Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002352.1 Hibiscus syriacus cultivar Beakdansim tig00004797_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: 2012169
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 10
Found at i:616930 original size:14 final size:15
Alignment explanation
Indices: 616906--616973 Score: 51
Period size: 14 Copynumber: 4.9 Consensus size: 15
616896 TTTAAAATTG
616906 TAGAT-ATAATATTT
1 TAGATAATAATATTT
616920 TA-ATAATAATA-TT
1 TAGATAATAATATTT
* *
616933 GATATAAATAATA--T
1 TAGAT-AATAATATTT
616947 TAGATAA-AATATTT
1 TAGATAATAATATTT
*
616961 TA-AAAATAATATT
1 TAGATAATAATATT
616974 ATTATTTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
12 4 0.09
13 10 0.23
14 23 0.52
15 7 0.16
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (15 bp):
TAGATAATAATATTT
Found at i:616944 original size:15 final size:15
Alignment explanation
Indices: 616924--616957 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
616914 ATATTTTAAT
616924 AATAATATT-GATATA
1 AATAATATTAGATA-A
616939 AATAATATTAGATAA
1 AATAATATTAGATAA
616954 AATA
1 AATA
616958 TTTTAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
AATAATATTAGATAA
Found at i:617801 original size:30 final size:27
Alignment explanation
Indices: 617735--617801 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 27
617725 GCATAAACAC
617735 TAAAAATATTATTATTTTAAATATTTAA
1 TAAAAATA-TATTATTTTAAATATTTAA
** *
617763 TATTAATATATTATTTTAGTATCATTTTAA
1 TAAAAATATATTATTTTA-AAT-A-TTTAA
617793 TAAAAATAT
1 TAAAAATAT
617802 TAATTATTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
27 10 0.32
28 8 0.26
29 1 0.03
30 12 0.39
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
TAAAAATATATTATTTTAAATATTTAA
Found at i:618370 original size:21 final size:21
Alignment explanation
Indices: 618346--618389 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
618336 CAGACCCTTA
618346 AACATGAATTATCAAGCAATC
1 AACATGAATTATCAAGCAATC
618367 AACATGAATTATCAAGCAATC
1 AACATGAATTATCAAGCAATC
618388 AA
1 AA
618390 GCTACATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.23
Consensus pattern (21 bp):
AACATGAATTATCAAGCAATC
Found at i:623085 original size:55 final size:55
Alignment explanation
Indices: 622946--623105 Score: 196
Period size: 57 Copynumber: 2.9 Consensus size: 55
622936 AGCGTATTTA
* * *
622946 CTCCCTATTCTTTTCAGGGAGTATAGAATTCAATAAATCTTCAGAAAAATAGGTTCG
1 CTCCCTATTC-TTTCAGGGAGTATAGAACTCAAGAAATCTTCAGAAAAATA-GTCCG
* * **
623003 CTCCCTATTCCTTTCAGGGAGTTTAGAACTCGAGAAATCTTCAGCAAACGTA-TCCG
1 CTCCCTATT-CTTTCAGGGAGTATAGAACTCAAGAAATCTTCAG-AAAAATAGTCCG
* *
623059 CTCTCTATTCTTTCAGGGAGTATAGAACTCAAGAAATCTTCTGAAAA
1 CTCCCTATTCTTTCAGGGAGTATAGAACTCAAGAAATCTTCAGAAAA
623106 CGGGTTTGCT
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
54 3 0.03
55 31 0.35
56 11 0.12
57 38 0.43
58 6 0.07
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (55 bp):
CTCCCTATTCTTTCAGGGAGTATAGAACTCAAGAAATCTTCAGAAAAATAGTCCG
Found at i:623107 original size:55 final size:56
Alignment explanation
Indices: 622946--623125 Score: 204
Period size: 55 Copynumber: 3.2 Consensus size: 56
622936 AGCGTATTTA
* * * *
622946 CTCCCTATTCTTTTCAGGGAGTATAGAATTCAATAAATCTTCAGAAAA-ATAGGTTCG
1 CTCCCTATTC-TTTCAGGGAGTATAGAACTCAAGAAATCTTCAGAAAACGTA-GTCCG
* * *
623003 CTCCCTATTCCTTTCAGGGAGTTTAGAACTCGAGAAATCTTCAGCAAACGTA-TCCG
1 CTCCCTATT-CTTTCAGGGAGTATAGAACTCAAGAAATCTTCAGAAAACGTAGTCCG
* * * **
623059 CTCTCTATTCTTTCAGGGAGTATAGAACTCAAGAAATCTTCTGAAAACG-GGTTTG
1 CTCCCTATTCTTTCAGGGAGTATAGAACTCAAGAAATCTTCAGAAAACGTAGTCCG
623114 CTCCCTATTCTT
1 CTCCCTATTCTT
623126 CTAAGAAGTC
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
55 49 0.47
56 11 0.11
57 41 0.39
58 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (56 bp):
CTCCCTATTCTTTCAGGGAGTATAGAACTCAAGAAATCTTCAGAAAACGTAGTCCG
Found at i:623542 original size:215 final size:215
Alignment explanation
Indices: 623170--623931 Score: 1161
Period size: 215 Copynumber: 3.5 Consensus size: 215
623160 ACCTTGGTGC
* * * * * * * *
623170 AAAACATCCTGCCCGAAGGTCTTATTGATGACCCGAAGGATTTATCATCTTGCTCGAGAGACTCA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
* * *
623235 CAAATAACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTATAA
* * *
623300 ATCGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
131 ATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTT
*
623365 CTCATTTTCAAATTCATTTG
196 TTCATTTTCAAATTCATTTG
* *
623385 AAAACATCCTACCCGAAGGTCTTATAGACGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
* * *
623450 CAGATGACCCTAAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGGCTTGAAGGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTATAA
*
623515 ATTATGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACGTCATCAT
131 ATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAA---CATCA-
* *
623580 TTTTTTTATTTTCAAATTCA-TGG
192 TTTTTTCATTTTCAAATTCATTTG
* * *
623603 AAAACA-CCATACCCGAAGGTCTTATGGATGGCCCGAAGGAATTATCATCTTGCTATAAACGCTT
1 AAAACATCC-TACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTT
*
623667 ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATA
65 ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTATA
* *
623732 AATTGTGAAATTTTGAAAATCGCATTATTCGTTTT-AAAAATTTTCATCTTCTTAAGACATCATT
130 AATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAA-TTTCATCTTCTTAAAACATCATT
* *
623796 TTTTCATTTCCAAATTCATGTG
194 TTTTCATTTTCAAATTCATTTG
*
623818 AAAACATCCTACCCGAATGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
623883 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
623932 GTTTGCTTCA
Statistics
Matches: 497, Mismatches: 42, Indels: 16
0.90 0.08 0.03
Matches are distributed among these distances:
214 18 0.04
215 280 0.56
216 2 0.00
217 7 0.01
218 172 0.35
219 18 0.04
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (215 bp):
AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTATAA
ATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTT
TTCATTTTCAAATTCATTTG
Found at i:623721 original size:42 final size:41
Alignment explanation
Indices: 623629--623725 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 41
623619 AGGTCTTATG
* * *
623629 GATGGCCCGAAGGAATTATCATCTTGCTATAAACGCTTACA
1 GATGGCCCGAAGGAATTAGCATCATGCTAGAAACGCTTACA
* * * *
623670 GATGACCCGAAGGATTTAAGCATCATGCTCGAAA-GACTTACT
1 GATGGCCCGAAGGAATT-AGCATCATGCTAGAAACG-CTTACA
623712 GATGGCCCGAAGGA
1 GATGGCCCGAAGGA
623726 CTTATAAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 16 0.35
42 30 0.65
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.23
Consensus pattern (41 bp):
GATGGCCCGAAGGAATTAGCATCATGCTAGAAACGCTTACA
Found at i:623925 original size:42 final size:41
Alignment explanation
Indices: 623844--623930 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 41
623834 ATGTCTTATG
* * * * *
623844 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGACCCGAAGGACTTAGCATCATGCTCGAAAGACTTACA
* *
623885 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGACTT-AGCATCATGCTCGAAAGACTTACA
623927 GATG
1 GATG
623931 GGTTTGCTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 15 0.39
42 23 0.61
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (41 bp):
GATGACCCGAAGGACTTAGCATCATGCTCGAAAGACTTACA
Found at i:624026 original size:37 final size:37
Alignment explanation
Indices: 623969--624121 Score: 211
Period size: 37 Copynumber: 4.1 Consensus size: 37
623959 CTTAAGGTGG
* *
623969 TGCTTCACTAC-TCTTCGGTGAAGGTTTAAGATTGATT
1 TGCTTCACTCCTTCTT-GGTGAAGGCTTAAGATTGATT
*
624006 TGCTTCACTTCTTCTTGGTGAAGGCTTAAGATTGATT
1 TGCTTCACTCCTTCTTGGTGAAGGCTTAAGATTGATT
*
624043 TACTTCACTCCTTCTTGGTGAAGGCTTAAGATTGATT
1 TGCTTCACTCCTTCTTGGTGAAGGCTTAAGATTGATT
* *
624080 TGCTT-ACCTCCTTTTTAGTGAAGGCTTAAGATTGAATT
1 TGCTTCA-CTCCTTCTTGGTGAAGGCTTAAGATTG-ATT
624118 TGCT
1 TGCT
624122 CCAATCTCAT
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
36 1 0.01
37 94 0.89
38 11 0.10
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (37 bp):
TGCTTCACTCCTTCTTGGTGAAGGCTTAAGATTGATT
Found at i:626168 original size:2 final size:2
Alignment explanation
Indices: 626157--626185 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
626147 TTGTATACAC
626157 AT AT -T 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
626186 TGTTGGGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:630407 original size:21 final size:21
Alignment explanation
Indices: 630375--630429 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
630365 ACCTCCAATG
630375 TGAAGTGGTCTTCATGTCTTTA
1 TGAAG-GGTCTTCATGTCTTTA
630397 TGAAGGGTCTTCATGTCTTTA
1 TGAAGGGTCTTCATGTCTTTA
*
630418 TGAATGGTCTTC
1 TGAAGGGTCTTC
630430 TCATCTTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 27 0.84
22 5 0.16
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.44
Consensus pattern (21 bp):
TGAAGGGTCTTCATGTCTTTA
Found at i:630436 original size:21 final size:21
Alignment explanation
Indices: 630375--630437 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
630365 ACCTCCAATG
*
