Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007952.1 Hibiscus syriacus cultivar Beakdansim tig00110377_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: 3169409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 16
Found at i:2818806 original size:30 final size:31
Alignment explanation
Indices: 2818757--2818827 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
2818747 ACATAATTTA
* *
2818757 TATCGCATAGACATATCA-TTTCCATACCTT
1 TATCACATAAACATATCATTTTCCATACCTT
*
2818787 TATCACATAAACATTTCATTTTCCATACCTT
1 TATCACATAAACATATCATTTTCCATACCTT
2818818 TATCACATAA
1 TATCACATAA
2818828 TTCATATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 15 0.41
31 22 0.59
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (31 bp):
TATCACATAAACATATCATTTTCCATACCTT
Found at i:2819310 original size:63 final size:63
Alignment explanation
Indices: 2819177--2819334 Score: 167
Period size: 63 Copynumber: 2.5 Consensus size: 63
2819167 CCTTAATGTG
* ** * * **
2819177 TGCATCGATGCACTATCTGTGCATCGGTACACAAATGTCATTCGATGTTTGTATTTAAGGGGG
1 TGCATCGATGCACTATCTGTGCATCGATACACAAATAACATTCGATGTTTCTATTTAAAGGAA
* ** **
2819240 TGTATCGATGCACTATCTGTGCATCGATACACGGATAACATTCGATGCTTTCT-TTTAAATTAA
1 TGCATCGATGCACTATCTGTGCATCGATACACAAATAACATTCGATG-TTTCTATTTAAAGGAA
*
2819303 TGCATCGATGCACT-TCATGTGCATCAATACAC
1 TGCATCGATGCACTATC-TGTGCATCGATACAC
2819335 CTAGCACAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
62 2 0.03
63 73 0.92
64 4 0.05
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (63 bp):
TGCATCGATGCACTATCTGTGCATCGATACACAAATAACATTCGATGTTTCTATTTAAAGGAA
Found at i:2823033 original size:22 final size:23
Alignment explanation
Indices: 2822995--2823059 Score: 82
Period size: 21 Copynumber: 3.0 Consensus size: 23
2822985 GTATAAATAC
*
2822995 CTTCCACATAGGTATCGATACCT
1 CTTCCATATAGGTATCGATACCT
2823018 CTTCCATAT-GGTATCGATA-CT
1 CTTCCATATAGGTATCGATACCT
* *
2823039 GTT-CATATAGGTATCAATACC
1 CTTCCATATAGGTATCGATACC
2823060 CCATACATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.14
21 13 0.35
22 11 0.30
23 8 0.22
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.34
Consensus pattern (23 bp):
CTTCCATATAGGTATCGATACCT
Found at i:2826032 original size:15 final size:15
Alignment explanation
Indices: 2826012--2826049 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
2826002 TGTACTTATA
2826012 TTATTATCCTCATTC
1 TTATTATCCTCATTC
2826027 TTATTATCCTCATTC
1 TTATTATCCTCATTC
2826042 TTATTATC
1 TTATTATC
2826050 ATATGATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATTATCCTCATTC
Found at i:2827221 original size:21 final size:22
Alignment explanation
Indices: 2827195--2827247 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
2827185 AAGTTCCCCG
2827195 GGTATCGATACC-CTCTACATA-
1 GGTATCGATACCTCT-TACATAT
*
2827216 GGTATCGATACCTCTTCCATAT
1 GGTATCGATACCTCTTACATAT
2827238 GGTATCGATA
1 GGTATCGATA
2827248 ATGTTCATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (22 bp):
GGTATCGATACCTCTTACATAT
Found at i:2829675 original size:103 final size:100
Alignment explanation
Indices: 2829431--2829884 Score: 229
Period size: 103 Copynumber: 4.4 Consensus size: 100
2829421 TGAGACAAAA
* * * *
2829431 TTTGTTTCAAGAGAAACAATCTCAAGTGAGAAAAGATTTTTCATTTTGAAGGAAATGATCTTGAA
1 TTTGTTTTAAGAGAAATAATCTCAAGTGA-AATA-ATTTTTCATTTTGAAGGAAATGATCTTCAA
* *
2829496 GTTTGTTTTTGAGGGAAACTATCTCGAGCGGGATGAT
64 GTTTGTCTTTGAGGGAAACTATCTCGAGCGAGATGAT
* * * * * * * *
2829533 TTT-TTTTCAATAGAAATGACCTTAAGTGAGATGGGATTTTTCTTTTTG-AGTGAAATGGTCTTC
1 TTTGTTTT-AAGAGAAATAATCTCAAGTGAAAT--AATTTTTCATTTTGAAG-GAAATGATCTTC
* *
2829596 AAGTTAATG-CTTTGAGGGAAATTATCTCTAGCGAGATGAAAT
62 AAGTT--TGTCTTTGAGGGAAACTATCTCGAGCGAGATG--AT
* ** * **
2829638 TTTGTTTTAAGGGAAATAATCTCAAGTGAAATAATTTTTTTTGTTTCAAGTGAAACAATC-TCAA
1 TTTGTTTTAAGAGAAATAATCTCAAGTGAAATAATTTTTCAT-TTTGAAG-GAAATGATCTTC-A
* * * * ** * **
2829702 AGTTTGTGTTTAAAAGGAGACGGTCTCAAGCGAGACAAAT
63 AGTTTGTCTTT-GAGGGAAACTATCTCGAGCGAGA-TGAT
* * * * *
2829742 TTTGTTTCAAGGGAAATAATCAT-AAGTGAGATGAGA-TTTTCTTTTTG-AGTGAAATGATCTTG
1 TTTGTTTTAAGAGAAATAATC-TCAAGTGAAAT-A-ATTTTTCATTTTGAAG-GAAATGATCTTC
* * * * * * * **
2829804 ATGTTTGTGTTTCAAAGGAAATTCTTTCGAGTAAGATGGAAT
62 AAGTTTGTCTTT-GAGGGAAACTATCTCGAGCGAGAT-G-AT
* * *
2829846 TTTGTTTTAAGAGAAACAATCTTAAGTGAGATAATTTTT
1 TTTGTTTTAAGAGAAATAATCTCAAGTGAAATAATTTTT
2829885 TTGGTTCAAG
Statistics
Matches: 269, Mismatches: 60, Indels: 45
0.72 0.16 0.12
Matches are distributed among these distances:
101 6 0.02
102 47 0.17
103 77 0.29
104 73 0.27
105 61 0.23
106 5 0.02
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.37
Consensus pattern (100 bp):
TTTGTTTTAAGAGAAATAATCTCAAGTGAAATAATTTTTCATTTTGAAGGAAATGATCTTCAAGT
TTGTCTTTGAGGGAAACTATCTCGAGCGAGATGAT
Found at i:2829826 original size:208 final size:205
Alignment explanation
Indices: 2829555--2830073 Score: 598
Period size: 207 Copynumber: 2.5 Consensus size: 205
2829545 GAAATGACCT
* * * ** * *
2829555 TAAGTGAGATGGGATTTTTCTTTTTGAGTGAAATGGTCTTCAAGTTAATGCTTTGAGGGAAATTA
1 TAAGTGAGATGAGA-TTTTCTTTTTGAGTGAAATGATCTTGAAGTTTGTG-TTTCAAGGAAATTA
* * * *
2829620 TCTCTAGCGAGATGAAATTTTGTTTTAAGGGAAATAATCTCAAGTGAAATAATTTTTTTTGTTTC
64 TCTCAAGCGAGATGGAATTTTGTTTTAAGGGAAACAATCTCAAGTGAAATAA-TTTTTTTGGTTC
* * *
2829685 AAGTGAAACAATCTCAAAGTTTGTGTTTAAAAGGAGACGGTCTCAAGCGAGA-CAAATTTTGTTT
128 AAGTGAAACAATCTCAAAGTTTGCGTTTAAAAGGAAACGGTCTCAAGAGAGATCAAA-TTTGTTT
* *
2829749 CAAGGGAAATAATC
192 CAAGAGAAACAATC
* *
2829763 ATAAGTGAGATGAGATTTTCTTTTTGAGTGAAATGATCTTGATGTTTGTGTTTCAAAGGAAATTC
1 -TAAGTGAGATGAGATTTTCTTTTTGAGTGAAATGATCTTGAAGTTTGTGTTTC-AAGGAAATTA
* * ** * * *
2829828 TTTCGAGTAAGATGGAATTTTGTTTTAAGAGAAACAATCTTAAGTGAGATAATTTTTTTGGTTCA
64 TCTCAAGCGAGATGGAATTTTGTTTTAAGGGAAACAATCTCAAGTGAAATAATTTTTTTGGTTCA
* * ** * *
2829893 AGTGAAGCAATCTCAAAGTTTGCGTTTAAAGGGAAATTGTCTCAGGAGAGATGAAATTTGTTTCA
129 AGTGAAACAATCTCAAAGTTTGCGTTTAAAAGGAAACGGTCTCAAGAGAGATCAAATTTGTTTCA
