27 bp):
GTTTAAGTTTAAGGTTTGGGATTTAGG
Found at i:4032258 original size:7 final size:7
Alignment explanation
Indices: 4032192--4032265 Score: 80
Period size: 7 Copynumber: 10.6 Consensus size: 7
4032182 ATGTTTAAGT
*
4032192 TTTAAGG
1 TTTAGGG
4032199 TTT-GGG
1 TTTAGGG
4032205 ATTTAGGG
1 -TTTAGGG
4032213 TTT-GGAG
1 TTTAGG-G
*
4032220 TTTGGGG
1 TTTAGGG
*
4032227 TTTGGGG
1 TTTAGGG
4032234 TTTAGGG
1 TTTAGGG
4032241 TTTAGGG
1 TTTAGGG
4032248 TTTAGGG
1 TTTAGGG
*
4032255 TTTAGAG
1 TTTAGGG
4032262 TTTA
1 TTTA
4032266 AGTTTGAAGT
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
6 4 0.07
7 51 0.85
8 5 0.08
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:4033206 original size:2 final size:2
Alignment explanation
Indices: 4033199--4033238 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4033189 AAATAAATAA
4033199 AT AT 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 AT AT
4033239 TCTTCCAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4036141 original size:21 final size:22
Alignment explanation
Indices: 4036096--4036143 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
4036086 ATTACATAAC
*
4036096 TTTAAAAAAAGTATCGATCATT
1 TTTAAAAAAAGTATCGATCACT
* *
4036118 TTTATAAAAAGTATGGA-CACT
1 TTTAAAAAAAGTATCGATCACT
4036139 TTTAA
1 TTTAA
4036144 TATAATAGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (22 bp):
TTTAAAAAAAGTATCGATCACT
Found at i:4036189 original size:23 final size:23
Alignment explanation
Indices: 4036158--4036230 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
4036148 ATAGGTAAAA
* *
4036158 ATATGATGTAATAGGTAACGCTT
1 ATATAATGTAATAGGTAGCGCTT
4036181 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
4036204 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
4036227 ATAT
1 ATAT
4036231 TGTAAAATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:4036271 original size:20 final size:20
Alignment explanation
Indices: 4036233--4036272 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
4036223 GCTTATATTG
*
4036233 TAAAATATCTATCCTTTTTA
1 TAAAATATCTATACTTTTTA
4036253 TAAAAGTATCTATACTTTTT
1 TAAAA-TATCTATACTTTTT
4036273 TCACTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (20 bp):
TAAAATATCTATACTTTTTA
Found at i:4036678 original size:23 final size:23
Alignment explanation
Indices: 4036647--4036742 Score: 183
Period size: 23 Copynumber: 4.2 Consensus size: 23
4036637 TCAGGTAAAA
*
4036647 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
4036670 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
4036693 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
4036716 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
4036739 ATAT
1 ATAT
4036743 TGTAAAGTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.35
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:4037127 original size:512 final size:512
Alignment explanation
Indices: 4036158--4037127 Score: 1719
Period size: 512 Copynumber: 1.9 Consensus size: 512
4036148 ATAGGTAAAA
* *
4036158 ATATGATGTAATAGGTAACGCTTATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGT
1 ATATAATGTAATAGGTAACGCTTATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGC
* *
4036223 GCTTATATTGTAAAATATCTATCCTTTTTATAAAAGTATCTATACTTTTTTCACTGTGGAAAATA
66 GCTTATATTGTAAAATATCTATCCTTTTTATAAAAGTATCTATACTTATTTCACTGTGGAAAACA
* *
4036288 TTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAATAATTATAGGTGTCTAATG
131 TTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAATAATTATAGGTATCTAATG
* * *
4036353 ATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACTTATATATTACAT
196 ATTTATTTTTTACGTTACAGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACAT
* *
4036418 ATTTATTATTATCTTTTGTTAATATTGTTAAATTTAAATTTTAAATAATATTTTATAAATATCAA
261 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAATATCAA
* *
4036483 AACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAA
326 AACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTAGAAAACATGAA
4036548 ACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAA
391 ACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAA
4036613 AAAGTATCGATATTTTACAATATATCAGGTAAAAATATGATGTAATAGGTAGCGCTT
456 AAAGTATCGATATTTTACAATATATCAGGTAAAAATATGATGTAATAGGTAGCGCTT
*
4036670 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGC
1 ATATAATGTAATAGGTAACGCTTATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGC
* * *
4036735 GCTTATATTGTAAAGTATCTATCCTTTTTATATAAGTGT-TCATACTTATTTCACTGTGGAAAAC
66 GCTTATATTGTAAAATATCTATCCTTTTTATAAAAGTATCT-ATACTTATTTCACTGTGGAAAAC
* *
4036799 ATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATATGTATCTAAT
130 ATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAATAATTATAGGTATCTAAT
*
4036864 GATTTATTTTTTATGTTACAGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACA
195 GATTTATTTTTTACGTTACAGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACA
*
4036929 TATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATC
260 TATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTAT-AAATATC
4036994 AAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTAGAAAACATG
324 AAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTAGAAAACATG
4037059 AAACACTATT-AAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTAT
389 AAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTAT
4037123 AAAAA
454 AAAAA
4037128 AATATGGACA