630375 TGAAGTGGTCTTCATGTCTTTA
1 TGAAG-GGTCTTCATATCTTTA
*
630397 TGAAGGGTCTTCATGTCTTTA
1 TGAAGGGTCTTCATATCTTTA
*
630418 TGAATGGTCTTC-TCATCTTT
1 TGAAGGGTCTTCAT-ATCTTT
630438 GGTATGACTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 1 0.03
21 32 0.84
22 5 0.13
ACGTcount: A:0.17, C:0.16, G:0.21, T:0.46
Consensus pattern (21 bp):
TGAAGGGTCTTCATATCTTTA
Found at i:635847 original size:37 final size:34
Alignment explanation
Indices: 635801--636012 Score: 119
Period size: 35 Copynumber: 5.8 Consensus size: 34
635791 ATAGTTTTTG
*
635801 AAAATATATAATATATAGTTTTTGAAAACGTATTTAAAA
1 AAAAAATATAATATATAGTTTTT-AAAA-GTATTT---A
635840 AAAATATATATAATATATAGTTTTTTTAAAA-TAGTTTCA
1 AAAA-A-ATATAATATATAG--TTTTTAAAAGTA-TTT-A
* ** *
635879 AAAAAGTATAATATATAGTTTTTAAAACGGGTTTG
1 AAAAAATATAATATATAGTTTTTAAAA-GTATTTA
* *
635914 AAAACATAT-ATAATATAGTTTTTTGAAATAGT-TTTG
1 AAAAAATATAAT-ATATAG-TTTTT-AAA-AGTATTTA
* *
635950 AAAACATATAATATATAGTTTTTAAAATGGT-TTTG
1 AAAAAATATAATATATAGTTTTTAAAA--GTATTTA
*
635985 AAAACATAT-ATAATATAGTTTTTTAAAA
1 AAAAAATATAAT-ATATAG-TTTTTAAAA
636013 ACGGTTTTGA
Statistics
Matches: 148, Mismatches: 9, Indels: 35
0.77 0.05 0.18
Matches are distributed among these distances:
33 1 0.01
34 7 0.05
35 48 0.32
36 36 0.24
37 18 0.12
38 2 0.01
39 9 0.06
40 2 0.01
41 16 0.11
42 4 0.03
43 5 0.03
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (34 bp):
AAAAAATATAATATATAGTTTTTAAAAGTATTTA
Found at i:635901 original size:35 final size:36
Alignment explanation
Indices: 635847--636115 Score: 259
Period size: 35 Copynumber: 7.3 Consensus size: 36
635837 AAAAAAATAT
* *
635847 ATATAATATATAGTTTTTTTAAAATAG-TTTCAAAAA
1 ATATAATATATAG-TTTTTTAAAATAGTTTTGAAAAC
** *
635883 AGTATAATATATAG-TTTTTAAAACGGGTTTGAAAAC
1 A-TATAATATATAGTTTTTTAAAATAGTTTTGAAAAC
*
635919 ATAT-ATAATATAGTTTTTTGAAATAGTTTTGAAAAC
1 ATATAAT-ATATAGTTTTTTAAAATAGTTTTGAAAAC
*
635955 ATATAATATATAG-TTTTTAAAATGGTTTTGAAAAC
1 ATATAATATATAGTTTTTTAAAATAGTTTTGAAAAC
635990 ATAT-ATAATATAGTTTTTTAAAA-ACGGTTTTGAAAAC
1 ATATAAT-ATATAGTTTTTTAAAATA--GTTTTGAAAAC
636027 ATAT-ATAATATAGGTTTTTTAAAA-ACGGTTTTGAAAAC
1 ATATAAT-ATATA-GTTTTTTAAAATA--GTTTTGAAAAC
* *
636065 ATATAGTATAT-GATTTTTTAAAAAAGAGGTTTTGAAAAC
1 ATATAATATATAG-TTTTTT--AAAATA-GTTTTGAAAAC
*
636104 TTATAATATATA
1 ATATAATATATA
636116 TATATATATA
Statistics
Matches: 203, Mismatches: 14, Indels: 28
0.83 0.06 0.11
Matches are distributed among these distances:
34 4 0.02
35 49 0.24
36 47 0.23
37 43 0.21
38 33 0.16
39 26 0.13
40 1 0.00
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (36 bp):
ATATAATATATAGTTTTTTAAAATAGTTTTGAAAAC
Found at i:636019 original size:37 final size:37
Alignment explanation
Indices: 635891--636113 Score: 270
Period size: 38 Copynumber: 6.1 Consensus size: 37
635881 AAAGTATAAT
*
635891 ATATAG-TTTTT-AAAACGGGTTTGAAAACATATATA
1 ATATAGTTTTTTAAAAACGGTTTTGAAAACATATATA
*
635926 ATATAGTTTTTTGAAATA--GTTTTGAAAACATATA-A
1 ATATAGTTTTTT-AAAAACGGTTTTGAAAACATATATA
*
635961 TATATAG-TTTTT-AAAATGGTTTTGAAAACATATATA
1 -ATATAGTTTTTTAAAAACGGTTTTGAAAACATATATA
635997 ATATAGTTTTTTAAAAACGGTTTTGAAAACATATATA
1 ATATAGTTTTTTAAAAACGGTTTTGAAAACATATATA
636034 ATATAGGTTTTTTAAAAACGGTTTTGAAAACATATAGT-
1 ATATA-GTTTTTTAAAAACGGTTTTGAAAACATATA-TA
*
636072 ATAT-GATTTTTTAAAAAAGAGGTTTTGAAAAC-T-TATA
1 ATATAG-TTTTTT-AAAAA-CGGTTTTGAAAACATATATA
636109 ATATA
1 ATATA
636114 TATATATATA
Statistics
Matches: 167, Mismatches: 5, Indels: 29
0.83 0.02 0.14
Matches are distributed among these distances:
33 3 0.02
35 34 0.20
36 34 0.20
37 40 0.24
38 43 0.26
39 13 0.08
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.41
Consensus pattern (37 bp):
ATATAGTTTTTTAAAAACGGTTTTGAAAACATATATA
Found at i:636116 original size:2 final size:2
Alignment explanation
Indices: 636105--636146 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
636095 TTTGAAAACT
636105 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
636146 T
1 T
636147 TAAAAATGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:636199 original size:5 final size:5
Alignment explanation
Indices: 636191--636253 Score: 62
Period size: 5 Copynumber: 13.2 Consensus size: 5
636181 ATATAGTCTT
* *
636191 TATTA TATT- TAGTA TA-TA TTATTA T-TTA TATTA TATTA TATTA TAATA
1 TATTA TATTA TATTA TATTA -TATTA TATTA TATTA TATTA TATTA TATTA
*
636239 TATTA TTTTA T-TTA T
1 TATTA TATTA TATTA T
636254 TTCATTTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
4 13 0.26
5 35 0.70
6 2 0.04
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:636212 original size:19 final size:18
Alignment explanation
Indices: 636190--636253 Score: 66
Period size: 17 Copynumber: 3.7 Consensus size: 18
636180 TATATAGTCT
636190 TTATTATATTTAGTATATA
1 TTATTATATTTA-TATATA
636209 TTA-T-TATTTATAT-TA
1 TTATTATATTTATATATA
636224 -TATTATA-TTATAATATA
1 TTATTATATTTAT-ATATA
*
636241 TTATTTTATTTAT
1 TTATTATATTTAT
636254 TTCATTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
14 2 0.05
15 7 0.18
16 7 0.18
17 8 0.21
18 7 0.18
19 7 0.18
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTATTATATTTATATATA
Found at i:636215 original size:22 final size:22
Alignment explanation
Indices: 636190--636272 Score: 59
Period size: 22 Copynumber: 3.8 Consensus size: 22
636180 TATATAGTCT
636190 TTATTATATTTAGTA-TATATTA
1 TTATTATATTTA-TATTATATTA
636212 TTATT-TATATTATATTATATTA
1 TTATTATAT-TTATATTATATTA
*
636234 TAATATATTATTT-TATT-TATT-
1 TTAT-TA-TATTTATATTATATTA
* * *
636255 TCATTTTATTTTTATTAT
1 TTATTATATTTATATTAT
636273 TTTCGGTCTA
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
19 5 0.10
20 5 0.10
21 9 0.18
22 22 0.43
23 5 0.10
24 2 0.04
25 3 0.06
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (22 bp):
TTATTATATTTATATTATATTA
Found at i:637526 original size:18 final size:19
Alignment explanation
Indices: 637492--637539 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
637482 ATAATCATTC
637492 TTTAATATTTTTAATTTAA
1 TTTAATATTTTTAATTTAA
* *
637511 TTTAATATTTTTATTTTAT
1 TTTAATATTTTTAATTTAA
*
637530 TTTATTATTT
1 TTTAATATTT
637540 AAGATTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTAATATTTTTAATTTAA
Found at i:637574 original size:23 final size:24
Alignment explanation
Indices: 637523--637574 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
637513 TAATATTTTT
637523 ATTTTATTTTATTATTTAAGATTA
1 ATTTTATTTTATTATTTAAGATTA
* * *
637547 A-TTTATTTTTTTGTTTAGGA-TA
1 ATTTTATTTTATTATTTAAGATTA
637569 ATTTTA
1 ATTTTA
637575 ATCTATCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 3 0.12
23 20 0.83
24 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (24 bp):
ATTTTATTTTATTATTTAAGATTA
Found at i:639152 original size:13 final size:13
Alignment explanation
Indices: 639134--639159 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
639124 CAAAGTTTAC
639134 CGTTGACTTTGAT
1 CGTTGACTTTGAT
639147 CGTTGACTTTGAT
1 CGTTGACTTTGAT
639160 TAAAAAGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (13 bp):
CGTTGACTTTGAT
Found at i:640418 original size:21 final size:22
Alignment explanation
Indices: 640392--640434 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
640382 TTGTTACCTA
*
640392 AGATTTTATCTTTACT-CGTTT
1 AGATTTTATATTTACTACGTTT
640413 AGATTTTATATTTACTACGTTT
1 AGATTTTATATTTACTACGTTT
640435 TAAAGATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.56
Consensus pattern (22 bp):
AGATTTTATATTTACTACGTTT
Found at i:645958 original size:17 final size:16
Alignment explanation
Indices: 645922--645957 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
645912 TTAAAGATTA
* *
645922 TTTTCAAATTTTTTAT
1 TTTTCAAAATTTATAT
645938 TTTTCAAAATTTATAT
1 TTTTCAAAATTTATAT
645954 TTTT
1 TTTT
645958 TAAATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTCAAAATTTATAT
Found at i:646076 original size:17 final size:19
Alignment explanation
Indices: 646047--646083 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
646037 AATTTTATTG
646047 AATTTTTACTATT-TTTTA
1 AATTTTTACTATTATTTTA
646065 AATTTTTA-TATTATTTTA
1 AATTTTTACTATTATTTTA
646083 A
1 A
646084 TAATTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
AATTTTTACTATTATTTTA
Found at i:647217 original size:15 final size:15
Alignment explanation
Indices: 647199--647228 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
647189 AAAACCATGT
647199 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
647214 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
647229 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:647235 original size:15 final size:15
Alignment explanation
Indices: 647202--647236 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
647192 ACCATGTTAG
* *
647202 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
647217 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
647232 ATAAA
1 ATAAA
647237 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:647354 original size:15 final size:15
Alignment explanation
Indices: 647334--647370 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
647324 TATAAAAAAT
*