2829958 AGAGAAACAATC
194 AGAGAAACAATC
* * **
2829970 TCAAGTGATATGAGA-TTT-TTTTT-AGTGGAATGATCTTGAAGTTTGTGTTTCAAGGAAAACAG
1 T-AAGTGAGATGAGATTTTCTTTTTGAGTGAAATGATCTTGAAGTTTGTGTTTCAAGGAAATTA-
* *
2830032 TCTCAAGCGAGATGGAA-TTTGTTTGAATGGAAACAATCTCAA
64 TCTCAAGCGAGATGGAATTTTGTTTTAAGGGAAACAATCTCAA
2830074 TGTTCTGACA
Statistics
Matches: 262, Mismatches: 44, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
203 28 0.11
204 39 0.15
205 5 0.02
206 4 0.02
207 89 0.34
208 84 0.32
209 13 0.05
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36
Consensus pattern (205 bp):
TAAGTGAGATGAGATTTTCTTTTTGAGTGAAATGATCTTGAAGTTTGTGTTTCAAGGAAATTATC
TCAAGCGAGATGGAATTTTGTTTTAAGGGAAACAATCTCAAGTGAAATAATTTTTTTGGTTCAAG
TGAAACAATCTCAAAGTTTGCGTTTAAAAGGAAACGGTCTCAAGAGAGATCAAATTTGTTTCAAG
AGAAACAATC
Found at i:2830065 original size:100 final size:102
Alignment explanation
Indices: 2829413--2830073 Score: 368
Period size: 104 Copynumber: 6.4 Consensus size: 102
2829403 AAGGGGAAAT
* * * **
2829413 GTCTCAAGTGAGA-CAAAATTTGTTTCAAGAGAAACAATCTCAAGTGAGAAAAGATTTTTCATTT
1 GTCTCAAGCGAGATGAAATTTTGTTTCAAGAGAAACAATCTCAAGTGAGATGAGATTTTT--TTT
* ** *
2829477 TGAAG-GAAATGATCTTGAAGTTTGT-TTTTGAGGGAAAC
64 T-AAGTGGAATGATCTTGAAGTTTGTGTTTAAAGGAAAAC
* * * * * ** * * *
2829515 TATCTCGAGCGGGATG--ATTTTTTTTCAATAGAAATGACCTTAAGTGAGATGGGATTTTTCTTT
1 -GTCTCAAGCGAGATGAAATTTTGTTTCAAGAGAAACAATCTCAAGTGAGATGAGA-TTTT-TTT
* * * * ** * * **
2829578 TTGAGTGAAATGGTCTTCAAGTTAATGCTTTGAGGGAAATT
63 TTAAGTGGAATGATCTTGAAGTTTGTG-TTTAAAGGAAAAC
* * * * * * * **
2829619 ATCTCTAGCGAGATGAAATTTTGTTTTAAGGGAAATAATCTCAAGTGAAATAATTTTTTTTGTTT
1 GTCTCAAGCGAGATGAAATTTTGTTTCAAGAGAAACAATCTCAAGTGAGATGAGATTTTTT-TTT
* ** ** *
2829684 CAAGTGAAACAATCTCAAAGTTTGTGTTTAAAAGG-AGAC
65 -AAGTGGAATGATCTTGAAGTTTGTGTTT-AAAGGAAAAC
* * *
2829723 GGTCTCAAGCGAGA-CAAATTTTGTTTCAAGGGAAATAATCAT-AAGTGAGATGAGATTTTCTTT
1 -GTCTCAAGCGAGATGAAATTTTGTTTCAAGAGAAACAATC-TCAAGTGAGATGAGATTTT-TTT
* * * *
2829786 TTGAGTGAAATGATCTTGATGTTTGTGTTTCAAAGGAAATTC
63 TTAAGTGGAATGATCTTGAAGTTTGTGTTT-AAAGGAAA-AC
* * ** * * *
2829828 -TTTCGAGTAAGATGGAATTTTGTTTTAAGAGAAACAATCTTAAGTGAGAT-A-ATTTTTTTGGT
1 GTCTCAAGCGAGATGAAATTTTGTTTCAAGAGAAACAATCTCAAGTGAGATGAGATTTTTTT--T
** * **
2829890 TCAAGT-GAA-GCAATCTCAAAGTTTGCGTTTAAAGGGAAATT
64 T-AAGTGGAATG--ATCTTGAAGTTTGTGTTTAAA-GGAAAAC
* * *
2829931 GTCTCAGGAGAGATGAAA-TTTGTTTCAAGAGAAACAATCTCAAGTGATATGAGA-TTTTTTTT-
1 GTCTCAAGCGAGATGAAATTTTGTTTCAAGAGAAACAATCTCAAGTGAGATGAGATTTTTTTTTA
*
2829993 AGTGGAATGATCTTGAAGTTTGTGTTTCAAGGAAAAC
66 AGTGGAATGATCTTGAAGTTTGTGTTTAAAGGAAAAC
* *
2830030 AGTCTCAAGCGAGATGGAA-TTTGTTTGAATG-GAAACAATCTCAA
1 -GTCTCAAGCGAGATGAAATTTTGTTTCAA-GAGAAACAATCTCAA
2830074 TGTTCTGACA
Statistics
Matches: 422, Mismatches: 105, Indels: 65
0.71 0.18 0.11
Matches are distributed among these distances:
99 5 0.01
100 57 0.14
101 9 0.02
102 57 0.14
103 102 0.24
104 130 0.31
105 62 0.15
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (102 bp):
GTCTCAAGCGAGATGAAATTTTGTTTCAAGAGAAACAATCTCAAGTGAGATGAGATTTTTTTTTA
AGTGGAATGATCTTGAAGTTTGTGTTTAAAGGAAAAC
Found at i:2833200 original size:37 final size:37
Alignment explanation
Indices: 2833159--2833230 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
2833149 AATTTTAAGC
*
2833159 TCACAAATTTTCAAATTACACTGAATTCAATTTAATT
1 TCACAAACTTTCAAATTACACTGAATTCAATTTAATT
* *
2833196 TCACAAACTTTCAAATTATATTGAATTCAATTTAA
1 TCACAAACTTTCAAATTACACTGAATTCAATTTAA
2833231 CTTTTAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (37 bp):
TCACAAACTTTCAAATTACACTGAATTCAATTTAATT
Found at i:2841969 original size:14 final size:14
Alignment explanation
Indices: 2841947--2841988 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
2841937 GAACACCAAT
2841947 GAACATAAACGAAC
1 GAACATAAACGAAC
* *
2841961 GAGCATAAACAAAC
1 GAACATAAACGAAC
2841975 GAACATAAACGAAC
1 GAACATAAACGAAC
2841989 AAATTATCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.57, C:0.21, G:0.14, T:0.07
Consensus pattern (14 bp):
GAACATAAACGAAC
Found at i:2844174 original size:19 final size:19
Alignment explanation
Indices: 2844146--2844182 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2844136 ACATTAGCAG
*
2844146 TGCATGTTCTAGAATGCAC
1 TGCATATTCTAGAATGCAC
2844165 TGCATATTCTAGAATGCA
1 TGCATATTCTAGAATGCA
2844183 TATTCCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (19 bp):
TGCATATTCTAGAATGCAC
Found at i:2844286 original size:36 final size:36
Alignment explanation
Indices: 2844239--2844356 Score: 200
Period size: 36 Copynumber: 3.3 Consensus size: 36
2844229 GAAAACGAAC
*
2844239 ACTTGGATCGGAAGTGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
2844275 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCA
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
2844311 ACTTGAATCGGAAGTGCCGATGCTTCCTTTCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
2844347 ATTTGAATCG
1 ACTTGAATCG
2844357 TCGGTGCACC
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 77 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (36 bp):
ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
Found at i:2845424 original size:19 final size:19
Alignment explanation
Indices: 2845396--2845432 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2845386 ACATTAGGAG
*
2845396 TGCATGTTCTAGAATGCAC
1 TGCATATTCTAGAATGCAC
2845415 TGCATATTCTAGAATGCA
1 TGCATATTCTAGAATGCA
2845433 TATTCCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (19 bp):
TGCATATTCTAGAATGCAC
Found at i:2848405 original size:3 final size:3
Alignment explanation
Indices: 2848394--2848454 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
2848384 TTTTTTATCG
** *
2848394 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2848439 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
2848455 CATATTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2848449 original size:29 final size:30