Statistics
Matches: 435, Mismatches: 21, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
511 1 0.00
512 354 0.81
513 80 0.18
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (512 bp):
ATATAATGTAATAGGTAACGCTTATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGC
GCTTATATTGTAAAATATCTATCCTTTTTATAAAAGTATCTATACTTATTTCACTGTGGAAAACA
TTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAATAATTATAGGTATCTAATG
ATTTATTTTTTACGTTACAGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACAT
ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAATATCAA
AACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTAGAAAACATGAA
ACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAA
AAAGTATCGATATTTTACAATATATCAGGTAAAAATATGATGTAATAGGTAGCGCTT
Found at i:4037247 original size:23 final size:23
Alignment explanation
Indices: 4037218--4037265 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
4037208 AAATAGGTCA
*
4037218 ATATAAGCGCTACCTATTATATT
1 ATATAAGCGCTACCTAATATATT
*
4037241 ATATAAGCGCTATCTAATATATT
1 ATATAAGCGCTACCTAATATATT
4037264 AT
1 AT
4037266 TGTACTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATATATT
Found at i:4039499 original size:24 final size:24
Alignment explanation
Indices: 4039467--4039512 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
4039457 GACACGTCAT
4039467 CACCACCCGAGTCAACAGCTACTC
1 CACCACCCGAGTCAACAGCTACTC
*
4039491 CACCACCCGAGTCATCAGCTAC
1 CACCACCCGAGTCAACAGCTAC
4039513 ATCGTCAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.46, G:0.13, T:0.13
Consensus pattern (24 bp):
CACCACCCGAGTCAACAGCTACTC
Found at i:4042327 original size:13 final size:13
Alignment explanation
Indices: 4042309--4042370 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
4042299 TTGTGGGTTA
*
4042309 TTGTTCTTTGTTT
1 TTGTTCTCTGTTT
4042322 TTGTTCTCTGTTT
1 TTGTTCTCTGTTT
* *
4042335 TTGCTGGTCTCTCTTCG
1 TTG-T--TCTCTGTT-T
*
4042352 TTGTTCTCTGTCT
1 TTGTTCTCTGTTT
4042365 TTGTTC
1 TTGTTC
4042371 GCAGATGGGG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
13 21 0.54
14 7 0.18
16 8 0.21
17 3 0.08
ACGTcount: A:0.00, C:0.19, G:0.18, T:0.63
Consensus pattern (13 bp):
TTGTTCTCTGTTT
Found at i:4043112 original size:40 final size:40
Alignment explanation
Indices: 4043068--4043292 Score: 394
Period size: 40 Copynumber: 5.8 Consensus size: 40
4043058 TGAGTAAGCT
4043068 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTC
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTC
4043108 CTTCTTCAGATGAGTTCTTCTCATTATGAAC-T-TTC-T-
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTC
4043144 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTC
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTC
4043184 CTTCTTCAGATGAGTTCTTCTCATTATGAAC-T-TTC-T-
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTC
4043220 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTC
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTC
4043260 CTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTT
4043293 TCTCTGGAAA
Statistics
Matches: 177, Mismatches: 0, Indels: 16
0.92 0.00 0.08
Matches are distributed among these distances:
36 62 0.35
37 4 0.02
38 12 0.07
39 4 0.02
40 95 0.54
ACGTcount: A:0.19, C:0.24, G:0.11, T:0.47
Consensus pattern (40 bp):
CTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTC
Found at i:4043151 original size:76 final size:76
Alignment explanation
Indices: 4043066--4043297 Score: 464
Period size: 76 Copynumber: 3.1 Consensus size: 76
4043056 GTTGAGTAAG
4043066 CTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
4043131 TTATGAACTTT
66 TTATGAACTTT
4043142 CTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
4043207 TTATGAACTTT
66 TTATGAACTTT
4043218 CTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
4043283 TTATGAACTTT
66 TTATGAACTTT
4043294 CTCT
1 CTCT
4043298 GGAAAAGCTG
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 156 1.00
ACGTcount: A:0.18, C:0.24, G:0.10, T:0.47
Consensus pattern (76 bp):
CTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTT
Found at i:4043388 original size:113 final size:113
Alignment explanation
Indices: 4043235--4044120 Score: 1422
Period size: 113 Copynumber: 7.8 Consensus size: 113
4043225 TCAGATGAGT
*
4043235 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT-TCTCTG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCT-TCTG
** *
4043299 GAAAAGCTGATCCATCGCGTGATGGATTTGATCAAAAGGTTGAACAAGC
65 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
*
4043348 TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTTATTATGAACTTC-TCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGG
4043412 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
*
4043460 TCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGG
4043525 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
4043573 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGG
4043638 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
4043686 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGG
4043751 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
4043799 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGG
* * **
4043864 AAAAGTTGATCCATCAAGTGATGGATTTGAGCATAAGGTTGAACAAAT
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
* * * *
4043912 TCTTCTCATTATGAATTTCTTCTTCCTCCTTCAAGTAATGAGTTCTTCTCATTATGAAC-TCTAC