647334 AAAGAAAAAGAAGAA
1 AAAGAAAAAAAAGAA
647349 AAAGAAAAAAAAGAA
1 AAAGAAAAAAAAGAA
647364 AAA-AAAA
1 AAAGAAAA
647371 TATAGAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAAGAA
Found at i:647377 original size:14 final size:14
Alignment explanation
Indices: 647338--647399 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 14
647328 AAAAATAAAG
*
647338 AAAAAGAAGAAAAA
1 AAAAAAAAGAAAAA
647352 GAAAAAAAAGAAAAA
1 -AAAAAAAAGAAAAA
* *
647367 AAAATATAGAAATAA
1 AAAAAAAAGAAA-AA
*
647382 AACAAATAAATAAAAA
1 AA-AAA-AAAGAAAAA
647398 AA
1 AA
647400 GTAAAATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
14 10 0.26
15 17 0.45
16 6 0.16
17 5 0.13
ACGTcount: A:0.82, C:0.02, G:0.08, T:0.08
Consensus pattern (14 bp):
AAAAAAAAGAAAAA
Found at i:647397 original size:39 final size:39
Alignment explanation
Indices: 647327--647439 Score: 113
Period size: 39 Copynumber: 2.9 Consensus size: 39
647317 AAATAAATAT
* * *
647327 AAAAAATAAAGAAA-AAGAAGAAAAAGA-AAAAAAAGAAA
1 AAAAAATATAGAAATAA-AACAAAAAAATAAAAAAAGAAA
* *
647365 AAAAAATATAGAAATAAAACAAATAAATAAAAAAAGTAA
1 AAAAAATATAGAAATAAAACAAAAAAATAAAAAAAGAAA
* * * * *
647404 AATATATATATATATAAAATAAAAAAATAAAAAAAG
1 AAAAAATATAGAAATAAAACAAAAAAATAAAAAAAG
647440 TAAATATATA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
38 20 0.32
39 42 0.68
ACGTcount: A:0.78, C:0.01, G:0.07, T:0.14
Consensus pattern (39 bp):
AAAAAATATAGAAATAAAACAAAAAAATAAAAAAAGAAA
Found at i:647406 original size:27 final size:25
Alignment explanation
Indices: 647321--647407 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 25
647311 TAAGTAAAAT
*
647321 AAATATAAAAAATAAAGAAAAAGAAGAA
1 AAATA-AAAAAATAAA-AAAAA-AAGTA
* *
647349 AAAGAAAAAAA-AGAAAAAAAAATATA
1 AAATAAAAAAATA-AAAAAAAAA-GTA
647375 GAAATAAAACAAATAAATAAAAAAAGTA
1 -AAATAAAA-AAATAAA-AAAAAAAGTA
647403 AAATA
1 AAATA
647408 TATATATATA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
25 2 0.04
26 7 0.15
27 20 0.42
28 11 0.23
29 8 0.17
ACGTcount: A:0.79, C:0.01, G:0.08, T:0.11
Consensus pattern (25 bp):
AAATAAAAAAATAAAAAAAAAAGTA
Found at i:647438 original size:9 final size:9
Alignment explanation
Indices: 647315--647443 Score: 55
Period size: 9 Copynumber: 13.4 Consensus size: 9
647305 AAATAGTAAG
*
647315 TAAAATAAA
1 TAAAAAAAA
*
647324 TATAAAAAA
1 TAAAAAAAA
647333 TAAAGAAAAA
1 TAAA-AAAAA
* *
647343 GAAGAAAAA
1 TAAAAAAAA
*
647352 GAAAAAAAA
1 TAAAAAAAA
*
647361 GAAAAAAAAA
1 -TAAAAAAAA
647371 TATAGAAATAAA
1 TA-A-AAA-AAA
*
647383 -ACAAATAAA
1 TA-AAAAAAA
*
647392 TAAAAAAAG
1 TAAAAAAAA
647401 TAAAATATATATA
1 TAAAA-A-A-A-A
* *
647414 TATATAAAA
1 TAAAAAAAA
647423 T-AAAAAAA
1 TAAAAAAAA
*
647431 TAAAAAAAG
1 TAAAAAAAA
647440 TAAA
1 TAAA
647444 TATATATATA
Statistics
Matches: 91, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
8 6 0.07
9 49 0.54
10 21 0.23
11 7 0.08
12 5 0.05
13 3 0.03
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.16
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:647445 original size:38 final size:39
Alignment explanation
Indices: 647354--647459 Score: 140
Period size: 39 Copynumber: 2.7 Consensus size: 39
647344 AAGAAAAAGA
* * * * * *
647354 AAAAAAAGAAAAAAAAATATAGAAATAAAACAAATAAAT
1 AAAAAAAGTAAAATATATATATATATAAAACAAAAAAAT
*
647393 AAAAAAAGTAAAATATATATATATATAAAATAAAAAAAT
1 AAAAAAAGTAAAATATATATATATATAAAACAAAAAAAT
647432 AAAAAAAGTAAATATATATATATATATA
1 AAAAAAAGTAAA-ATATATATATATATA
647460 TAAATTAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
39 44 0.75
40 15 0.25
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.23
Consensus pattern (39 bp):
AAAAAAAGTAAAATATATATATATATAAAACAAAAAAAT
Found at i:647543 original size:24 final size:23
Alignment explanation
Indices: 647509--647575 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
647499 TATAAATCTA
*
647509 AAAAAAAAAAATATATACTAAA-GT
1 AAAAAAAAAAATACATA--AAATGT
*
647533 AAAAAAGAAAATACATAAAATGT
1 AAAAAAAAAAATACATAAAATGT
* *
647556 AAAAAAAATATTACATAAAA
1 AAAAAAAAAAATACATAAAA
647576 AAAAAGAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 3 0.08
23 19 0.51
24 15 0.41
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.19
Consensus pattern (23 bp):
AAAAAAAAAAATACATAAAATGT
Found at i:647920 original size:37 final size:36
Alignment explanation
Indices: 647877--647978 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
647867 ATAGTAGAAC
647877 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
* *
647914 TTTATCCTATTTTTAAGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
647948 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
647979 TAGGACGAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
34 32 0.54
37 27 0.46
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:648932 original size:106 final size:105
Alignment explanation
Indices: 648526--649043 Score: 724
Period size: 106 Copynumber: 5.0 Consensus size: 105
648516 CATTGTTCCA
* * * ** *
648526 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGTTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * * *
648590 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
648632 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
648692 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
648732 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
648797 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
648837 AGTCCAATATCCTTCGTTTTGAAGTTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAG-TTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
648902 CAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGA
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
648943 AGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
* * *
649008 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
649044 CCTCGAGTGC
Statistics
Matches: 375, Mismatches: 29, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
100 84 0.22
101 1 0.00
102 7 0.02
104 5 0.01
105 102 0.27
106 176 0.47
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:649776 original size:68 final size:65
Alignment explanation
Indices: 649686--649843 Score: 192
Period size: 68 Copynumber: 2.4 Consensus size: 65
649676 AAGATATCTG
* * *
649686 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAAATT-GAAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATT-TGTTTTAAGGGAAAT-AAATTCAAAG-
*
649750 TTT
63 GTT
* * * *
649753 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAGGT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGGT
649818 T
65 T
*
649819 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
649844 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
65 22 0.28
66 8 0.10
67 18 0.23
68 31 0.39
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGGTT
Found at i:649859 original size:65 final size:67
Alignment explanation
Indices: 649687--649870 Score: 178
Period size: 65 Copynumber: 2.8 Consensus size: 67
649677 AGATATCTGT
* * * * * * *
649687 TGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAAATTGAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATT-TGTTTTAAGGGAAATAAAATTAAAGAGT
649752 TTG
65 TTG
* * * *
649755 TGTTTCAAGAGTAACTGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAAT-AAATTCAAAG-GT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAATAAAATT-AAAGAGT
649818 TT-
65 TTG
* * * *
649820 TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAAT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-GAAAATTTGTTTTAAGGGAAAT
649871 TGTCTCAAGA
Statistics
Matches: 98, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
65 38 0.39
66 12 0.12
67 17 0.17
68 31 0.32
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAATAAAATTAAAGAGTT
TG
Found at i:649872 original size:15 final size:15
Alignment explanation
Indices: 649852--649882 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
649842 AGATAGACGA
*
649852 AAATTGTTTCAAGAG
1 AAATTGTCTCAAGAG
649867 AAATTGTCTCAAGAG
1 AAATTGTCTCAAGAG
649882 A
1 A
649883 GACAAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (15 bp):
AAATTGTCTCAAGAG
Found at i:649875 original size:36 final size:35
Alignment explanation
Indices: 649819--650135 Score: 297
Period size: 36 Copynumber: 9.0 Consensus size: 35
649809 TTCAAAGGTT
*
649819 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAA
* *
649855 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* ** * * * *
649890 CTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAA
*** * * **
649928 TTGTTTCAAATAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
649957 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
649992 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAA
* *
650029 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
650064 TTCGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TT-GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
650100 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
650136 CTCTTCTAGT
Statistics
Matches: 233, Mismatches: 33, Indels: 30
0.79 0.11 0.10
Matches are distributed among these distances:
28 2 0.01
29 17 0.07
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 9 0.04
36 163 0.70
37 35 0.15
38 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:649931 original size:138 final size:138
Alignment explanation
Indices: 649770--650079 Score: 345
Period size: 138 Copynumber: 2.2 Consensus size: 138
649760 CAAGAGTAAC
* * ** * * *
649770 TGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
* * *
649835 TGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTAGTTCC
66 TGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCC
649899 AAAAGAAAT
130 AAAAGAAAT
** * * *
649908 TGTCTCAAGGGAGACGGAATTTGTTTCAAATAAAACATATTCAAATATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
* * * * *
649973 TGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAA-TTTGTTTCA
66 TGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCA
** *
650037 AGGGAAAC
131 AAAGAAAT
** * *
650045 TGTCTCAAGATAGACGAAATTCGTTTCAAGAGAAA
1 TGTCTCAAGGGAGACAAAATTTGTTTCAA-AGAAA
650080 CTGTCTCAAG
Statistics
Matches: 142, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
137 41 0.29
138 101 0.71
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.28
Consensus pattern (138 bp):
TGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
TGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCA
AAAGAAAT
Found at i:650037 original size:21 final size:21
Alignment explanation
Indices: 650013--650075 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
650003 GGAAACTGTC
650013 TCAAGATAGACGAAATTTGTT
1 TCAAGATAGACGAAATTTGTT
* *
650034 TCAAG---G--GAAA-CTGTC
1 TCAAGATAGACGAAATTTGTT
*
650049 TCAAGATAGACGAAATTCGTT
1 TCAAGATAGACGAAATTTGTT
650070 TCAAGA
1 TCAAGA
650076 GAAACTGTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 12
0.65 0.10 0.25
Matches are distributed among these distances:
15 8 0.26
16 4 0.13
18 2 0.06
20 4 0.13
21 13 0.42
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (21 bp):
TCAAGATAGACGAAATTTGTT
Found at i:650073 original size:72 final size:72
Alignment explanation
Indices: 649956--650177 Score: 297
Period size: 72 Copynumber: 3.1 Consensus size: 72
649946 ATTCAAATAT
* * *
649956 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGAGAAACTGTCTCAAGAGA
*
650021 GACGAAA
66 GACAAAA
* * *
650028 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAATTCGTTTCAAGAGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGAGAAACTGTCTCAAGAGA
650093 GACAAAA
66 GACAAAA
* * * * *
650100 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTC--TTCTAGTGAAAACGGTCTCAAGCG
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGAG-AAACTGTCTCAAGAG
650163 AGAC-AAA
65 AGACAAAA
650170 TCTTGTTT
1 T-TTGTTT
650178 TAAGAAAAAC
Statistics
Matches: 134, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
70 10 0.07
71 23 0.17
72 101 0.75
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.27
Consensus pattern (72 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGAGAAACTGTCTCAAGAGA
GACAAAA
Found at i:651142 original size:22 final size:22
Alignment explanation
Indices: 651065--651135 Score: 124
Period size: 22 Copynumber: 3.2 Consensus size: 22
651055 TTGTGTTTGG
*
651065 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
651087 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
651109 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
651131 TCAAA
1 TCAAA
651136 AGATTGATGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:651760 original size:16 final size:17
Alignment explanation
Indices: 651737--651776 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
651727 TCTTTGCATG
651737 TGCTTTTTGTCCTTTTT
1 TGCTTTTTGTCCTTTTT
*
651754 T-CTTTTTGTTCTTTTT
1 TGCTTTTTGTCCTTTTT
651770 TGCTTTT
1 TGCTTTT
651777 GTTTTTTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.00, C:0.15, G:0.10, T:0.75
Consensus pattern (17 bp):
TGCTTTTTGTCCTTTTT
Found at i:651775 original size:33 final size:33
Alignment explanation
Indices: 651737--651838 Score: 100
Period size: 38 Copynumber: 2.9 Consensus size: 33
651727 TCTTTGCATG
*
651737 TGCTTTTTGTCCTT-TTTTCTTTTTGTTCTTTTT
1 TGCTTTTT-TGCTTCTTTTCTTTTTGTTCTTTTT
*
651770 TGCTTTTGTTTTTTGCTTCTTTT-TTTTGTGTTTTTTTT
1 TGC-----TTTTTTGCTTCTTTTCTTTT-TGTTCTTTTT
651808 TGCTTTTTTGCTTCTTTTCTTTTTTGTTCTT
1 TGCTTTTTTGCTTCTTTTC-TTTTTGTTCTT
651839 GATTGGATCT
Statistics
Matches: 57, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
33 18 0.32
34 6 0.11
35 4 0.07
37 8 0.14
38 21 0.37
ACGTcount: A:0.00, C:0.13, G:0.11, T:0.76
Consensus pattern (33 bp):
TGCTTTTTTGCTTCTTTTCTTTTTGTTCTTTTT
Found at i:651777 original size:16 final size:16
Alignment explanation
Indices: 651741--651833 Score: 56
Period size: 16 Copynumber: 5.9 Consensus size: 16
651731 TGCATGTGCT
*
651741 TTTTGTCCTTTTTT-C
1 TTTTGTTCTTTTTTGC
651756 TTTTTGTTCTTTTTTGC
1 -TTTTGTTCTTTTTTGC
651773 TTTTG---TTTTTTGC
1 TTTTGTTCTTTTTTGC
* *
651786 TTCTT-TT-TTTTGTGTT
1 TT-TTGTTCTTTTTTG-C
*
651802 TTTTTTTGCTTTTTTGC
1 TTTTGTT-CTTTTTTGC
651819 TTCTT-TTCTTTTTTG
1 TT-TTGTTCTTTTTTG
651834 TTCTTGATTG
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
13 10 0.16
14 2 0.03
15 8 0.13
16 30 0.48
17 5 0.08
18 8 0.13
ACGTcount: A:0.00, C:0.12, G:0.11, T:0.77
Consensus pattern (16 bp):
TTTTGTTCTTTTTTGC
Found at i:651783 original size:13 final size:12
Alignment explanation
Indices: 651765--651816 Score: 70
Period size: 13 Copynumber: 4.2 Consensus size: 12
651755 CTTTTTGTTC
651765 TTTTTTGCTTTT
1 TTTTTTGCTTTT
651777 GTTTTTTGCTTCTT
1 -TTTTTTGCTT-TT
651791 TTTTTTG-TGTTT
1 TTTTTTGCT-TTT
651803 TTTTTTGCTTTT
1 TTTTTTGCTTTT
651815 TT
1 TT
651817 GCTTCTTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
12 15 0.42
13 19 0.53
14 2 0.06
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.81
Consensus pattern (12 bp):
TTTTTTGCTTTT
Found at i:651806 original size:25 final size:25
Alignment explanation
Indices: 651765--651833 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
651755 CTTTTTGTTC
651765 TTTTTTGCTTTTGTTTTTTGCTTCTT
1 TTTTTTGCTTTTGTTTTTTGCTT-TT
651791 TTTTTTG-TGTTT-TTTTTTGCTTTT
1 TTTTTTGCT-TTTGTTTTTTGCTTTT
** *
651815 TTGCTT-CTTTTCTTTTTTG
1 TTTTTTGCTTTTGTTTTTTG
651834 TTCTTGATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
23 3 0.08
24 14 0.37
25 11 0.29
26 10 0.26
ACGTcount: A:0.00, C:0.10, G:0.12, T:0.78
Consensus pattern (25 bp):
TTTTTTGCTTTTGTTTTTTGCTTTT
Found at i:652945 original size:8 final size:8
Alignment explanation
Indices: 652929--652967 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
652919 AATGTAGATG
652929 AAAATGCA
1 AAAATGCA
*
652937 AAAAGGCA
1 AAAATGCA
652945 AAAATGC-
1 AAAATGCA
652952 AAAATGCA
1 AAAATGCA
*
652960 AGAATGCA
1 AAAATGCA
652968 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:652955 original size:15 final size:15
Alignment explanation
Indices: 652929--652967 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
652919 AATGTAGATG
652929 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
652945 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
652960 AGAATGCA
1 AAAATGCA
652968 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:654764 original size:15 final size:15
Alignment explanation
Indices: 654746--654775 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
654736 AAAACCATGT
654746 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
654761 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
654776 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:654782 original size:15 final size:15
Alignment explanation
Indices: 654749--654783 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
654739 ACCATGTTAG
* *
654749 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
654764 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
654779 ATAAA
1 ATAAA
654784 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:654933 original size:28 final size:28
Alignment explanation
Indices: 654872--654935 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
654862 TAAAATAAAT
*
654872 ATAAAAAATAAAGAAAAAGAAGAAAAAG
1 ATAAAAAATAAAGAAAAAGAACAAAAAG
* *
654900 AAAAAAAATATAGAAATAA-AACAAATAA-
1 ATAAAAAATAAAGAAA-AAGAACAAA-AAG
654928 ATAAAAAA
1 ATAAAAAA
654936 AGTAAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.80, C:0.02, G:0.08, T:0.11
Consensus pattern (28 bp):
ATAAAAAATAAAGAAAAAGAACAAAAAG
Found at i:654943 original size:9 final size:8
Alignment explanation
Indices: 654862--654980 Score: 51
Period size: 9 Copynumber: 13.5 Consensus size: 8
654852 AAATAGTAAG
654862 TAAAATAAA
1 TAAAA-AAA
654871 TATAAAAAA
1 TA-AAAAAA
654880 TAAAGAAAAA
1 T-AA-AAAAA
*
654890 GAAGAAAAA
1 TAA-AAAAA
*
654899 GAAAAAAAA
1 -TAAAAAAA
* *
654908 TATAGAAA
1 TAAAAAAA
654916 TAAAACAAA
1 TAAAA-AAA
654925 TAAATAAAA
1 TAAA-AAAA
*
654934 AAAGTAAAAA
1 TAA--AAAAA
* *
654944 T-AATATA
1 TAAAAAAA
*
654951 TATATAAAA
1 TA-AAAAAA
654960 TAAAAAAA
1 TAAAAAAA
654968 TAAAAAAA
1 TAAAAAAA
654976 GTAAA
1 -TAAA
654981 TATATATATA
Statistics
Matches: 84, Mismatches: 15, Indels: 22