Alignment explanation
Indices: 2848387--2848449 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
2848377 TCCGGGTTTT
*
2848387 TTTATCGTTATTTTATTATTATTATTATTA
1 TTTATCGTTATCTTATTATTATTATTATTA
2848417 -TTATCGTTATCTTATTATT-TTATTATTA
1 TTTATCGTTATCTTATTATTATTATTATTA
2848445 TTTAT
1 TTTAT
2848450 TATTACATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (30 bp):
TTTATCGTTATCTTATTATTATTATTATTA
Found at i:2848460 original size:28 final size:28
Alignment explanation
Indices: 2848400--2848465 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
2848390 ATCGTTATTT
* *
2848400 TATTATTATTATTATTATTATCGTTATCT
1 TATTATT-TTATTATTATTATCATTATCA
*
2848429 TATTATTTTATTATTATTTATTATTA-CA
1 TATTATTTTATTATTA-TTATCATTATCA
*
2848457 TATTTTTTT
1 TATTATTTT
2848466 GCAGGCCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (28 bp):
TATTATTTTATTATTATTATCATTATCA
Found at i:2856203 original size:36 final size:35
Alignment explanation
Indices: 2856146--2856249 Score: 115
Period size: 36 Copynumber: 3.0 Consensus size: 35
2856136 CTTGAGATCG
2856146 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAA-TTTGTCTCGCTTGAGACAA
** *
2856181 TTTCTCTAAAAACAAATGTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAAT-TTGTCTCGCTTGAGACAA
* *
2856217 TATCT-T-AAAGCAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTT-GTCTCGCTTGAGACA
2856250 TCATTTTCTC
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
33 2 0.03
34 20 0.34
35 8 0.14
36 28 0.48
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (35 bp):
TTTCTCTAAAAACAAATTTGTCTCGCTTGAGACAA
Found at i:2856519 original size:28 final size:28
Alignment explanation
Indices: 2856496--2856596 Score: 120
Period size: 28 Copynumber: 3.7 Consensus size: 28
2856486 ACAGTTTCTC
2856496 TTGAAAAAAATCTTTGAGTTAGTTCCTT
1 TTGAAAAAAATCTTTGAGTTAGTTCCTT
* *
2856524 TT-AAATAAAATCTTGGAGTTTGTTCCTT
1 TTGAAA-AAAATCTTTGAGTTAGTTCCTT
* *
2856552 TTGAATAAATATCTTTGAGTT-GTTTCTT
1 TTGAA-AAAAATCTTTGAGTTAGTTCCTT
2856580 TTG--AAAAATCTTTGAGT
1 TTGAAAAAAATCTTTGAGT
2856597 CTATTTATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
25 13 0.20
27 3 0.05
28 33 0.52
29 14 0.22
30 1 0.02
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.47
Consensus pattern (28 bp):
TTGAAAAAAATCTTTGAGTTAGTTCCTT
Found at i:2856608 original size:54 final size:56
Alignment explanation
Indices: 2856496--2856611 Score: 130
Period size: 54 Copynumber: 2.1 Consensus size: 56
2856486 ACAGTTTCTC
* * *
2856496 TTGAAAAAAATCTTTGAGTTAGTTCCTTTTAAATAAAATCTTGGAGTTTGTTCCTT
1 TTGAAAAAAATCTTTGAGTTAGTTCCTTTTAAATAAAATCTTGGAGTCTATTCATT
* * * * *
2856552 TTGAATAAATATCTTTGAGTT-GTTTCTTTT-GA-AAAATCTTTGAGTCTATTTATT
1 TTGAA-AAAAATCTTTGAGTTAGTTCCTTTTAAATAAAATCTTGGAGTCTATTCATT
2856606 TTGAAA
1 TTGAAA
2856612 CAAAGTTTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
53 1 0.02
54 22 0.43
55 1 0.02
56 13 0.25
57 14 0.27
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (56 bp):
TTGAAAAAAATCTTTGAGTTAGTTCCTTTTAAATAAAATCTTGGAGTCTATTCATT
Found at i:2856766 original size:28 final size:28
Alignment explanation
Indices: 2856692--2856756 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
2856682 CTTTAGACAA
2856692 TTTTGTGAAAAAATCTTTGAGATTGTTTC
1 TTTTG-GAAAAAATCTTTGAGATTGTTTC
*
2856721 TTTTGGAAAAAATCTTTGAGTTTGTTTC
1 TTTTGGAAAAAATCTTTGAGATTGTTTC
2856749 -TTTGGAAA
1 TTTTGGAAA
2856757 CAAAATTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 8 0.23
28 22 0.63
29 5 0.14
ACGTcount: A:0.28, C:0.06, G:0.18, T:0.48
Consensus pattern (28 bp):
TTTTGGAAAAAATCTTTGAGATTGTTTC
Found at i:2856794 original size:37 final size:37
Alignment explanation
Indices: 2856744--2856860 Score: 115
Period size: 37 Copynumber: 3.4 Consensus size: 37
2856734 CTTTGAGTTT
2856744 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* * * *
2856781 GTTTCTTTTGAAACAAAA------ATCT-TTGAG-TCT
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT-A
2856811 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* *
2856848 ATTTCTTTTGAAA
1 GTTTCTTTGGAAA
2856861 AAATCTTTGA
Statistics
Matches: 61, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
29 1 0.02
30 21 0.34
31 3 0.05
36 3 0.05
37 32 0.52
38 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (37 bp):
GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
Found at i:2856804 original size:67 final size:65
Alignment explanation
Indices: 2856711--2856934 Score: 276
Period size: 67 Copynumber: 3.4 Consensus size: 65
2856701 AAAATCTTTG
* * *
2856711 AGATTGTTTCTTTTGGAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
2856776 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1 AGATAGTTTCTTTTG-AA-AAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
2856841 TA
64 TA
* * * *
2856843 AGATAATTTCTTTTG-AAAAAATCTTTGAATCTGTTT-TTCT-TAAA-ATAAATTTTGTATCTCT
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCTT-TGGAAACA-AAATTTTGTCTCTCT
*
2856904 TG
64 TA
* * **
2856906 AGACAGTTTCTCTTGAAGTAAATCTTTGA
1 AGATAGTTTCTTTTGAAAAAAATCTTTGA
2856935 ATATGTTCAT
Statistics
Matches: 141, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
62 1 0.01
63 32 0.23
64 31 0.22
65 15 0.11
66 1 0.01
67 61 0.43
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (65 bp):
AGATAGTTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
Found at i:2857117 original size:63 final size:62
Alignment explanation
Indices: 2857019--2857136 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 62
2857009 GAAACAAAAC
*
2857019 AAACATCTTTGAGATCATTTCCCTTTAAACGAATTTTGTCTCATTCGAGACAGTTTTCCTTT
1 AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCATTCGAGACAGTTTTCCTTT
* * *
2857081 AAACAATCTTTGAG-TCATTT-CTTTTGAAACAAAATTTTGTCTCTTTTGAGACAGTT
1 AAAC-ATCTTTGAGATCATTTCCCTTT-AAAC-AAATTTTGTCTCATTCGAGACAGTT
2857137 GCTTTTGAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
61 4 0.08
62 14 0.29
63 31 0.63
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (62 bp):
AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCATTCGAGACAGTTTTCCTTT
Found at i:2857369 original size:46 final size:45
Alignment explanation
Indices: 2857273--2857486 Score: 198
Period size: 46 Copynumber: 4.9 Consensus size: 45
2857263 AGACCAGATC
* *
2857273 TCCTCATCACGTAGGAGCCGTGTCA--ACCATAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCATCACCTTAGATAACCAGCCG
* **
2857316 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCATCACC-TTAGATAACCAGCCG
* * *
2857362 TCCTCATCATGTAGGAACCGTGTCATC-CC-CAG---ACCAGATC-
1 TCCTCATCACGTAGGAACCGTGTCATCACCTTAGATAACCAG-CCG
* * **
2857402 TCTTCATCACGTATGAGTCGTGTCA-C-CC-TAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCATCACCTTAGATAACCAGCCG
* *
2857444 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATAGCCAG
1 TCCTCATCACGTAGGAACCGTGTCATCACC-TTAGATAACCAG
2857487 AACTCTTCAT
Statistics
Matches: 136, Mismatches: 23, Indels: 21
0.76 0.13 0.12
Matches are distributed among these distances:
39 5 0.04
40 24 0.18
41 2 0.01
42 25 0.18
43 26 0.19
44 2 0.01
45 5 0.04
46 47 0.35
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (45 bp):
TCCTCATCACGTAGGAACCGTGTCATCACCTTAGATAACCAGCCG
Found at i:2857451 original size:82 final size:86
Alignment explanation
Indices: 2857355--2857514 Score: 238
Period size: 82 Copynumber: 1.9 Consensus size: 86
2857345 CTTTAGATGG
* *
2857355 CCAGCCGTCCTCATCATGTAGGAACCGTGTCATC-CC-CAG-A-CCAGATCTCTTCATCACGTAT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCACCTCAGAAGCCAGAACTCTTCATCACGTAT
2857416 GAGTCGTGTCACCCTAGATAA
66 GAGTCGTGTCACCCTAGATAA
* *
2857437 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATAGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCACC-TCAGA-AGCCAGAACTCTTCATCACGT
2857502 ATGAGTCGTGTCA
64 ATGAGTCGTGTCA
2857515 TTCCCCGACC
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
82 32 0.47
83 2 0.03
85 2 0.03
87 1 0.01
88 31 0.46
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (86 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCACCTCAGAAGCCAGAACTCTTCATCACGTAT
GAGTCGTGTCACCCTAGATAA
Found at i:2857463 original size:128 final size:129
Alignment explanation
Indices: 2857214--2857569 Score: 538
Period size: 128 Copynumber: 2.8 Consensus size: 129
2857204 AACCATAACT
* * *
2857214 CCTTTAGATGACCAGATCTCCTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCCTCA
1 CCTTTAGATGGCCAGAACTCCTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTCA
* *
2857279 TCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
66 TCACGTATGAGCCGTGTC-ACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
* * * *
2857344 CCTTTAGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTC
1 CCTTTAGATGGCCAGAAC-TCCTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTC
*
2857407 ATCACGTATGAGTCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
65 ATCACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
* * *
2857472 CCTTTAGATAGCCAGAACTCTTCATCACGTATGAGTCGTGTCATTCCCC-GACCAGATCTCTTCA
1 CCTTTAGATGGCCAGAACTCCTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTCA
*
2857536 TCACGTATGAGCCGTGTCACCCTTAGATGACCAG
66 TCACGTATGAGCCGTGTCACCC-TAGATAACCAG
2857570 ACCTCTTCAT
Statistics
Matches: 204, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
128 115 0.56
129 53 0.26
130 36 0.18
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (129 bp):
CCTTTAGATGGCCAGAACTCCTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTCA
TCACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
Found at i:2857512 original size:46 final size:43
Alignment explanation
Indices: 2857394--2857672 Score: 165
Period size: 40 Copynumber: 6.6 Consensus size: 43
2857384 TCATCCCCAG
*
2857394 ACCAGATCTCTTCATCACGTATGAGTCGTG-TCACCCTAGATA
1 ACCAGAACTCTTCATCACGTATGAGTCGTGTTCACCCTAGATA
* * * ** *
2857436 ACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATA
1 ACCAGAAC-TCTTCATCACGTATGAGTCGTG-T-TCACC-CTAGATA
* *
2857482 GCCAGAACTCTTCATCACGTATGAGTCGTG-TCATTCCC-CG---
1 ACCAGAACTCTTCATCACGTATGAGTCGTGTTCA--CCCTAGATA
* * *
2857522 ACCAGATCTCTTCATCACGTATGAGCCGTG-TCACCCTTAGATG
1 ACCAGAACTCTTCATCACGTATGAGTCGTGTTCACCC-TAGATA
* **
2857565 ACCAGACCTCTTCATTGCGTATGAGTCGTG-TCATTTCCC--G---
1 ACCAGAACTCTTCATCACGTATGAGTCGTGTTCA---CCCTAGATA
* * *
2857605 ACCAGATCTCTTCATCACGTATGAGCCGTG-TCACCCTTAGATG
1 ACCAGAACTCTTCATCACGTATGAGTCGTGTTCACCC-TAGATA
* **
2857648 ACCAGACCTCTTCATTGCGTATGAG
1 ACCAGAACTCTTCATCACGTATGAG
2857673 CAGTGTCGTC
Statistics
Matches: 186, Mismatches: 29, Indels: 43
0.72 0.11 0.17
Matches are distributed among these distances:
37 3 0.02
38 3 0.02
40 61 0.33
41 1 0.01
42 23 0.12
43 56 0.30
45 7 0.04
46 31 0.17
47 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (43 bp):
ACCAGAACTCTTCATCACGTATGAGTCGTGTTCACCCTAGATA
Found at i:2857586 original size:43 final size:43
Alignment explanation
Indices: 2857217--2857679 Score: 280
Period size: 43 Copynumber: 10.9 Consensus size: 43
2857207 CATAACTCCT
* *
2857217 TTAGATGACCAGATCTCCTCATCACGTATGAGCCGTGTCATTCCC
1 TTAGATGACCAGACCTCTTCATCACGTATGAGCCGTGTCA--CCC
* * * * *
2857262 ---CA-GACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
1 TTAGATGACCAGACCTCTTCATCACGTATGAGCCGTGTCACCC
* * * * * *
2857301 ATAGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCT
1 TTAGATGACCAGACC-TCTTCATCACGTATGAGCCGTG---TCACCC
* * * * *
2857347 TTAGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTCATCCC
1 TTAGATGACCAGACC-TCTTCATCACGTATGAGCCGTGTCA-CCC
* * *
2857391 ---CA-GACCAGATCTCTTCATCACGTATGAGTCGTGTCACCC
1 TTAGATGACCAGACCTCTTCATCACGTATGAGCCGTGTCACCC
* * * * *
2857430 -TAGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCT
1 TTAGATGACCAGACC-TCTTCATCACGTATGAGCCGTG---TCACCC
* *
2857475 TTAGAT-AGCCAGAACTCTTCATCACGTATGAGTCGTGTCA---
1 TTAGATGA-CCAGACCTCTTCATCACGTATGAGCCGTGTCACCC
**** *
2857515 TTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC
1 TTAGATGACCAGACCTCTTCATCACGTATGAGCCGTGTCACCC
** *
2857558 TTAGATGACCAGACCTCTTCATTGCGTATGAGTCGTGTCA---
1 TTAGATGACCAGACCTCTTCATCACGTATGAGCCGTGTCACCC
**** *
2857598 TTTCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC
1 TTAGATGACCAGACCTCTTCATCACGTATGAGCCGTGTCACCC
** *
2857641 TTAGATGACCAGACCTCTTCATTGCGTATGAGCAGTGTC
1 TTAGATGACCAGACCTCTTCATCACGTATGAGCCGTGTC
2857680 GTCCCCACCA
Statistics
Matches: 326, Mismatches: 65, Indels: 56
0.73 0.15 0.13
Matches are distributed among these distances:
39 5 0.02
40 89 0.27
41 38 0.12
42 26 0.08
43 95 0.29
44 2 0.01
45 6 0.02
46 64 0.20
47 1 0.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (43 bp):
TTAGATGACCAGACCTCTTCATCACGTATGAGCCGTGTCACCC
Found at i:2857679 original size:83 final size:83
Alignment explanation
Indices: 2857469--2857672 Score: 347
Period size: 83 Copynumber: 2.5 Consensus size: 83
2857459 AACCGTGTTA
* * **
2857469 TCACCTTTAGAT-AGCCAGAACTCTTCATCACGTATGAGTCGTGTCATTCCCCGACCAGATCTCT
1 TCACCCTTAGATGA-CCAGACCTCTTCATTGCGTATGAGTCGTGTCATTCCCCGACCAGATCTCT
2857533 TCATCACGTATGAGCCGTG
65 TCATCACGTATGAGCCGTG
*
2857552 TCACCCTTAGATGACCAGACCTCTTCATTGCGTATGAGTCGTGTCATTTCCCGACCAGATCTCTT
1 TCACCCTTAGATGACCAGACCTCTTCATTGCGTATGAGTCGTGTCATTCCCCGACCAGATCTCTT
2857617 CATCACGTATGAGCCGTG
66 CATCACGTATGAGCCGTG
2857635 TCACCCTTAGATGACCAGACCTCTTCATTGCGTATGAG
1 TCACCCTTAGATGACCAGACCTCTTCATTGCGTATGAG
2857673 CAGTGTCGTC
Statistics
Matches: 115, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
83 114 0.99
84 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.29
Consensus pattern (83 bp):
TCACCCTTAGATGACCAGACCTCTTCATTGCGTATGAGTCGTGTCATTCCCCGACCAGATCTCTT
CATCACGTATGAGCCGTG
Found at i:2857848 original size:3 final size:3
Alignment explanation
Indices: 2857837--2857900 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
2857827 TTTTTTATCG
** *
2857837 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2857882 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
2857901 CATATTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2857869 original size:32 final size:32
Alignment explanation
Indices: 2857831--2857898 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
2857821 CCGGGTTTTT
*
2857831 TTATCGTTATTTTATTATTATTATTATTA-TTA
1 TTATCGTTATCTTATTATT-TTATTATTATTTA
2857863 TTATCGTTATCTTATTATTTTATTATTATTTA
1 TTATCGTTATCTTATTATTTTATTATTATTTA
2857895 TTAT
1 TTAT
2857899 TACATATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 9 0.26
32 25 0.74
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.66
Consensus pattern (32 bp):
TTATCGTTATCTTATTATTTTATTATTATTTA
Found at i:2857906 original size:28 final size:28
Alignment explanation
Indices: 2857846--2857911 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
2857836 GTTATTTTAT
* *
2857846 TATTATTATTATTATTATTATCGTTATCT
1 TATTATT-TTATTATTATTATCATTATCA
*
2857875 TATTATTTTATTATTATTTATTATTA-CA
1 TATTATTTTATTATTA-TTATCATTATCA
*
2857903 TATTTTTTT
1 TATTATTTT
2857912 GCAGGCCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (28 bp):
TATTATTTTATTATTATTATCATTATCA
Found at i:2866202 original size:25 final size:24
Alignment explanation
Indices: 2866144--2866202 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
2866134 ATAAAAAATA
* *
2866144 AAAAAATCACAAAAAAATAAATTT
1 AAAAAATTACAAAAAAATAAATGT
**
2866168 AAAATTTTACTAAAAAAAT-AATGGT
1 AAAAAATTAC-AAAAAAATAAAT-GT
2866193 AAAAAATTAC
1 AAAAAATTAC
2866203 CTTGTGGCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.64, C:0.07, G:0.03, T:0.25
Consensus pattern (24 bp):
AAAAAATTACAAAAAAATAAATGT
Found at i:2866682 original size:32 final size:32
Alignment explanation
Indices: 2866646--2866715 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
2866636 AAGGTGACCT
* *
2866646 TTAGGTAAGCTCATGGGTCCCAAGATACTCCC
1 TTAGGTAAGCTCATAGGCCCCAAGATACTCCC
* * *
2866678 TTAGGTAGGCTCTTAGGCCCCAAGGTACTCCC
1 TTAGGTAAGCTCATAGGCCCCAAGATACTCCC
2866710 TTAGGT
1 TTAGGT
2866716 TGACTTCTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.27
Consensus pattern (32 bp):
TTAGGTAAGCTCATAGGCCCCAAGATACTCCC
Found at i:2868635 original size:2 final size:2
Alignment explanation
Indices: 2868628--2868656 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2868618 TCAAACTACC
2868628 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2868657 AATGCCAAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2874076 original size:22 final size:22
Alignment explanation
Indices: 2874056--2874102 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2874046 TAAATATATT
2874056 TATTAATATTTCTAATAATATAA
1 TATT-ATATTTCTAATAATATAA
* *
2874079 TATTATATTTTTAATATTATAA
1 TATTATATTTCTAATAATATAA
2874101 TA
1 TA
2874103 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTATATTTCTAATAATATAA
Found at i:2874086 original size:32 final size:33
Alignment explanation
Indices: 2874050--2874127 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 33
2874040 AATATTTAAA
* *
2874050 TATATTTATTAATATTTCTAATAATATAAT-AT
1 TATATTTATTAATATTTATAATAAAATAATAAT
2874082 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT-AAT
*
2874114 TATATATA-TAATAT
1 TATATTTATTAATAT
2874128 AAGTAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.33
31 6 0.15
32 20 0.51
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (33 bp):
TATATTTATTAATATTTATAATAAAATAATAAT
Found at i:2874691 original size:29 final size:29
Alignment explanation
Indices: 2874658--2874716 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2874648 TTTCAGAAAT
*
2874658 GTAATTCATTTTCCAGAATTCAAATTCAA
1 GTAATTCATTTTCCAAAATTCAAATTCAA
* * *
2874687 GTAATTTATTTTTCAAAATTCAATTTCAA
1 GTAATTCATTTTCCAAAATTCAAATTCAA
2874716 G
1 G
2874717 AAACCCAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (29 bp):
GTAATTCATTTTCCAAAATTCAAATTCAA
Found at i:2875238 original size:18 final size:19
Alignment explanation