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTC-AG--ATGAGTTCTTCTTATTATGAACTTCT-T
*** * * ** * * **
4043976 CTGGAAATTTTAATCCATCACA-TGATGAATTCAAACAAAAGGTTAAACAAAT
62 CTGGAAAAGCTGATCCATCA-AGTGATGGATTTGAGCAAAAGGTTGAACAAGC
* * *
4044028 TCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTT-TCTCTG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCT-TCTG
4044092 GAAAAGCTGATCCATCAAGTGATGGATTT
65 GAAAAGCTGATCCATCAAGTGATGGATTT
4044121 AAATCTTTGC
Statistics
Matches: 727, Mismatches: 37, Indels: 18
0.93 0.05 0.02
Matches are distributed among these distances:
112 108 0.15
113 519 0.71
114 3 0.00
115 5 0.01
116 91 0.13
117 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (113 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGG
AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
Found at i:4044500 original size:52 final size:52
Alignment explanation
Indices: 4044422--4044522 Score: 202
Period size: 52 Copynumber: 1.9 Consensus size: 52
4044412 ATGTTAATTC
4044422 TGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACATTA
1 TGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACATTA
4044474 TGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACA
1 TGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACA
4044523 GATATCGATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36
Consensus pattern (52 bp):
TGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACATTA
Found at i:4045162 original size:83 final size:83
Alignment explanation
Indices: 4045014--4045490 Score: 688
Period size: 83 Copynumber: 5.6 Consensus size: 83
4045004 GGTTTCATAT
*
4045014 CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTACT-AGCACATTCCTCTTCCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCCTCTTCCAA
*
4045078 ATTCAATAACTGGTTTTAC
65 ATTCAATAATTGGTTTTAC
* ** *
4045097 CAAACCAGATCACATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
*
4045162 TTCAATGATTGGTTTTAC
66 TTCAATAATTGGTTTTAC
*
4045180 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTACT-AGAACATTCCTCTTCCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCCTCTTCCAA
4045244 ATTCAATAATTGGTTTTAC
65 ATTCAATAATTGGTTTTAC
** *
4045263 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
*
4045328 TTCAATAACTGGTTCTGTGGTTCATAC
66 TTCAATAA-------T-TGGTT-TTAC
*
4045355 CAAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
* *
4045420 TTCAATGATTGATTTTAC
66 TTCAATAATTGGTTTTAC
* *
4045438 CAAATCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGAGCACAT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
4045491 GGCATTTGTT
Statistics
Matches: 356, Mismatches: 26, Indels: 24
0.88 0.06 0.06
Matches are distributed among these distances:
82 2 0.01
83 271 0.76
84 5 0.01
85 1 0.00
90 1 0.00
91 5 0.01
92 71 0.20
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.26
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
TTCAATAATTGGTTTTAC
Found at i:4045440 original size:175 final size:173
Alignment explanation
Indices: 4044962--4045490 Score: 804
Period size: 166 Copynumber: 3.1 Consensus size: 173
4044952 CTTATTTCTA
* * * * * *
4044962 CTATGAGCAAATTCATCTTTCAAATTTAATGATTAGTTCTGTGGTTTCATATCAAACCAGATCAA
1 CTATGAGCACATTTATCTTTCAAATTCAAT-AAT-GTTCTGTGG-TTCATACCAAACCAGATCAG
*
4045027 ATAACTCAAAGAACACTTCCAGAAGATGCTACTAGCACATTCCTCTTCCAAATTCAATAACTGGT
63 ATAACTCAAAGAACACTTCCAGAAGATGCTACTAGCACATTCCTCTTCCAAATTCAATAATTGGT
*
4045092 TTTACCAAACCAGATCACATAACTCAAAGAACACTTCCAGAAGATG
128 TTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
* *
4045138 CTATGAGCACATTTATCTTTCAAATTC---AATG--AT-TGGTT-TTACCAAACCAGATCAGATA
1 CTATGAGCACATTTATCTTTCAAATTCAATAATGTTCTGTGGTTCATACCAAACCAGATCAGATA
*
4045196 ACTCAAAGAACACTTCCAGAAGATGCTACTAGAACATTCCTCTTCCAAATTCAATAATTGGTTTT
66 ACTCAAAGAACACTTCCAGAAGATGCTACTAGCACATTCCTCTTCCAAATTCAATAATTGGTTTT
4045261 ACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
131 ACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
*
4045304 CTATGAGCACATTTATCTTTCAAATTCAATAACTGGTTCTGTGGTTCATACCAAAACAGATCAGA
1 CTATGAGCACATTTATCTTTCAAATTCAATAA-T-GTTCTGTGGTTCATACCAAACCAGATCAGA
* *
4045369 TAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCCTCTTCCAAATTCAATGATTGAT
64 TAACTCAAAGAACACTTCCAGAAGATGCTACT-AGCACATTCCTCTTCCAAATTCAATAATTGGT
* *
4045433 TTTACCAAATCAGATCAGATAACTCAAAGAACACTTCTAGAAGATG
128 TTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
4045479 CTATGAGCACAT
1 CTATGAGCACAT
4045491 GGCATTTGTT
Statistics
Matches: 324, Mismatches: 19, Indels: 21
0.89 0.05 0.06
Matches are distributed among these distances:
166 149 0.46
167 2 0.01
168 3 0.01
169 3 0.01
170 1 0.00
171 2 0.01
172 2 0.01
173 1 0.00
174 6 0.02
175 131 0.40
176 24 0.07
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.28
Consensus pattern (173 bp):
CTATGAGCACATTTATCTTTCAAATTCAATAATGTTCTGTGGTTCATACCAAACCAGATCAGATA
ACTCAAAGAACACTTCCAGAAGATGCTACTAGCACATTCCTCTTCCAAATTCAATAATTGGTTTT
ACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
Found at i:4045462 original size:258 final size:249
Alignment explanation
Indices: 4045014--4045481 Score: 731
Period size: 258 Copynumber: 1.8 Consensus size: 249
4045004 GGTTTCATAT
*
4045014 CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTACTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTACTAGCACATTCATCTTCCAAA
*