0.69 0.12 0.18
Matches are distributed among these distances:
7 4 0.05
8 21 0.25
9 42 0.50
10 16 0.19
11 1 0.01
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (8 bp):
TAAAAAAA
Found at i:654958 original size:30 final size:29
Alignment explanation
Indices: 654924--654986 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
654914 AATAAAACAA
* * *
654924 ATAAATAAAAAAAGTAAAAATAATATATAT
1 ATAAATAAAAAAA-TAAAAAAAGTAAATAT
654954 ATAAAATAAAAAAATAAAAAAAGTAAATAT
1 ATA-AATAAAAAAATAAAAAAAGTAAATAT
654984 ATA
1 ATA
654987 TATATATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (29 bp):
ATAAATAAAAAAATAAAAAAAGTAAATAT
Found at i:654958 original size:39 final size:39
Alignment explanation
Indices: 654885--654996 Score: 136
Period size: 39 Copynumber: 2.8 Consensus size: 39
654875 AAAAATAAAG
* * * *
654885 AAAAAGAAGAAAAAG-AAAAAAAATATAGAAATAAAACAA
1 AAAAATAA-AAAAAGTAAAAATAATATATATATAAAACAA
* *
654924 ATAAATAAAAAAAGTAAAAATAATATATATATAAAATAA
1 AAAAATAAAAAAAGTAAAAATAATATATATATAAAACAA
*
654963 AAAAATAAAAAAAGTAAATATATATATATATATA
1 AAAAATAAAAAAAGTAAAAATA-ATATATATATA
654997 TAAATTAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
38 6 0.10
39 46 0.73
40 11 0.17
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (39 bp):
AAAAATAAAAAAAGTAAAAATAATATATATATAAAACAA
Found at i:655097 original size:23 final size:23
Alignment explanation
Indices: 655055--655115 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
655045 TAAAAAAAAT
655055 AAAAATATATAC-T-AAA-GTAAA
1 AAAAATA-ATACATAAAATGTAAA
655076 AAAGAA-AATACATAAAATGTAAA
1 AAA-AATAATACATAAAATGTAAA
*
655099 AAAAATATTACATAAAA
1 AAAAATAATACATAAAA
655116 AAGAAAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 4 0.12
21 5 0.15
22 7 0.21
23 18 0.53
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (23 bp):
AAAAATAATACATAAAATGTAAA
Found at i:655457 original size:37 final size:36
Alignment explanation
Indices: 655411--655515 Score: 160
Period size: 34 Copynumber: 2.9 Consensus size: 36
655401 ATAATAGTAG
655411 AATTCTATCCTATTTTTAGGAGTTTGAATCCTAGCAA
1 AATTCTATCCTATTTTTAGGAGTTTGAATCCTAG-AA
* **
655448 AATTTTATCCTATTTTTAAAAGTTTGAATCCT--AA
1 AATTCTATCCTATTTTTAGGAGTTTGAATCCTAGAA
655482 AATTCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 AATTCTATCCTATTTTTAGGAGTTTGAATCCTAG
655516 TAGGACGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
34 31 0.52
37 29 0.48
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.44
Consensus pattern (36 bp):
AATTCTATCCTATTTTTAGGAGTTTGAATCCTAGAA
Found at i:662375 original size:58 final size:56
Alignment explanation
Indices: 662208--662351 Score: 227
Period size: 58 Copynumber: 2.5 Consensus size: 56
662198 TTTTATTACG
**
662208 TAATTTATTTATTGAACATGATTAATTAAATTAATTATAATCATTGCAAGTTAAAA
1 TAATTTATTTATTGAACATGATTAATTAAATTAATTATAATCATTAAAAGTTAAAA
*
662264 TAATTTATTGACATTGAACATGATTAATTAAATTAATTATAATCATTAAAAGTTAAAA
1 TAATTTATT--TATTGAACATGATTAATTAAATTAATTATAATCATTAAAAGTTAAAA
662322 TAATTTATTTATTGAAC-TAGATTAATTAAA
1 TAATTTATTTATTGAACAT-GATTAATTAAA
662352 AAATAATTTA
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
55 1 0.01
56 27 0.33
58 53 0.65
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (56 bp):
TAATTTATTTATTGAACATGATTAATTAAATTAATTATAATCATTAAAAGTTAAAA
Found at i:663686 original size:20 final size:19
Alignment explanation
Indices: 663658--663696 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
663648 TCAAAATTCT
663658 AAAAAAAATAAAGAAAACA
1 AAAAAAAATAAAGAAAACA
* *
663677 AAAAACAAATTATGAAAACA
1 AAAAA-AAATAAAGAAAACA
663697 TAGTAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.77, C:0.08, G:0.05, T:0.10
Consensus pattern (19 bp):
AAAAAAAATAAAGAAAACA
Found at i:663829 original size:3 final size:3
Alignment explanation
Indices: 663821--663848 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
663811 TACTTTGGAT
663821 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
663849 CCACAAGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:664962 original size:103 final size:102
Alignment explanation
Indices: 664855--665149 Score: 308
Period size: 102 Copynumber: 2.9 Consensus size: 102
664845 TAAAGGTTAA
* * *
664855 GGGTTTGGGTGTTTATAAAGATCAAAGATGAGTTTTGAGGATGAATATAAATAAACAAAGGTTGA
1 GGGTTTGGGTGTTTGTAAAGATCAAAGATG-GTTTTGAGGATGAATACAAATAAACAAGGGTTGA
* * * * *
664920 GGGTTTGTGTGCTTGATCGAGAAAATAGGTTGGGTTTT
65 GGGTTTGGGTGCTTGATCGAAAAAAAAAGTTGAGTTTT
* * * * * * *
664958 GGGTTTGGGT-TTTGGTAAAGATCAAATAAGGGTTTGAGGATGGATACGAATAAATAAGGGTTAA
1 GGGTTTGGGTGTTT-GTAAAGATCAAAGATGGTTTTGAGGATGAATACAAATAAACAAGGGTTGA
* *
665022 GGGTTTGGGTGTTTGATTGAAAAAAAAAGTTGAGTTTT
65 GGGTTTGGGTGCTTGATCGAAAAAAAAAGTTGAGTTTT
* * * * *
665060 GGGTTTGGATGTTTGTAAATATCAAAGATGGGTTTTGGGGGATGTACACAAATAAACAAGGGTTG
1 GGGTTTGGGTGTTTGTAAAGATCAAAGAT-GGTTTT-GAGGATGAATACAAATAAACAAGGGTTG
* *
665125 A--ATTTGGGGTGTTTGATCGAAAAAA
64 AGGGTTT-GGGTGCTTGATCGAAAAAA
665150 TCAAATAATT
Statistics
Matches: 157, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
102 85 0.54
103 49 0.31
104 23 0.15
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.33
Consensus pattern (102 bp):
GGGTTTGGGTGTTTGTAAAGATCAAAGATGGTTTTGAGGATGAATACAAATAAACAAGGGTTGAG
GGTTTGGGTGCTTGATCGAAAAAAAAAGTTGAGTTTT
Found at i:665560 original size:2 final size:2
Alignment explanation
Indices: 665553--666159 Score: 220
Period size: 2 Copynumber: 304.0 Consensus size: 2
665543 ATTTATAGTT
665553 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
665595 TA TA TA TA TA TA TA TA TA TA TA GTT TA TA T- TA -A TA AA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * *
665635 TA TA GTT TA TA T- TA TA AA CTA TA TA GTT TT TA TA TA TA -A T-
1 TA TA -TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
* *
665675 TA TA TA TA GTT TA TA TA GTA TA TA TA TA TA TA TA TA TA AA CTA
1 TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA
* *
665718 TA TA GTA TA AA TA TA TA TA -A TA GTT TA TA T- TA -A TA -A TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
** * * *
665758 TA TA TA GC T- TA TA TA TA GTT TA TA TA CT- TGA CA TA TA TT TCA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA T-A TA TA TA TA T-A
* * * *
665800 T- TA -A TA AA CTA TT TA GTT TA TA TA -A TA TA TA TA TA TA TA AA
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
665841 TA GTT TA TG T- TA -A TA AA T- TA TA TA GTT TA TA GA TA TA -A TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * *
665881 TA TA TA GT- TT TA AA CTA TA TA -A TA TA TA AA TA GTA TA TA AA
1 TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * *
665922 TA -A TT TA TA CA TA GTA TA TA AA TA TA AA CTA TA TA -A TC TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * *
665964 TC TA GTT TA TA T- TA -A TA AA CTA TA TA GTT TA TA CA TA -A TA
1 TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
* *
666004 TA TA TA -A TT TA TA CA TA -A TA TA TA TA -A T- TCA TA TA TA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA -TA
* * * * *
666044 TA TA AA TA TA AA T- TA CA TA GTT TA TA TA T- TA TA TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * *
666084 TA -A TA TA TA GTT TA CA TA CTA TA TA GTT TA TA GA TA GTA TA TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA -TA TA TA
* *
666127 AA TA TA AA CTA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
666160 ATTGTTTTAA
Statistics
Matches: 442, Mismatches: 96, Indels: 134
0.66 0.14 0.20
Matches are distributed among these distances:
1 34 0.08
2 369 0.83
3 39 0.09
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:665958 original size:33 final size:33
Alignment explanation
Indices: 665903--666069 Score: 106
Period size: 33 Copynumber: 4.8 Consensus size: 33
665893 AACTATATAA
* *
665903 TATATAAATAGTATA-TAAATAATTTATACATAG
1 TATATAAATA-TAAACTATATAATTTATACATAG
*
665936 TATATAAATATAAACTATATAATCTATATC-TAG
1 TATATAAATATAAACTATATAATTTATA-CATAG
* * * *
665969 TTTAT-ATTAATAAACTATATAGTTTATACATAA
1 TATATAAAT-ATAAACTATATAATTTATACATAG
* * *
666002 TATATATAATTTATACATAATATATATAATTCATATATAG
1 TATATA-AA--TAT--A-AA-CTATATAATTTATACATAG
* * *
666042 TATATAAATATAAATTACATAGTTTATA
1 TATATAAATATAAACTATATAATTTATA
666070 TATTATATAT
Statistics
Matches: 103, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
32 6 0.06
33 61 0.59
34 3 0.03
35 2 0.02
36 2 0.02
37 4 0.04
38 1 0.01
39 4 0.04
40 20 0.19
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.43
Consensus pattern (33 bp):
TATATAAATATAAACTATATAATTTATACATAG
Found at i:667793 original size:4 final size:4
Alignment explanation
Indices: 667784--667817 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
667774 GCTAATTGCA
667784 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
667818 TCTATCTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:668070 original size:2 final size:2
Alignment explanation
Indices: 668063--668088 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
668053 TAAATTATTA
668063 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