Indices: 2875200--2875240 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2875190 TTTTTCAGAA
*
2875200 TTTTTTTATTATTTTTCCT
1 TTTTTTTATTATTGTTCCT
*
2875219 TTTTTTTCTTATTGTT-CT
1 TTTTTTTATTATTGTTCCT
2875237 TTTT
1 TTTT
2875241 ATTTTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTTTATTATTGTTCCT
Found at i:2877063 original size:19 final size:20
Alignment explanation
Indices: 2877039--2877089 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2877029 AATGACCAAT
2877039 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* * *
2877058 AAAATCGCAACGTGATTTAG
1 AAAATCGCAACGCGATATAC
2877078 AAAATCGCAACG
1 AAAATCGCAACG
2877090 TTAAAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:2877083 original size:20 final size:20
Alignment explanation
Indices: 2877039--2877336 Score: 161
Period size: 20 Copynumber: 14.6 Consensus size: 20
2877029 AATGACCAAT
* *
2877039 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
*
2877058 AAAATCGCAACGTGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
2877078 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
2877098 AAAATCGCAACG-G-TCAAACG
1 AAAATCGCAACGCGAT-TTA-G
* **
2877118 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
2877139 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
2877162 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
2877182 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
2877202 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
2877225 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
2877245 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
2877265 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
2877285 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
2877305 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
2877325 AAAATCGCAACG
1 AAAATCGCAACG
2877337 TTAAAAAGAA
Statistics
Matches: 224, Mismatches: 43, Indels: 23
0.77 0.15 0.08
Matches are distributed among these distances:
19 19 0.08
20 162 0.72
21 14 0.06
23 29 0.13
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:2877218 original size:40 final size:40
Alignment explanation
Indices: 2877164--2877334 Score: 216
Period size: 40 Copynumber: 4.2 Consensus size: 40
2877154 TTTAGAAGAA
*
2877164 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* * * *
2877204 AGTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGA-TT-G-AGAGAATCGCAATGCGATTGAGAG
* * *
2877247 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* * *
2877287 AATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAA
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
2877327 AATCGCAA
1 AATCGCAA
2877335 CGTTAAAAAG
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 75 0.67
41 3 0.03
42 2 0.02
43 32 0.29
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.20
Consensus pattern (40 bp):
AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
Found at i:2877226 original size:63 final size:63
Alignment explanation
Indices: 2877143--2877336 Score: 286
Period size: 63 Copynumber: 3.1 Consensus size: 63
2877133 GCTTCCAAGT
* *
2877143 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAGAA
* *
2877206 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAGAA
* * * * *
2877269 TCGCAATGCGATTTA-TAG--AATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAGAA
2877329 TCGCAACG
1 TCGCAACG
2877337 TTAAAAAGAA
Statistics
Matches: 119, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
60 44 0.37
62 2 0.02
63 73 0.61
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.20
Consensus pattern (63 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAGAA
Found at i:2877346 original size:20 final size:20
Alignment explanation
Indices: 2877323--2877366 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2877313 AACGCGATTT
*
2877323 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
* *
2877343 AGAAAATCTCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
2877363 AGAA
1 AGAA
2877367 TAGTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.14
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:2877454 original size:6 final size:6
Alignment explanation
Indices: 2877443--2877515 Score: 123
Period size: 6 Copynumber: 12.5 Consensus size: 6
2877433 GACACGTATT
*
2877443 ACCACG ACCACG ACCACG ACCAAG A-CACG ACCACG ACCACG A-CACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2877489 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
2877516 TATCATCCAT
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
5 9 0.14
6 54 0.86
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2877471 original size:23 final size:24
Alignment explanation
Indices: 2877443--2877515 Score: 114
Period size: 23 Copynumber: 3.1 Consensus size: 24
2877433 GACACGTATT
2877443 ACCACGACCACGACCACGACCAAG
1 ACCACGACCACGACCACGACCAAG
*
2877467 A-CACGACCACGACCACGA-CACG
1 ACCACGACCACGACCACGACCAAG
*
2877489 ACCACGACCACGACCACGACCACG
1 ACCACGACCACGACCACGACCAAG
2877513 ACC
1 ACC
2877516 TATCATCCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
22 4 0.09
23 34 0.74
24 8 0.17
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (24 bp):
ACCACGACCACGACCACGACCAAG
Found at i:2877473 original size:17 final size:17
Alignment explanation
Indices: 2877443--2877515 Score: 119
Period size: 17 Copynumber: 4.2 Consensus size: 17
2877433 GACACGTATT
2877443 ACCACGACCACGACCACG
1 ACCACGA-CACGACCACG
*
2877461 ACCAAGACACGACCACG
1 ACCACGACACGACCACG
2877478 ACCACGACACGACCACG
1 ACCACGACACGACCACG
2877495 ACCACGACCACGACCACG
1 ACCACGA-CACGACCACG
2877513 ACC
1 ACC
2877516 TATCATCCAT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
17 33 0.63
18 19 0.37
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (17 bp):
ACCACGACACGACCACG
Found at i:2878048 original size:6 final size:6
Alignment explanation
Indices: 2878027--2878175 Score: 217
Period size: 6 Copynumber: 26.3 Consensus size: 6