4045079 TTCAATAACTGGTTTTACCAAACCAGATCACATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATAACTGGTTTTACCAAAACAGATCACATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* * *
4045144 GCACATTTATCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
131 GCACATTCATCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACAC
4045209 TTCCAGAAGATGCTACTAGAACATTCCTCTTCCAAATTCAATAATTGGTTTTAC
196 TTCCAGAAGATGCTACTAGAACATTCCTCTTCCAAATTCAATAATTGGTTTTAC
* * *
4045263 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTTATCTTTCAA
1 CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTACT-AGCACATTCATCTTCCAA
*
4045327 ATTCAATAACTGGTTCTGTGGTTCATACCAAAACAGATCAGATAACTCAAAGAACACTTCCAGAA
65 ATTCAATAACT-G----GT--TT--TACCAAAACAGATCACATAACTCAAAGAACACTTCCAGAA
* *
4045392 GATGCTATGAGCACATTCCTCTTCCAAATTCAATGATTGATTTTACCAAATCAGATCAGATAACT
121 GATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACT
*
4045457 CAAAGAACACTTCTAGAAGATGCTA
186 CAAAGAACACTTCCAGAAGATGCTA
4045482 TGAGCACATG
Statistics
Matches: 197, Mismatches: 12, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
248 1 0.01
249 69 0.35
250 1 0.01
254 2 0.01
256 2 0.01
258 122 0.62
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.26
Consensus pattern (249 bp):
CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTACTAGCACATTCATCTTCCAAA
TTCAATAACTGGTTTTACCAAAACAGATCACATAACTCAAAGAACACTTCCAGAAGATGCTATGA
GCACATTCATCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTACTAGAACATTCCTCTTCCAAATTCAATAATTGGTTTTAC
Found at i:4046651 original size:9 final size:8
Alignment explanation
Indices: 4046637--4046696 Score: 52
Period size: 9 Copynumber: 7.0 Consensus size: 8
4046627 CTTGACCCCC
4046637 CTTTTTCTT
1 CTTTTT-TT
4046646 C-TTTTTT
1 CTTTTTTT
4046653 CTCTTTTTT
1 CT-TTTTTT
4046662 C-TTTTTT
1 CTTTTTTT
4046669 CTTTTTCTCT
1 CTTTTT-T-T
4046679 CTTTTTTTT
1 C-TTTTTTT
4046688 CTCTTTTTT
1 CT-TTTTTT
4046697 TTCTTCAAGC
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
7 10 0.23
8 9 0.20
9 17 0.39
10 3 0.07
11 5 0.11
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
CTTTTTTT
Found at i:4046666 original size:24 final size:23
Alignment explanation
Indices: 4046638--4046700 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
4046628 TTGACCCCCC
4046638 TTTTTCTTCTTTTTTCTCTTTTT
1 TTTTTCTTCTTTTTTCTCTTTTT
4046661 TCTTTT-TTCTTTTTCTCTCTTTTT
1 T-TTTTCTTCTTTTT-TCTCTTTTT
*
4046685 TTTCTCTT-TTTTTTCT
1 TTTTTCTTCTTTTTTCT
4046701 TCAAGCATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 3 0.08
23 17 0.47
24 16 0.44
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTCTTCTTTTTTCTCTTTTT
Found at i:4046671 original size:26 final size:28
Alignment explanation
Indices: 4046637--4046701 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 28
4046627 CTTGACCCCC
*
4046637 CTTTTTCTTCTTT-TTTCTCTTTTTTCT
1 CTTTTTCTTCTTTCTCTCTCTTTTTTCT
*
4046664 -TTTTTCTT-TTTCTCTCTTTTTTTTCT
1 CTTTTTCTTCTTTCTCTCTCTTTTTTCT
*
4046690 CTTTTTTTTCTT
1 CTTTTTCTTCTT
4046702 CAAGCATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 3 0.09
26 20 0.62
27 7 0.22
28 2 0.06
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (28 bp):
CTTTTTCTTCTTTCTCTCTCTTTTTTCT
Found at i:4046696 original size:13 final size:13
Alignment explanation
Indices: 4046656--4046698 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
4046646 CTTTTTTCTC
4046656 TTTTTTCT-TTTT
1 TTTTTTCTCTTTT
*
4046668 TCTTTTTCTCTCTT
1 T-TTTTTCTCTTTT
4046682 TTTTTTCTCTTTT
1 TTTTTTCTCTTTT
4046695 TTTT
1 TTTT
4046699 CTTCAAGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 1 0.04
13 22 0.81
14 4 0.15
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTCTCTTTT
Found at i:4046701 original size:9 final size:9
Alignment explanation
Indices: 4046638--4046697 Score: 61
Period size: 10 Copynumber: 6.6 Consensus size: 9
4046628 TTGACCCCCC
4046638 TTTTTCTTCT
1 TTTTTCTT-T
*
4046648 TTTTTCTCT
1 TTTTTCTTT
4046657 TTTTTC--T
1 TTTTTCTTT
4046664 TTTTTCTTT
1 TTTTTCTTT
*
4046673 TTCTCTCTTT
1 TT-TTTCTTT
4046683 TTTTTCTCTT
1 TTTTTCT-TT
4046693 TTTTT
1 TTTTT
4046698 TCTTCAAGCA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
7 7 0.16
9 14 0.33
10 22 0.51
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:4053964 original size:15 final size:15
Alignment explanation
Indices: 4053941--4053972 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4053931 TGAAATGAAT
4053941 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
4053956 AATGCATGTATGCAA
1 AATGAATGTATGCAA
4053971 AA
1 AA
4053973 AGGTATTGAT
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:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:4058093 original size:25 final size:25
Alignment explanation
Indices: 4058031--4058093 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
4058021 ATAATAAAAA
*
4058031 AAATATTTAAATATACAAGTAAAATT
1 AAATATTTAAA-ATACAAGTAAAACT
* * * *
4058057 AAATAATAAAAATACAATTAGAACT
1 AAATATTTAAAATACAAGTAAAACT
*
4058082 ATATATTTAAAA
1 AAATATTTAAAA
4058094 GCAATAAAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
25 20 0.69
26 9 0.31
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (25 bp):
AAATATTTAAAATACAAGTAAAACT
Found at i:4058874 original size:13 final size:13
Alignment explanation
Indices: 4058856--4058917 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
4058846 TTGTGGGTTA
*
4058856 TTGTTCTTTGTTT