668089 CAGAAGAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:672291 original size:3 final size:3
Alignment explanation
Indices: 672283--672307 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
672273 TGATAAATAT
672283 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
672308 AACCCAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:674065 original size:23 final size:22
Alignment explanation
Indices: 674035--674118 Score: 73
Period size: 23 Copynumber: 3.8 Consensus size: 22
674025 AAAATCTATT
*
674035 TTCATTTATGTTCATTTATTGTG
1 TTCATTTACGTTC-TTTATTGTG
* *
674058 TTCTTTTACGTTC-GT-TTGTG
1 TTCATTTACGTTCTTTATTGTG
* *
674078 TTCGTTAACGTTCTTTTATTGTG
1 TTCATTTACGTTC-TTTATTGTG
*
674101 TTCATTTATGTTCGTTTA
1 TTCATTTACGTTC-TTTA
674119 CATCCGTTCG
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
20 16 0.33
21 1 0.02
22 1 0.02
23 30 0.62
ACGTcount: A:0.13, C:0.12, G:0.15, T:0.60
Consensus pattern (22 bp):
TTCATTTACGTTCTTTATTGTG
Found at i:674078 original size:20 final size:20
Alignment explanation
Indices: 674053--674090 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
674043 TGTTCATTTA
* *
674053 TTGTGTTCTTTTACGTTCGT
1 TTGTGTTCGTTAACGTTCGT
674073 TTGTGTTCGTTAACGTTC
1 TTGTGTTCGTTAACGTTC
674091 TTTTATTGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.08, C:0.16, G:0.21, T:0.55
Consensus pattern (20 bp):
TTGTGTTCGTTAACGTTCGT
Found at i:678231 original size:17 final size:17
Alignment explanation
Indices: 678199--678232 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
678189 AAATAAATAA
678199 AATAAATAAGTAAAAAC
1 AATAAATAAGTAAAAAC
678216 AATAACATAAGTAAAAA
1 AATAA-ATAAGTAAAAA
678233 TAAATTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (17 bp):
AATAAATAAGTAAAAAC
Found at i:679234 original size:20 final size:23
Alignment explanation
Indices: 679206--679254 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
679196 AAGGTAAAAC
679206 TTTTCTTTC-T-TCTCT-TTTTT
1 TTTTCTTTCGTATCTCTCTTTTT
*
679226 TTTTGTTTCGTATCTCTCTTTTT
1 TTTTCTTTCGTATCTCTCTTTTT
679249 TTTTCT
1 TTTTCT
679255 CTATTCTCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 5 0.21
23 10 0.42
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTTCTTTCGTATCTCTCTTTTT
Found at i:679262 original size:21 final size:21
Alignment explanation
Indices: 679206--679274 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
679196 AAGGTAAAAC
* * *
679206 TTTTCTTTCTTCTCTTTTTTT
1 TTTTCTCTATTCTCTCTTTTT
*
679227 TTTGTTTCGTA-TCTCTCTTTTT
1 TTT-TCTC-TATTCTCTCTTTTT
* *
679249 TTTTCTCTATTCTCTGTTGTT
1 TTTTCTCTATTCTCTCTTTTT
679270 TTTTC
1 TTTTC
679275 GTTTTGGTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
20 2 0.05
21 20 0.53
22 15 0.39
23 1 0.03
ACGTcount: A:0.03, C:0.19, G:0.06, T:0.72
Consensus pattern (21 bp):
TTTTCTCTATTCTCTCTTTTT
Found at i:679701 original size:3 final size:3
Alignment explanation
Indices: 679693--679747 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
679683 GTATATTGTA
679693 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
679741 AA- AAT AA
1 AAT AAT AA
679748 ATATAAAAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:680270 original size:98 final size:99
Alignment explanation
Indices: 680090--680272 Score: 289
Period size: 98 Copynumber: 1.9 Consensus size: 99
680080 ATGACACGAC
* **
680090 TCATACGTGATGAAGAGTTCTTGGACATCTTTAGGAAAGGTGATAACTCGGTTCCTACGTGATGA
1 TCATACATGATGAAGAACTCTTGGACATCTTTAGGAAAGGTGATAACTCGGTTCCTACGTGATGA
* *
680155 GGACGTCTGTTCGTCTAAGGGTAGATGACATGGT
66 GGACGGCTGTTCATCTAAGGGTAGATGACATGGT
*
680189 TCATACATGATGAAGAACTC-TGGCCATCTTTAGGAAAGGTGATAACTCGGTTCCTACGTGATGA
1 TCATACATGATGAAGAACTCTTGGACATCTTTAGGAAAGGTGATAACTCGGTTCCTACGTGATGA
680253 GGACGGCTGATT-ATCTAAGG
66 GGACGGCTG-TTCATCTAAGG
680273 TTGACACGGC
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
98 58 0.75
99 19 0.25
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (99 bp):
TCATACATGATGAAGAACTCTTGGACATCTTTAGGAAAGGTGATAACTCGGTTCCTACGTGATGA
GGACGGCTGTTCATCTAAGGGTAGATGACATGGT
Found at i:690453 original size:107 final size:105
Alignment explanation
Indices: 690253--690457 Score: 376
Period size: 107 Copynumber: 1.9 Consensus size: 105
690243 CTGGATTCAC
690253 CTCTTCCTAACTTCTCAACCAAATGACTACTGCTATTCGATCAGCCCCAAACATTTGGAAAGATT
1 CTCTTCCTAACTTCTCAACCAAATGACTACTGCTATTCGATCAGCCCCAAACATTTGGAAAGATT
690318 ACCAAACCATATATACCCAAGGCAAATACATCTATCACCT
66 ACCAAACCATATATACCCAAGGCAAATACATCTATCACCT
690358 CTCTTCCTAACTTCTCAACCAAATCGACTACTGCTAGTTCGATCAGCCCCAAACATTTTGGAAAG
1 CTCTTCCTAACTTCTCAACCAAAT-GACTACTGCTA-TTCGATCAGCCCCAAACA-TTTGGAAAG
690423 ATTACCAAACCATATATACCC-AGGCAAATACATCT
63 ATTACCAAACCATATATACCCAAGGCAAATACATCT
690458 CTACGCACGT
Statistics
Matches: 97, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
105 24 0.25
106 11 0.11
107 32 0.33
108 30 0.31
ACGTcount: A:0.35, C:0.30, G:0.09, T:0.26
Consensus pattern (105 bp):
CTCTTCCTAACTTCTCAACCAAATGACTACTGCTATTCGATCAGCCCCAAACATTTGGAAAGATT
ACCAAACCATATATACCCAAGGCAAATACATCTATCACCT
Found at i:693032 original size:20 final size:18
Alignment explanation
Indices: 692986--693024 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
692976 TAAAATAAAT
692986 AAATAA-ATAAGTAAAAA
1 AAATAACATAAGTAAAAA
*
693003 CAATAACATAAGTAAAAA
1 AAATAACATAAGTAAAAA
693021 AAAT
1 AAAT
693025 TATACATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (18 bp):
AAATAACATAAGTAAAAA
Found at i:694028 original size:18 final size:19
Alignment explanation
Indices: 694001--694051 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
693991 TTTTTTTTTT
694001 TTTTTGTTTCGTA-TCTCTC
1 TTTTT-TTTCGTATTCTCTC
* *
694020 TTTTTTTTCTCTATTCTCTG
1 TTTTTTTTC-GTATTCTCTC
694040 TTGTTTTTTCGT
1 TT-TTTTTTCGT
694052 TTTGGTTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 4 0.15
19 7 0.27
20 8 0.31
21 7 0.27
ACGTcount: A:0.04, C:0.18, G:0.10, T:0.69
Consensus pattern (19 bp):
TTTTTTTTCGTATTCTCTC
Found at i:694475 original size:3 final size:3
Alignment explanation
Indices: 694467--694551 Score: 147
Period size: 3 Copynumber: 28.7 Consensus size: 3
694457 GTATATTGTA
694467 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
694514 AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
694552 ATATAAAAGA
Statistics
Matches: 79, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.05
3 72 0.91
4 3 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:695851 original size:89 final size:89
Alignment explanation
Indices: 695700--695877 Score: 338
Period size: 89 Copynumber: 2.0 Consensus size: 89
695690 TGGAGCTCCA
695700 GTATGTTATGTACATATACACACATTCTTATAGATGCAACTGTTTAGACTGAAATTTTTATGAAA
1 GTATGTTATGTACATATACACACATTCTTATAGATGCAACTGTTTAGACTGAAATTTTTATGAAA
*
695765 AAAATATTTCGTTTTATCATTAAG
66 AAAATATTTCATTTTATCATTAAG
*
695789 GTATGTTATGTACATATACATACATTCTTATAGATGCAACTGTTTAGACTGAAATTTTTATGAAA
1 GTATGTTATGTACATATACACACATTCTTATAGATGCAACTGTTTAGACTGAAATTTTTATGAAA
695854 AAAATATTTCATTTTATCATTAAG
66 AAAATATTTCATTTTATCATTAAG
695878 ATCGTTTAAT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.41
Consensus pattern (89 bp):
GTATGTTATGTACATATACACACATTCTTATAGATGCAACTGTTTAGACTGAAATTTTTATGAAA
AAAATATTTCATTTTATCATTAAG
Found at i:699863 original size:15 final size:17
Alignment explanation
Indices: 699838--699874 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
699828 TAAAGGTCCT
*
699838 AAATAACTAATGAA-TA
1 AAATAACTAATAAACTA
699854 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
699870 AAATA
1 AAATA
699875 TCTTAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:701649 original size:96 final size:96
Alignment explanation
Indices: 701478--701660 Score: 237
Period size: 96 Copynumber: 1.9 Consensus size: 96
701468 TGTGATGCCG
* * * *
701478 ATATTTAGGTCGAACAAGCTGTTAGTTGAATTCCTTCCCCTTGAACTTGAAGGCATCGTGCTATA
1 ATATTGAGGTCGAACAAGCTGTCAGTTGAATGCCTTCCCCTTGAACTTGAAGGCATCGTGCTAAA
* *
701543 CGGGTTTTGAACTGAGTGTTGTGTCGCATGC
66 CGGGTATTGAACAGAGTGTTGTGTCGCATGC
*
701574 ATATTGAGGTCGAAGAAGCTCG-CAGTTGAATGCC-TCCCCTTGGAACTTGAAGGCATCGTG-TC
1 ATATTGAGGTCGAACAAGCT-GTCAGTTGAATGCCTTCCCCTT-GAACTTGAAGGCATCGTGCT-
* *
701636 AAATGGGTATTGAACAGATTGTTGT
63 AAACGGGTATTGAACAGAGTGTTGT
701661 ATCAATGGCA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
95 8 0.11
96 66 0.88
97 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (96 bp):
ATATTGAGGTCGAACAAGCTGTCAGTTGAATGCCTTCCCCTTGAACTTGAAGGCATCGTGCTAAA
CGGGTATTGAACAGAGTGTTGTGTCGCATGC
Found at i:704834 original size:30 final size:30
Alignment explanation
Indices: 704800--704872 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
704790 AGTAGACCAC
*
704800 ATTTTTAAATTTTTTCTTTTAATTTTATAT
1 ATTTTTAAATTCTTTCTTTTAATTTTATAT
*
704830 ATTTTTAAATTCTTTCTTTTACTTTTATAT
1 ATTTTTAAATTCTTTCTTTTAATTTTATAT
704860 ATTTTTAAATTCT
1 ATTTTTAAATTCT
704873 AGATAATATC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (30 bp):
ATTTTTAAATTCTTTCTTTTAATTTTATAT
Found at i:719115 original size:34 final size:31
Alignment explanation
Indices: 719077--719148 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 31