2878017 TCTCGTCTCG
*
2878027 GGTCG- GGTCG- GGTCGT GGTCGT CGTCGT GGTCGT GGTCG- GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2878072 GGTCGT GGTC-- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
*
2878118 GGTAGT GGTC-- GGTCGT GGTCGT GGTCGT GGTC-- GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2878162 GGTCGT GGTCGT GG
1 GGTCGT GGTCGT GG
2878176 AGTGGTAATA
Statistics
Matches: 132, Mismatches: 4, Indels: 15
0.87 0.03 0.10
Matches are distributed among these distances:
4 12 0.09
5 15 0.11
6 105 0.80
ACGTcount: A:0.01, C:0.17, G:0.51, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:2878053 original size:22 final size:23
Alignment explanation
Indices: 2878027--2878172 Score: 221
Period size: 22 Copynumber: 6.5 Consensus size: 23
2878017 TCTCGTCTCG
2878027 GGTCG-GGTCGGGTCGTGGTCGT
1 GGTCGTGGTCGGGTCGTGGTCGT
*
2878049 CGTCGTGGTCGTGGTCG-GGTCGT
1 GGTCGTGGTCG-GGTCGTGGTCGT
2878072 GGTCGTGGTC-GGTCGTGGTCGT
1 GGTCGTGGTCGGGTCGTGGTCGT
2878094 GGTCGTGGTCGTGGTCGTGGTCGT
1 GGTCGTGGTCG-GGTCGTGGTCGT
*
2878118 GGTAGTGGTC-GGTCGTGGTCGT
1 GGTCGTGGTCGGGTCGTGGTCGT
2878140 GGTCGTGGTC-GGTCGTGGTCGT
1 GGTCGTGGTCGGGTCGTGGTCGT
2878162 GGTCGTGGTCG
1 GGTCGTGGTCG
2878173 TGGAGTGGTA
Statistics
Matches: 114, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
21 5 0.04
22 63 0.55
23 20 0.18
24 26 0.23
ACGTcount: A:0.01, C:0.18, G:0.51, T:0.31
Consensus pattern (23 bp):
GGTCGTGGTCGGGTCGTGGTCGT
Found at i:2878330 original size:23 final size:23
Alignment explanation
Indices: 2878297--2878340 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2878287 TGATTTTCTA
*
2878297 AATCGCGTTGCGATTCTCTCAAT
1 AATCGCATTGCGATTCTCTCAAT
2878320 AATCGCATTGCGATTCTCTCA
1 AATCGCATTGCGATTCTCTCA
2878341 GTCGTGGTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (23 bp):
AATCGCATTGCGATTCTCTCAAT
Found at i:2878352 original size:6 final size:6
Alignment explanation
Indices: 2878341--2878443 Score: 199
Period size: 6 Copynumber: 17.3 Consensus size: 6
2878331 GATTCTCTCA
2878341 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
2878389 GTCGTG GTCGT- GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
2878436 GTCGTG GT
1 GTCGTG GT
2878444 AATACGTGTC
Statistics
Matches: 96, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.05
6 91 0.95
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:2878545 original size:19 final size:19
Alignment explanation
Indices: 2878521--2878559 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2878511 TTTTTAACTA
*
2878521 TCTTTTGACCGTTGAGATT
1 TCTTTTGAACGTTGAGATT
* *
2878540 TCTTTTTAACGTTGCGATT
1 TCTTTTGAACGTTGAGATT
2878559 T
1 T
2878560 TCTAAATCGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (19 bp):
TCTTTTGAACGTTGAGATT
Found at i:2878599 original size:53 final size:52
Alignment explanation
Indices: 2878532--2878636 Score: 192
Period size: 53 Copynumber: 2.0 Consensus size: 52
2878522 CTTTTGACCG
2878532 TTGAGATTTCTTTTTAACGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTC
1 TTGAGATTTCTTTTTAACGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTC
*
2878584 TTGAGATTTTCTTTTTAACGTTGTGATTTTCTAAATCGCGTTGCGATTCTCTC
1 TTGAGA-TTTCTTTTTAACGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTC
2878637 AATAAATCGC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 6 0.12
53 45 0.88
ACGTcount: A:0.17, C:0.18, G:0.17, T:0.48
Consensus pattern (52 bp):
TTGAGATTTCTTTTTAACGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTC
Found at i:2878627 original size:320 final size:322
Alignment explanation
Indices: 2878264--2878905 Score: 1197
Period size: 320 Copynumber: 2.0 Consensus size: 322
2878254 TCTTTGACCG
2878264 TTGAGATTTTCTTTTTAACGTTGTGATTTTCTAAATCGCGTTGCGATTCTCTCAAT-AATCGCAT
1 TTGAGATTTTCTTTTTAACGTTGTGATTTTCTAAATCGCGTTGCGATTCTCTCAATAAATCGCAT
*
2878328 TGCGATTCTCTCAGTCGTGGTCGTGGTCGTGGTCGTGGTCGTGGTCGTGGTCGTGGTCGTGGTCG
66 TGCGATTCTCTCAGTCGTGG-CGTGGTCGTGGGCGTGGTCGTGGTCGTGGTCGTGGTCGTGGT-G
2878393 TGGTCGT-GTCGTGGTCGTGGTCGTGGTCGTGGTCGTGGTCGT-GGTCGTGGTAATACGTGTCTT
129 TGGTCGTGGTCGTGGTCGTGGTCGT-GTCGTGGTCGTGGTCGTGGGTCGTGGTAATACGTGTCTT
2878456 CGACACGTCCGCGCGGATACTATC-TTTTAGAGAAAATTCTTAAGAAACAAAATTTTTTTTAACT
193 CGACACGTCCGCGCGGATACTATCTTTTTAGAGAAAATTCTTAAGAAACAAAA-TTTTTTTAACT
2878520 A-TCTTTTGACCGTTGAGA-TTTCTTTTTAACGTTGCGATTTTCTAAATCGCGTTGCGATTCTCT
257 ATTCTTTTGACCGTTGAGATTTTCTTTTTAACGTTGCGATTTTCTAAATCGCGTTGCGATTCTCT
2878583 C
322 C
2878584 TTGAGATTTTCTTTTTAACGTTGTGATTTTCTAAATCGCGTTGCGATTCTCTCAATAAATCGCAT
1 TTGAGATTTTCTTTTTAACGTTGTGATTTTCTAAATCGCGTTGCGATTCTCTCAATAAATCGCAT
2878649 TGCGATTCTCTCAGTCGTGGCGTGGTCGTGGGCGTGGTCGTGGTCGTGGTCGTGGTCGTGGTGTG
66 TGCGATTCTCTCAGTCGTGGCGTGGTCGTGGGCGTGGTCGTGGTCGTGGTCGTGGTCGTGGTGTG
2878714 GTCGTGGTCGTGGTCGTGGTCGTGTCGTGGTCGTGGTCGTGGGTCGTGGTAATACGTGTCTTCGA
131 GTCGTGGTCGTGGTCGTGGTCGTGTCGTGGTCGTGGTCGTGGGTCGTGGTAATACGTGTCTTCGA
2878779 CACGTCCGCGCGGATACTATCTTTTTAGAGAAAATTCTTAAGAAACAAAATTTTTTTAACTATTC
196 CACGTCCGCGCGGATACTATCTTTTTAGAGAAAATTCTTAAGAAACAAAATTTTTTTAACTATTC
2878844 TTTTGACCGTTGAGATTTTCTTTTTAACGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTC
261 TTTTGACCGTTGAGATTTTCTTTTTAACGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTC
2878906 AATAAATCGC
Statistics
Matches: 315, Mismatches: 1, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
319 25 0.08
320 171 0.54
321 73 0.23
322 46 0.15
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.39
Consensus pattern (322 bp):
TTGAGATTTTCTTTTTAACGTTGTGATTTTCTAAATCGCGTTGCGATTCTCTCAATAAATCGCAT
TGCGATTCTCTCAGTCGTGGCGTGGTCGTGGGCGTGGTCGTGGTCGTGGTCGTGGTCGTGGTGTG
GTCGTGGTCGTGGTCGTGGTCGTGTCGTGGTCGTGGTCGTGGGTCGTGGTAATACGTGTCTTCGA
CACGTCCGCGCGGATACTATCTTTTTAGAGAAAATTCTTAAGAAACAAAATTTTTTTAACTATTC
TTTTGACCGTTGAGATTTTCTTTTTAACGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTC
Found at i:2878651 original size:24 final size:24
Alignment explanation