1 TTGTTCTCTGTTT
4058869 TTGTTCTCTGTTT
1 TTGTTCTCTGTTT
* *
4058882 TTGCTGGTCTCTCTTCG
1 TTG-T--TCTCTGTT-T
*
4058899 TTGTTCTCTGTCT
1 TTGTTCTCTGTTT
4058912 TTGTTC
1 TTGTTC
4058918 GCAGATGGGG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
13 21 0.54
14 7 0.18
16 8 0.21
17 3 0.08
ACGTcount: A:0.00, C:0.19, G:0.18, T:0.63
Consensus pattern (13 bp):
TTGTTCTCTGTTT
Found at i:4059379 original size:24 final size:24
Alignment explanation
Indices: 4059311--4059379 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 24
4059301 TGTAATATTA
* *
4059311 AATAA-TA-TATATTAATATTAAT
1 AATAATTATTATATAAATAATAAT
4059333 AATAATTATTATTATAATTATAATAAT
1 AATAATTATTA-TATAA--ATAATAAT
4059360 AATAATTATTATATAAATAA
1 AATAATTATTATATAAATAA
4059380 CATAAAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 5 0.12
23 2 0.05
24 6 0.15
25 4 0.10
26 5 0.12
27 18 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AATAATTATTATATAAATAATAAT
Found at i:4061723 original size:19 final size:19
Alignment explanation
Indices: 4061701--4061745 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4061691 TTTATTACTA
4061701 TAATTT-TAAGTAAATTTAT
1 TAATTTATAAG-AAATTTAT
*
4061720 TAATTTATAAGATATTTAT
1 TAATTTATAAGAAATTTAT
*
4061739 TTATTTA
1 TAATTTA
4061746 GAAATATCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
TAATTTATAAGAAATTTAT
Found at i:4063521 original size:2 final size:2
Alignment explanation
Indices: 4063514--4063547 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4063504 TGGGCTTGTA
4063514 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
4063548 TAATAATAAA
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:4063854 original size:76 final size:76
Alignment explanation
Indices: 4063723--4064899 Score: 2048
Period size: 76 Copynumber: 15.5 Consensus size: 76
4063713 GATGGAAATG
* * *
4063723 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
4063788 CCTGAAGGCTT
66 CCCGAAGGCTT
*
4063799 TTTGGAAACATCATGCACTGAAAGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
4063864 CCCGAAGGGTT
66 CCCGAAGGCTT
*
4063875 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
4063940 CCCGAAGGGTT
66 CCCGAAGGCTT
* *
4063951 TTTGGAAACAGCATGCACTGAAGGACTTACAGATGACCTTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
4064016 CCCGAAGGCTTT
66 CCCGAAGGC-TT
* *
4064028 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
4064093 CCTGAAGGCTT
66 CCCGAAGGCTT
*
4064104 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
4064169 CCCGAAGGCTTT
66 CCCGAAGGC-TT
* *
4064181 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
4064246 CCTGAAGGCTT
66 CCCGAAGGCTT
4064257 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
4064322 CCCGAAGGCTT
66 CCCGAAGGCTT
*
4064333 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
4064398 CCTGAAGGCTT
66 CCCGAAGGCTT
*
4064409 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCTTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
4064474 CCCGAAGGCTT
66 CCCGAAGGCTT
*
4064485 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
4064550 CCTGAAGGCTT
66 CCCGAAGGCTT
*
4064561 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCTTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
4064626 CCCGAAGGCTT
66 CCCGAAGGCTT
* * * *
4064637 TTTGGAAACATCATGCACTAAAGGGCTTACAGATGATCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
4064702 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
4064713 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
4064778 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
4064789 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
4064854 CCTGAAGGCTT
66 CCCGAAGGCTT
4064865 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
4064900 TAGGAAATAG
Statistics
Matches: 1050, Mismatches: 49, Indels: 4
0.95 0.04 0.00
Matches are distributed among these distances:
76 907 0.86
77 143 0.14
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:4065603 original size:22 final size:22
Alignment explanation
Indices: 4065578--4065632 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
4065568 CATAAAGTTT
*
4065578 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
4065600 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
4065622 TCATCTTTGAA
1 TCATCTTTGAA
4065633 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:4066082 original size:54 final size:52
Alignment explanation
Indices: 4066000--4066109 Score: 166
Period size: 54 Copynumber: 2.1 Consensus size: 52
4065990 AGAATAACAG
***
4066000 GTTCGTAAAACATTTGACAGTGCATTCATCTTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCAT-TTTT-CTGTGGCTTCTGCTCAGAT
*
4066054 GTTCGTAAAACATTTGACAACACATTCATTTTTTTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATTTTTCTGTGGCTTCTGCTCAGAT
4066106 GTTC
1 GTTC
4066110 TCAATCATTG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 22 0.42
53 4 0.08
54 26 0.50
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (52 bp):
GTTCGTAAAACATTTGACAACACATTCATTTTTCTGTGGCTTCTGCTCAGAT
Found at i:4067085 original size:157 final size:157
Alignment explanation
Indices: 4066799--4067112 Score: 610
Period size: 157 Copynumber: 2.0 Consensus size: 157
4066789 TTGAAAACAT
*
4066799 ACTTGCTGAGTAAACATTTATTCAACATCATGATCATAAATGTAATTGCCTGATGAATGAAGCAA
1 ACTTGCTGAGTAAACATTTATTCAACATCATGATCATAAATGTAATTGCCTGATGAACGAAGCAA
*