719067 GTACAAAAAG
*
719077 AAAGAAAAGACA-AAAAGAAGAAGAAAATTCAGGA
1 AAAGAAAAGA-AGAAAAGAAAAAG-AAATTCA--A
719111 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
1 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
719142 AAAGAAA
1 AAAGAAA
719149 GTAAGCCAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 8 0.22
33 8 0.22
34 20 0.56
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (31 bp):
AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
Found at i:722354 original size:29 final size:29
Alignment explanation
Indices: 722316--722380 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
722306 GTGCAAAAAG
* *
722316 AAAGAAAAG-ATAAAAG-AAGAAATTCAGAA
1 AAAGAAAAGAAGAAAAGAAAAAAATTC--AA
722345 AAAGAAAAGAAGAAAAGAAAAAAATTCAA
1 AAAGAAAAGAAGAAAAGAAAAAAATTCAA
722374 AAAGAAA
1 AAAGAAA
722381 GCAAGCCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 18 0.56
30 6 0.19
31 8 0.25
ACGTcount: A:0.74, C:0.03, G:0.15, T:0.08
Consensus pattern (29 bp):
AAAGAAAAGAAGAAAAGAAAAAAATTCAA
Found at i:725886 original size:20 final size:19
Alignment explanation
Indices: 725846--725889 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
725836 TCTATATCAT
* *
725846 TTATTTATTCATTCTTTTA
1 TTATTTATTCATACTTATA
725865 TTATTTATTTCATACTTATA
1 TTATTTA-TTCATACTTATA
725885 TTATT
1 TTATT
725890 ATCCCCTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTTATTCATACTTATA
Found at i:726171 original size:19 final size:19
Alignment explanation
Indices: 726137--726185 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
726127 AAAATTGGAG
726137 TACAAAAAG-A-AAGAAAA
1 TACAAAAAGAAGAAGAAAA
726154 TACAAAAAGAAGAAGAAAA
1 TACAAAAAGAAGAAGAAAA
*
726173 TTCAAAAA-AAGAA
1 TACAAAAAGAAGAA
726186 AAGAAGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 9 0.31
18 6 0.21
19 14 0.48
ACGTcount: A:0.73, C:0.06, G:0.12, T:0.08
Consensus pattern (19 bp):
TACAAAAAGAAGAAGAAAA
Found at i:726212 original size:33 final size:34
Alignment explanation
Indices: 726141--726219 Score: 99
Period size: 34 Copynumber: 2.3 Consensus size: 34
726131 TTGGAGTACA
* *
726141 AAAAGAAAGAAAATACAAAAAGAAGAAGAAAATTC
1 AAAA-AAAGAAAAGACAAAAAGAAAAAGAAAATTC
726176 AAAAAAAGAAAAGA-AGAAAAGAAAAAG-AAATTC
1 AAAAAAAGAAAAGACA-AAAAGAAAAAGAAAATTC
*
726209 AAAAGAAGAAA
1 AAAAAAAGAAA
726220 GGAAAGTGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
33 17 0.43
34 19 0.47
35 4 0.10
ACGTcount: A:0.75, C:0.04, G:0.15, T:0.06
Consensus pattern (34 bp):
AAAAAAAGAAAAGACAAAAAGAAAAAGAAAATTC
Found at i:726224 original size:19 final size:19
Alignment explanation
Indices: 726143--726224 Score: 59
Period size: 19 Copynumber: 4.6 Consensus size: 19
726133 GGAGTACAAA
* *
726143 AAGAAAGAAAATACAAAAAG
1 AAGAAAGGAAATTC-AAAAG
* *
726163 AAG-AAGAAAATTCAAAAA
1 AAGAAAGGAAATTCAAAAG
* *
726181 AAGAAAAG-AA--GAAAAG
1 AAGAAAGGAAATTCAAAAG
726197 AA-AAA-GAAATTCAAAAG
1 AAGAAAGGAAATTCAAAAG
726214 AAGAAAGGAAA
1 AAGAAAGGAAA
726225 GTGCTCTACC
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
14 1 0.02
15 5 0.10
16 6 0.12
17 7 0.14
18 12 0.24
19 15 0.31
20 3 0.06
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.06
Consensus pattern (19 bp):
AAGAAAGGAAATTCAAAAG
Found at i:728255 original size:86 final size:86
Alignment explanation
Indices: 728110--728281 Score: 344
Period size: 86 Copynumber: 2.0 Consensus size: 86
728100 ACCATCACAA
728110 GCCCAAAGGACTTATTCATTCATCTCAAGCATTATGTATTTTCCTAGAGACATGTATCTAGCCGA
1 GCCCAAAGGACTTATTCATTCATCTCAAGCATTATGTATTTTCCTAGAGACATGTATCTAGCCGA
728175 ACAACTTGTAACCATTCGGCC
66 ACAACTTGTAACCATTCGGCC
728196 GCCCAAAGGACTTATTCATTCATCTCAAGCATTATGTATTTTCCTAGAGACATGTATCTAGCCGA
1 GCCCAAAGGACTTATTCATTCATCTCAAGCATTATGTATTTTCCTAGAGACATGTATCTAGCCGA
728261 ACAACTTGTAACCATTCGGCC
66 ACAACTTGTAACCATTCGGCC
728282 AAGCCCTCTC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (86 bp):
GCCCAAAGGACTTATTCATTCATCTCAAGCATTATGTATTTTCCTAGAGACATGTATCTAGCCGA
ACAACTTGTAACCATTCGGCC
Found at i:728988 original size:22 final size:19
Alignment explanation
Indices: 728960--729008 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 19
728950 TAAAGGGGAT
728960 AATAATATAAGTAATGAAAATA
1 AATAA-ATAAG-AAT-AAAATA
728982 AAT-AATAAGAATAAAATA
1 AATAAATAAGAATAAAATA
729000 AATAAATAA
1 AATAAATAA
729009 ATGATAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 9 0.35
19 8 0.31
20 5 0.19
21 1 0.04
22 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.24
Consensus pattern (19 bp):
AATAAATAAGAATAAAATA
Found at i:729460 original size:19 final size:21
Alignment explanation
Indices: 729417--729468 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
729407 GAAACCCCTT
729417 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
729438 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
729457 TGAAGATACATG
1 TGAAAATACATG
729469 CTCTTGGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:731157 original size:19 final size:21
Alignment explanation
Indices: 731133--731184 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
731123 CGTCCAAGAG
*
731133 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
731152 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
731173 CATGTATTTTCA
1 CATGTATTTTCA
731185 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:731624 original size:19 final size:19
Alignment explanation
Indices: 731596--731634 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
731586 TATCATTTAT
731596 TTATTTATTTCATT-CTTA
1 TTATTTATTTCATTACTTA
731614 TTATTTAATTTCATTACTTA
1 TTATTT-ATTTCATTACTTA
731634 T
1 T
731635 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 8 0.42
20 5 0.26
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTATTTCATTACTTA
Found at i:731637 original size:22 final size:20
Alignment explanation
Indices: 731592--731640 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
731582 TCTCTATCAT
731592 TTAT-TTATTTATTTCATTC
1 TTATATTATTTATTTCATTC
731611 -T-TATTATTTAATTTCATTAC
1 TTATATTATTT-ATTTCATT-C
731631 TTATATTATT
1 TTATATTATT
731641 ATCCCCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.04
18 7 0.28
19 8 0.32
20 1 0.04
21 1 0.04
22 7 0.28
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATATTATTTATTTCATTC
Found at i:731923 original size:17 final size:17
Alignment explanation
Indices: 731891--731922 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
731881 AAATTGGAGT
731891 ACAAAAAGAAAGAAAAG
1 ACAAAAAGAAAGAAAAG
731908 ACAAAAAG-AAGAAAA
1 ACAAAAAGAAAGAAAA
731923 AAATTCAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (17 bp):
ACAAAAAGAAAGAAAAG
Found at i:731932 original size:28 final size:29
Alignment explanation
Indices: 731901--731967 Score: 86
Period size: 28 Copynumber: 2.3 Consensus size: 29
731891 ACAAAAAGAA
*
731901 AGAAAAGACAAAAAGAAG-AAAA-AAATTC
1 AGAAAAGA-AAAAAAAAGAAAAAGAAATTC
731929 AGAAAAAGAAAAAAAAAGAAAAAGAAATTC
1 AG-AAAAGAAAAAAAAAGAAAAAGAAATTC
731959 A-AAAAGAAA
1 AGAAAAGAAA
731968 GCAAGCCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
28 18 0.51
29 10 0.29
30 7 0.20
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.06
Consensus pattern (29 bp):
AGAAAAGAAAAAAAAAGAAAAAGAAATTC
Found at i:732731 original size:31 final size:34
Alignment explanation
Indices: 732696--732770 Score: 93
Period size: 37 Copynumber: 2.2 Consensus size: 34
732686 GGTGCTGCCC
*
732696 ATGAAGAT-GCCT-TTTC-ACAAGGAACACGTGG
1 ATGAAGATACCCTATTTCAACAAGGAACACGTGG
732727 ATGAAGAGATCACCCTATTTCAACAAGGAACACGTGG
1 ATG-A-AGAT-ACCCTATTTCAACAAGGAACACGTGG
732764 ATGAAGA
1 ATGAAGA
732771 GATCACACCT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
31 3 0.08
32 1 0.03
33 4 0.11
35 6 0.16
36 5 0.14
37 18 0.49
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (34 bp):
ATGAAGATACCCTATTTCAACAAGGAACACGTGG
Found at i:732757 original size:37 final size:37
Alignment explanation
Indices: 732708--732783 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
732698 GAAGATGCCT
732708 TTTCACAAGGAACACGTGGATGAAGAGATCAC-CCTA
1 TTTCACAAGGAACACGTGGATGAAGAGATCACACCTA
732744 TTTCAACAAGGAACACGTGGATGAAGAGATCACACCTA
1 TTTC-ACAAGGAACACGTGGATGAAGAGATCACACCTA
732782 TT
1 TT
732784 GGAAGCTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 4 0.11
37 28 0.74
38 6 0.16
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (37 bp):
TTTCACAAGGAACACGTGGATGAAGAGATCACACCTA
Found at i:733481 original size:18 final size:20
Alignment explanation
Indices: 733458--733496 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
733448 TATCATTTAT
733458 TTATTTA-TTTCATT-CTTA
1 TTATTTATTTTCATTACTTA
733476 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
733496 T
1 T
733497 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 7 0.37
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:733499 original size:22 final size:20
Alignment explanation
Indices: 733454--733502 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
733444 TCTCTATCAT
733454 TTAT-TTATTTATTTCATTC
1 TTATATTATTTATTTCATTC
733473 -T-TATTATTTATTTTCATTAC
1 TTATATTATTTA-TTTCATT-C