4066864 TTATGTATAGTCAGCTAGACTGTCACTGTTTCACCATTTTCATTCTTCATATCTTTCTGTCTCAT
66 TTATGTATAGTCAGCTAGACTGTCACTGTTTCACCATTTTCATTCTTCATAACTTTCTGTCTCAT
4066929 TGGAAATATTTGTTCAAGTCAATGATC
131 TGGAAATATTTGTTCAAGTCAATGATC
4066956 ACTTGCTGAGTAAACATTTATTCAACATCATGATCATAAATGTAATTGCCTGATGAACGAAGCAA
1 ACTTGCTGAGTAAACATTTATTCAACATCATGATCATAAATGTAATTGCCTGATGAACGAAGCAA
4067021 TTATGTATAGTCAGCTAGACTGTCACTGTTTCACCATTTTCATTCTTCATAACTTTCTGTCTCAT
66 TTATGTATAGTCAGCTAGACTGTCACTGTTTCACCATTTTCATTCTTCATAACTTTCTGTCTCAT
4067086 TGGAAATATTTGTTCAAGTCAATGATC
131 TGGAAATATTTGTTCAAGTCAATGATC
4067113 TTTACACAGG
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (157 bp):
ACTTGCTGAGTAAACATTTATTCAACATCATGATCATAAATGTAATTGCCTGATGAACGAAGCAA
TTATGTATAGTCAGCTAGACTGTCACTGTTTCACCATTTTCATTCTTCATAACTTTCTGTCTCAT
TGGAAATATTTGTTCAAGTCAATGATC
Found at i:4068648 original size:93 final size:93
Alignment explanation
Indices: 4068489--4068674 Score: 284
Period size: 93 Copynumber: 2.0 Consensus size: 93
4068479 TATGAGCAAA
* * * *
4068489 ATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAG
1 ATTCATCTTCCAAATCCAATGATTGAATCTGGAGTTCATACCAAACCAGATCAGATAACTCAAAG
*
4068554 AACACTTCCAGAAGATGCTATTGAGCCT
66 AACACTTCCAAAAGATGCTATTGAGCCT
* * *
4068582 ATTCATCTTCCAAATTCAATGATTGAATCTGTG-GTTTATCCCAAACCAGATCAGATAACTCAAA
1 ATTCATCTTCCAAATCCAATGATTGAATCTG-GAGTTCATACCAAACCAGATCAGATAACTCAAA
4068646 GAACACTTCCAAAAGATGCTATTGAGCCT
65 GAACACTTCCAAAAGATGCTATTGAGCCT
4068675 CCTTATTTCT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
93 83 0.99
94 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (93 bp):
ATTCATCTTCCAAATCCAATGATTGAATCTGGAGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAAAAGATGCTATTGAGCCT
Found at i:4068762 original size:207 final size:207
Alignment explanation
Indices: 4068414--4068873 Score: 798
Period size: 206 Copynumber: 2.2 Consensus size: 207
4068404 GGGGTTCCTA
* * * * * *
4068414 CCAAATCAGATCAGATAACTCAAATAACATTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTAC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCCTCCTTATTTCTAC
*
4068479 TATGAGCAAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGA
66 CATGAGCAAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGA
4068544 TAACTCAAAGAACACTTCCAGAAGATGCTATTGAGC-CTATTCATCTTCCAAATTCAATGATTGA
131 TAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCAC-ATTCATCTTCCAAATTCAATGATTGA
4068608 ATCTGTGGTTTATC
194 ATCTGTGGTTTATC
4068622 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCCTCCTTATTTCTAC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCCTCCTTATTTCTAC
4068687 CATGAGC-AAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGA
66 CATGAGCAAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGA
* * *
4068751 TAATTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATTTTCCAAATTCAATGATTGATT
131 TAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGAAT
4068816 CTGTGGTTTATC
196 CTGTGGTTTATC
4068828 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTAT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTAT
4068874 AAGCACATTC
Statistics
Matches: 241, Mismatches: 10, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
206 89 0.37
207 87 0.36
208 65 0.27
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (207 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCCTCCTTATTTCTAC
CATGAGCAAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGA
TAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGAAT
CTGTGGTTTATC
Found at i:4068965 original size:93 final size:93
Alignment explanation
Indices: 4068691--4068966 Score: 423
Period size: 92 Copynumber: 3.0 Consensus size: 93
4068681 TTCTACCATG
* * * * *
4068691 AGCAAATTCATCTTTCAAATCCAATGATTGATT-T-TGGAGTTCATACCAAATCAGATCAGATAA
1 AGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGG-TTTCATACCAAACCAGATCAGATAA
* *
4068754 TTCAAAGAACACTTCCAGAAGATGCTATG
65 CTCAAAGAACACTTCCAGAAGATGCTATA
* *
4068783 AGCACATTCATTTTCCAAATTCAATGATTGATTCTGTGGTTT-ATCCCAAACCAGATCAGATAAC
1 AGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAGATAAC
*
4068847 TCAAAGAACACTTCCAAAAGATGCTATA
66 TCAAAGAACACTTCCAGAAGATGCTATA
*
4068875 AGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAAC
1 AGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAGATAAC
4068940 TCAAAGAACACTTCCAGAAGATGCTAT
66 TCAAAGAACACTTCCAGAAGATGCTAT
4068967 TGGGTCTCCT
Statistics
Matches: 167, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
92 114 0.68
93 50 0.30
94 3 0.02
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (93 bp):
AGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAGATAAC
TCAAAGAACACTTCCAGAAGATGCTATA
Found at i:4075608 original size:18 final size:19
Alignment explanation
Indices: 4075582--4075627 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
4075572 TGAAATATTA
4075582 ATAAGAAATATATAA-TAT-T
1 ATAA-AAATA-ATAAGTATAT
*
4075601 ATGAAAATAATAAGTATAT
1 ATAAAAATAATAAGTATAT
4075620 ATAAAAAT
1 ATAAAAAT
4075628 TTTGAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.33
Consensus pattern (19 bp):
ATAAAAATAATAAGTATAT
Found at i:4075633 original size:28 final size:28
Alignment explanation
Indices: 4075571--4075635 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 28
4075561 TGCAAATAAA
*
4075571 ATGAAATATTAATAAGAAATATATAATATT
1 ATGAAA-A-TAATAAGAAATATATAAAATT
*
4075601 ATGAAAATAATAAG-TATATATAAAAATT
1 ATGAAAATAATAAGAAATATAT-AAAATT
*
4075629 TTGAAAA
1 ATGAAAA
4075636 GAAAGAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 6 0.19
28 18 0.58
29 1 0.03
30 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (28 bp):
ATGAAAATAATAAGAAATATATAAAATT
Found at i:4076110 original size:19 final size:19
Alignment explanation
Indices: 4076088--4076132 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4076078 TTTATTACTA
4076088 TAATTT-TAAGTAAATTTAT
1 TAATTTATAAG-AAATTTAT
*
4076107 TAATTTATAAGATATTTAT
1 TAATTTATAAGAAATTTAT
*
4076126 TTATTTA
1 TAATTTA
4076133 GAAATATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
TAATTTATAAGAAATTTAT
Found at i:4076512 original size:15 final size:15
Alignment explanation
Indices: 4076487--4076522 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
4076477 TAAACATATC
4076487 AAAAGTAATAATAAAT
1 AAAA-TAATAATAAAT
*
4076503 AAAATAATAATAATT
1 AAAATAATAATAAAT
4076518 AAAAT
1 AAAAT
4076523 GAAAGAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAATAATAATAAAT
Found at i:4077876 original size:2 final size:2
Alignment explanation
Indices: 4077863--4077920 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
4077853 TGGGCTTGTA
*
4077863 AT AT AT AG 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 AT AT AT
4077905 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
4077921 TAATAATAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4077952 original size:15 final size:15
Alignment explanation
Indices: 4077927--4077968 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
4077917 ATATTAATAA
4077927 TAATAAT-ATAATTT
1 TAATAATAATAATTT
* *
4077941 TAGTAATAATAAATT
1 TAATAATAATAATTT
4077956 TAATAATAATAAT
1 TAATAATAATAAT
4077969 AAAATTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
TAATAATAATAATTT
Found at i:4085546 original size:32 final size:35
Alignment explanation
Indices: 4085481--4085549 Score: 117
Period size: 32 Copynumber: 2.1 Consensus size: 35
4085471 CCAAAAAAGA
4085481 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
4085516 AGAGTTGGATTA-GACTC-AATA-TAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
4085548 AG
1 AG
4085550 GGTTTTTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 13 0.38
33 4 0.12
34 5 0.15
35 12 0.35
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:4086198 original size:2 final size:2
Alignment explanation
Indices: 4086193--4086221 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4086183 CTTATAACTT
4086193 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 T
4086222 TATTTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4086268 original size:23 final size:21
Alignment explanation
Indices: 4086213--4086270 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
4086203 TATATATATA
4086213 TATATATATTATTTTTTATTAT
1 TATAT-TATTATTTTTTATTAT
*
4086235 T-T-TCATT-TTTTATTCATTAT
1 TATATTATTATTTT-TT-ATTAT
4086255 TATATTATTATTTTTT
1 TATATTATTATTTTTT
4086271 TAAATCTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 4 0.14
19 5 0.17
20 7 0.24
21 2 0.07
22 7 0.24
23 4 0.14
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (21 bp):
TATATTATTATTTTTTATTAT
Found at i:4086484 original size:38 final size:40
Alignment explanation
Indices: 4086433--4086512 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
4086423 AGTGAGAGGG
*
4086433 TAGCTTTTCTATTTT-TAAATA-TTTGTTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
4086471 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
4086511 TA
1 TA
4086513 TATTTTCCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.56
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:4086589 original size:9 final size:9
Alignment explanation
Indices: 4086577--4086605 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
4086567 CCTTATCTTA
4086577 TTTATTTAT
1 TTTATTTAT
4086586 TTTATTTAT
1 TTTATTTAT
4086595 TTTATTT-T
1 TTTATTTAT
4086603 TTT
1 TTT
4086606 CCCTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTATTTAT
Found at i:4086626 original size:15 final size:15
Alignment explanation
Indices: 4086581--4086626 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
4086571 ATCTTATTTA
*
4086581 TTTATTTTATT-TAT
1 TTTATTTTATTCTCT
* *
4086595 TTTATTTTTTTCCCT
1 TTTATTTTATTCTCT
4086610 TTTATTTTATTCTCT
1 TTTATTTTATTCTCT
4086625 TT
1 TT
4086627 ATCTTATTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTTATTCTCT
Found at i:4087577 original size:10 final size:10
Alignment explanation
Indices: 4087564--4087592 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
4087554 CATTTTTTTA
4087564 TTTTTATTTG
1 TTTTTATTTG
4087574 TTTTTATTTG
1 TTTTTATTTG
4087584 TTTTTATTT
1 TTTTTATTT
4087593 TACTAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (10 bp):
TTTTTATTTG
Found at i:4087610 original size:28 final size:26
Alignment explanation
Indices: 4087558--4087622 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
4087548 TTTTTCCATT
* **
4087558 TTTTTATTTTTATTTGTTTTTATTTG
1 TTTTTATTTTTAATTGTTTGCATTTG
4087584 TTTTTATTTTACTAATTGTTTGCATTTG
1 TTTTTATTTT--TAATTGTTTGCATTTG
* *
4087612 TATTTGTTTTT
1 TTTTTATTTTT
4087623 TAGCATTTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
26 11 0.34
28 21 0.66
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (26 bp):
TTTTTATTTTTAATTGTTTGCATTTG
Found at i:4095173 original size:106 final size:106