733493 TTATATTATT
1 TTATATTATT
733503 ATCCCCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.04
18 8 0.32
19 7 0.28
20 1 0.04
21 1 0.04
22 7 0.28
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATATTATTTATTTCATTC
Found at i:733797 original size:29 final size:29
Alignment explanation
Indices: 733764--733833 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 29
733754 AAAAAGAAAG
*
733764 AAAAGACAAA-AAG-AAGAAGAAAATTCAGA
1 AAAAGA-AAAGAAGAAAGAAAAAAATTCA-A
733793 AAAAGAAAAGAAGAAAGAAAAAAATTC-A
1 AAAAGAAAAGAAGAAAGAAAAAAATTCAA
*
733821 AAAAGAAATGAAG
1 AAAAGAAAAGAAG
733834 CCAAGCAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
28 16 0.43
29 9 0.24
30 12 0.32
ACGTcount: A:0.71, C:0.04, G:0.17, T:0.07
Consensus pattern (29 bp):
AAAAGAAAAGAAGAAAGAAAAAAATTCAA
Found at i:737346 original size:7 final size:7
Alignment explanation
Indices: 737296--737326 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
737286 ATTGGCATAC
737296 AAAGCAA
1 AAAGCAA
737303 AAAGCAA
1 AAAGCAA
737310 AAAGCAA
1 AAAGCAA
737317 AAAG-AA
1 AAAGCAA
737323 AAAG
1 AAAG
737327 AAGTTCGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.74, C:0.10, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAGCAA
Found at i:740317 original size:2 final size:2
Alignment explanation
Indices: 740310--740343 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
740300 AATTATTTTC
740310 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
740344 CCTATAGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:747926 original size:13 final size:13
Alignment explanation
Indices: 747908--747932 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
747898 TATAGGCGTG
747908 ATATGGTGATGAA
1 ATATGGTGATGAA
747921 ATATGGTGATGA
1 ATATGGTGATGA
747933 TATAGGCGTG
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:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (13 bp):
ATATGGTGATGAA
Found at i:751976 original size:11 final size:11
Alignment explanation
Indices: 751938--751986 Score: 55
Period size: 11 Copynumber: 4.2 Consensus size: 11
751928 AATATAGGCT
751938 TGATATGGTGA
1 TGATATGGTGA
751949 TGGAATATGGTGA
1 T-G-ATATGGTGA
751962 TGATATAGGTG-
1 TGATAT-GGTGA
751973 TGATAATGGTGA
1 TGAT-ATGGTGA
751985 TG
1 TG
751987 GACAGATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 13 0.39
12 10 0.30
13 10 0.30
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:752004 original size:36 final size:35
Alignment explanation
Indices: 751923--752004 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 35
751913 TTAGAAGTTT
* *
751923 GTGATAATATAGGCTTGATATGGTGATGGAATATG
1 GTGATCATATAGGCTTGATATGGTGATGGAAGATG
* *
751958 GTGATGATATAGG-TGTGATAATGGTGATGGACAGATT
1 GTGATCATATAGGCT-TGAT-ATGGTGATGGA-AGATG
751995 GT-ATCATATA
1 GTGATCATATA
752005 AAACTAAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
34 1 0.03
35 16 0.40
36 18 0.45
37 5 0.12
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (35 bp):
GTGATCATATAGGCTTGATATGGTGATGGAAGATG
Found at i:756675 original size:20 final size:21
Alignment explanation
Indices: 756629--756683 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
756619 ATGAAACCCC
756629 TTTGAAAATACATGATTTTTA
1 TTTGAAAATACATGATTTTTA
**
756650 AATGAAAATACATGA-TTTTA
1 TTTGAAAATACATGATTTTTA
*
756670 TTTGAAGATACATG
1 TTTGAAAATACATG
756684 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.40
Consensus pattern (21 bp):
TTTGAAAATACATGATTTTTA
Found at i:759707 original size:18 final size:17
Alignment explanation
Indices: 759686--759734 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
759676 TTGAAATTTC
759686 TTTTTTCTTTTTCGAATT
1 TTTTTTCTTTTT-GAATT
**
759704 TTTTCTTCTTTTTGTCTT
1 TTTT-TTCTTTTTGAATT
759722 TTTCTTTCTTTTT
1 TTT-TTTCTTTTT
759735 TTGAAGGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.78
Consensus pattern (17 bp):
TTTTTTCTTTTTGAATT
Found at i:763568 original size:18 final size:17
Alignment explanation
Indices: 763547--763596 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
763537 TTGAAATTTC
763547 TTTTTTCTTTTCTGAATT
1 TTTTTTCTTTT-TGAATT
**
763565 TTTTCTTCTTTTTGTCTT
1 TTTT-TTCTTTTTGAATT
763583 TTTCTTTCTTTTTG
1 TTT-TTTCTTTTTG
763597 CATTCCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.04, C:0.14, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTTTCTTTTTGAATT
Found at i:767456 original size:74 final size:75
Alignment explanation
Indices: 767334--767482 Score: 291
Period size: 74 Copynumber: 2.0 Consensus size: 75
767324 CTATATGTTC
767334 TTCAAAAGTCACATCTTTTAGTCCTCCAAAAGACACGATTCTTGAATCATCTCCTTGAAAAGATA
1 TTCAAAAGTCACATCTTTTAGTCCTCCAAAAGACACGATTCTTGAATCATCTCCTTGAAAAGATA
767399 TGTCTCTTGA
66 TGTCTCTTGA
767409 TTCAAAAGTCACATC-TTTAGTCCTCCAAAAGACACGATTCTTGAATCATCTCCTTGAAAAGATA
1 TTCAAAAGTCACATCTTTTAGTCCTCCAAAAGACACGATTCTTGAATCATCTCCTTGAAAAGATA
767473 TGTCTCTTGA
66 TGTCTCTTGA
767483 ATTGTCCTGC
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 59 0.80
75 15 0.20
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (75 bp):
TTCAAAAGTCACATCTTTTAGTCCTCCAAAAGACACGATTCTTGAATCATCTCCTTGAAAAGATA
TGTCTCTTGA
Found at i:768626 original size:19 final size:19
Alignment explanation
Indices: 768603--768650 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
768593 CTTTTCTTCT
768603 TTTCTTTTTTCTGAATTTTC
1 TTTCTTTTTT-TGAATTTTC
**
768623 -TTCTTCTTTTTGTCTTTTC
1 TTTCTT-TTTTTGAATTTTC
768642 TTTCTTTTT
1 TTTCTTTTT
768651 GTACTCCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (19 bp):
TTTCTTTTTTTGAATTTTC
Found at i:768630 original size:35 final size:33
Alignment explanation
Indices: 768576--768649 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 33
768566 GCTTGCTTTC
*
768576 TTTTTGAATTTCTTTTTCTTTTCT-TCTTTTCTT
1 TTTTTGAATTTCTTCTTCTTTT-TGTCTTTTCTT
768609 TTTTCTGAATTTTCTTCTTCTTTTTGTCTTTTCTT
1 TTTT-TGAA-TTTCTTCTTCTTTTTGTCTTTTCTT
768644 TCTTTT
1 T-TTTT
768650 TGTACTCCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
33 4 0.11
34 5 0.14
35 24 0.67
36 3 0.08
ACGTcount: A:0.05, C:0.16, G:0.04, T:0.74
Consensus pattern (33 bp):
TTTTTGAATTTCTTCTTCTTTTTGTCTTTTCTT
Found at i:772025 original size:34 final size:32
Alignment explanation
Indices: 771968--772039 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 32
771958 CTTGGCTTGC
*
771968 TTTC-TTTTTGAATTTCTTTTTCTTTTCT-TCT
1 TTTCTTTTTTGAATTTCTTCTTCTTTT-TGTCT
771999 TTTCTTTTTCTGAATTTTCTTCTTCTTTTTGTCT
1 TTTCTTTTT-TGAA-TTTCTTCTTCTTTTTGTCT
772033 TTTCTTT
1 TTTCTTT
772040 CTTTTTGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 4 0.11
32 4 0.11
33 5 0.14
34 23 0.64
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.74
Consensus pattern (32 bp):
TTTCTTTTTTGAATTTCTTCTTCTTTTTGTCT
Found at i:779436 original size:19 final size:20
Alignment explanation
Indices: 779396--779440 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
779386 GACCCTCCAA
*
779396 TATCGATACTCCTACTTTAG
1 TATCGATACTCCTACTTGAG
779416 TATCGATAC-CCTA-TATGAG
1 TATCGATACTCCTACT-TGAG
779435 TATCGA
1 TATCGA
779441 ATGCCAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 13 0.57
20 9 0.39
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (20 bp):
TATCGATACTCCTACTTGAG
Found at i:787244 original size:20 final size:20
Alignment explanation
Indices: 787216--787253 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
787206 TGGAACTTGC
*
787216 AACAAAATTAGGTAATAATT
1 AACAAAATTAGATAATAATT
*
787236 AACATAATTAGATAATAA
1 AACAAAATTAGATAATAA
787254 CACCTGAGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.29
Consensus pattern (20 bp):
AACAAAATTAGATAATAATT
Found at i:788611 original size:25 final size:25
Alignment explanation
Indices: 788583--788630 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
788573 TTAATTAGCC
788583 CTTCAATTTT-TTTTCATCTTGTTTT
1 CTTCAATTTTATTTT-ATCTTGTTTT
*
788608 CTTCAATTTTATTTTATTTTGTT
1 CTTCAATTTTATTTTATCTTGTT
788631 AAATTAAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.15, C:0.12, G:0.04, T:0.69
Consensus pattern (25 bp):
CTTCAATTTTATTTTATCTTGTTTT
Found at i:789893 original size:39 final size:39
Alignment explanation
Indices: 789828--789924 Score: 122
Period size: 39 Copynumber: 2.5 Consensus size: 39
789818 ATAGTATAAA
* *
789828 GACATGTGGTAAAGACTTATCATGTGCACAAAGCAGAGG
1 GACATGCGGTAAAGACTTATCATGTGCACAAAGCAGAAG
* * * *
789867 GACCTGCGGTAAGGACTTATCTTGTGCACAATGCAGAAG
1 GACATGCGGTAAAGACTTATCATGTGCACAAAGCAGAAG
* *
789906 GACATGCGATAAAGTCTTA
1 GACATGCGGTAAAGACTTA
789925 CAAGTCATAA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.23
Consensus pattern (39 bp):
GACATGCGGTAAAGACTTATCATGTGCACAAAGCAGAAG
Found at i:792910 original size:22 final size:21
Alignment explanation
Indices: 792885--792937 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
792875 TGTTCCAAAT
*
792885 GACCTGTGAATATGTCCCGAAG
1 GACCTATGAAT-TGTCCCGAAG
* *
792907 GACCTATGAGTTGTCCCGAAT
1 GACCTATGAATTGTCCCGAAG
792928 GACCTATGAA
1 GACCTATGAA
792938 ACCCTCGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
GACCTATGAATTGTCCCGAAG
Done.