Alignment explanation
Indices: 4094938--4095774 Score: 1069
Period size: 106 Copynumber: 8.0 Consensus size: 106
4094928 CGCGCCACTA
* * * *
4094938 GAGACAACACAAGTTCAACTTCACAATGAAGGGACAGCTGGTTGTCAACAAACCACTTT-TCAGT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAA-CAATTTCCCA--
*
4095002 TTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
63 AT--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* *
4095048 GGGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAATAAACAATTTCCCAATT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATT
* * * *
4095113 TCAGAGCCAATTTCAACTTCACATCGAAAGATGTTAGACTC
66 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
*
4095154 GGGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATT
* * *
4095219 TCAGAGTCAATTTCAACTTCACAGCAAAGGATATTAGACTC
66 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* *
4095260 AAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATCTCCCAATT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATT
* *
4095325 TCAGAG-C-----CAA--T---AGCAAAGGATATTGGACTT
66 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
** * *
4095355 GAGATGACACAAGTTCAACTTCACAACGAAGGGACGGCT-GCT-T-ATCAAACAATTTCCCAATT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATT
* * * *
4095417 TTAGAGTCAATTTCTACTTCACATCGAAGGATATTGGACTC
66 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* *
4095458 GAGAC--CACAAGTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAACAAATAATTTCCCAATT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATT
4095521 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
66 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* * *
4095562 GAGACGACACAAGTTCAACTTCACAACGAAGGGATGACTGGTTGTCAACAAACAATTTCCCAATT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATT
* * * *
4095627 TCAGGGTCAATTTCAACTTCACATCGAAGGATATTAGACTC
66 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* * * * * * * * *
4095668 AAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGTTGGCTGTCAACAAACAATTTTCCAGTT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATT
* * * *
4095733 CCAAAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTC
66 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
4095774 G
1 G
4095775 GAACAATACA
Statistics
Matches: 640, Mismatches: 70, Indels: 38
0.86 0.09 0.05
Matches are distributed among these distances:
92 22 0.03
93 2 0.00
94 2 0.00
95 53 0.08
98 3 0.00
100 4 0.01
101 32 0.05
102 2 0.00
103 21 0.03
104 59 0.09
105 1 0.00
106 383 0.60
108 1 0.00
109 5 0.01
110 50 0.08
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATT
TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
Found at i:4095584 original size:302 final size:304
Alignment explanation
Indices: 4095033--4095630 Score: 948
Period size: 302 Copynumber: 2.0 Consensus size: 304
4095023 CTTCACAGCG
* * *
4095033 AAGGATATTGGACTCGGGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAATA
1 AAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTATC-A-A
* *
4095098 AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAAGATGTTAGACTCGGGACAACA
64 AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAAGATATTAGACTCGAGAC-ACA
* *
4095163 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTCA
128 CAAGTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
4095228 ATTTCAACTTCACAGCAAAGGATATTAGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
193 ATTTCAACTTCACAGCAAAGGATATTAGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
*
4095293 ACGGCTGGTTGTCAACAAACAATCTCCCAATTTCAGAGCCAATAGCA
258 ACGACTGGTTGTCAACAAACAATCTCCCAATTTCAGAGCCAATAGCA
* **
4095340 AAGGATATTGGACTTGAGATGACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTATC-AAA
1 AAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTATCAAAA
* * * * *
4095404 CAATTTCCCAATTTTAGAGTCAATTTCTACTTCACATCGAAGGATATTGGACTCGAGAC-CACAA
66 CAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAAGATATTAGACTCGAGACACACAA
*
4095468 GTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAACAAATAATTTCCCAATTTCAGAGCCAATT
131 GTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATT
* * * * *
4095533 TCAACTTCACAGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGATG
196 TCAACTTCACAGCAAAGGATATTAGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACG
*
4095598 ACTGGTTGTCAACAAACAATTTCCCAATTTCAG
261 ACTGGTTGTCAACAAACAATCTCCCAATTTCAG
4095631 GGTCAATTTC
Statistics
Matches: 268, Mismatches: 23, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
302 158 0.59
304 55 0.21
307 55 0.21
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (304 bp):
AAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTATCAAAA
CAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAAGATATTAGACTCGAGACACACAA
GTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATT
TCAACTTCACAGCAAAGGATATTAGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACG
ACTGGTTGTCAACAAACAATCTCCCAATTTCAGAGCCAATAGCA
Found at i:4096350 original size:35 final size:35
Alignment explanation
Indices: 4096258--4096329 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
4096248 CCAAAAAAGA
4096258 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
4096293 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
4096328 AG
1 AG
4096330 GGTTTTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Done.