Indices: 2878615--2878661 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2878605 TGTGATTTTC
*
2878615 TAAATCGCGTTGCGATTCTCTCAA
1 TAAATCGCATTGCGATTCTCTCAA
2878639 TAAATCGCATTGCGATTCTCTCA
1 TAAATCGCATTGCGATTCTCTCA
2878662 GTCGTGGCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (24 bp):
TAAATCGCATTGCGATTCTCTCAA
Found at i:2878684 original size:6 final size:6
Alignment explanation
Indices: 2878662--2878763 Score: 165
Period size: 6 Copynumber: 17.3 Consensus size: 6
2878652 GATTCTCTCA
*
2878662 GTCGTG G-CGTG GTCGTG GGCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
2878709 GT-GTG GTCGTG GTCGTG GTCGTG GTCGT- GTCGTG GTCGTG GTCGTGG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGT-G
2878756 GTCGTG GT
1 GTCGTG GT
2878764 AATACGTGTC
Statistics
Matches: 90, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
5 15 0.17
6 69 0.77
7 6 0.07
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GTCGTG
Found at i:2878714 original size:29 final size:29
Alignment explanation
Indices: 2878662--2878763 Score: 154
Period size: 29 Copynumber: 3.5 Consensus size: 29
2878652 GATTCTCTCA
*
2878662 GTCGTGG-CGTGGTCGTGGGCGTGGTCGTG
1 GTCGTGGTCGTGGTCGT-GGTGTGGTCGTG
2878691 GTCGTGGTCGTGGTCGTGGTGTGGTCGTG
1 GTCGTGGTCGTGGTCGTGGTGTGGTCGTG
2878720 GTCGTGGTCGTGGTCGT-GTCGTGGTCGTG
1 GTCGTGGTCGTGGTCGTGGT-GTGGTCGTG
2878749 GTCGTGGGTCGTGGT
1 GTCGT-GGTCGTGGT
2878764 AATACGTGTC
Statistics
Matches: 69, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
28 2 0.03
29 49 0.71
30 18 0.26
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (29 bp):
GTCGTGGTCGTGGTCGTGGTGTGGTCGTG
Found at i:2878866 original size:20 final size:20
Alignment explanation
Indices: 2878841--2878884 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2878831 TTTTTAACTA
*
2878841 TTCTTTTGACCGTTGAGATT
1 TTCTTTTGAACGTTGAGATT
* *
2878861 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGAGATT
2878881 TTCT
1 TTCT
2878885 AAATCGCGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.16, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGAGATT
Found at i:2878894 original size:20 final size:20
Alignment explanation
Indices: 2878871--2879218 Score: 171
Period size: 20 Copynumber: 16.6 Consensus size: 20
2878861 TTCTTTTTAA
2878871 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
2878891 CGTTGCGATTCTCTCAATAAATCG
1 CGTTGCGATT-T-TC--TAAATCG
* * * *
2878915 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
2878935 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* *
2878955 CATTGTGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
2878978 CGTTGCGACTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
*
2879001 CGTTGCGGCTTTCTTCTAAATCG
1 CGTTGC-G-ATT-TTCTAAATCG
* * *
2879024 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
2879044 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
2879064 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
2879084 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
2879107 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
2879128 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
2879146 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
*
2879168 CGTTGCGATTTTTTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
2879188 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
2879207 CGTTGCGATTTT
1 CGTTGCGATTTT
2879219 ATTGGTCATT
Statistics
Matches: 265, Mismatches: 46, Indels: 35
0.77 0.13 0.10
Matches are distributed among these distances:
18 2 0.01
19 17 0.06
20 137 0.52
21 15 0.06
22 11 0.04
23 66 0.25
24 17 0.06
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:2878978 original size:23 final size:22
Alignment explanation
Indices: 2878873--2879114 Score: 188
Period size: 20 Copynumber: 11.3 Consensus size: 22
2878863 CTTTTTAACG
*
2878873 TTGCGA-TT-TTCTAAATCGCG
1 TTGCGATTTCTTCTAAATCGCA
2878893 TTGCGA-TTCTCTCAATAAATCGCA
1 TTGCGATTTCT-TC--TAAATCGCA
* *
2878917 TTGCGA-TTC-TCTCAGTCGCA
1 TTGCGATTTCTTCTAAATCGCA
* *
2878937 TTGCGA-TTC-TCTCAGTCGCA
1 TTGCGATTTCTTCTAAATCGCA
* *
2878957 TTGTGATTTTCTTCTAAATCGCG
1 TTGCGA-TTTCTTCTAAATCGCA
*
2878980 TTGCGACTTTCTTCTAAATCGCG
1 TTGCGA-TTTCTTCTAAATCGCA
* *
2879003 TTGCGGCTTTCTTCTAAATCGCG
1 TTGC-GATTTCTTCTAAATCGCA
* *
2879026 TTGCGA-CTC-TCTCAATCGCA
1 TTGCGATTTCTTCTAAATCGCA
*
2879046 TTGCGA-TTC-TATAAATCGCA
1 TTGCGATTTCTTCTAAATCGCA
2879066 TTGCGA-TTCTATC--AATCGCA
1 TTGCGATTTCT-TCTAAATCGCA
*
2879086 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA-TTTCTTCTAAATCGCA
2879109 TTGCGA
1 TTGCGA
2879115 ACTTGGAAGC
Statistics
Matches: 189, Mismatches: 19, Indels: 25
0.81 0.08 0.11
Matches are distributed among these distances:
20 88 0.47
21 5 0.03
22 13 0.07
23 65 0.34
24 18 0.10
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (22 bp):
TTGCGATTTCTTCTAAATCGCA
Found at i:2879206 original size:19 final size:19
Alignment explanation
Indices: 2879168--2879218 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
2879158 TTCTTTTTAA
*
2879168 CGTTGCGATTTTTTAAATCG
1 CGTTGCGA-TTTTGAAATCG
*
2879188 CGTTGCGATTTTGATATCG
1 CGTTGCGATTTTGAAATCG
2879207 CGTTGCGATTTT
1 CGTTGCGATTTT
2879219 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTGAAATCG
Found at i:2882673 original size:27 final size:27
Alignment explanation
Indices: 2882643--2882700 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
2882633 ATATTTTGTC
2882643 TGTATCAATGTCTGGATTGTAGTTTAA
1 TGTATCAATGTCTGGATTGTAGTTTAA
2882670 TGTATCAATGTCTGGATTGTAGTTTAA
1 TGTATCAATGTCTGGATTGTAGTTTAA
2882697 TGTA
1 TGTA
2882701 GTTTGTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.45
Consensus pattern (27 bp):
TGTATCAATGTCTGGATTGTAGTTTAA
Found at i:2887720 original size:21 final size:21
Alignment explanation
Indices: 2887696--2887770 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
2887686 TTCCCATATA
2887696 AGTATCAATACTTGAAATGAG
1 AGTATCAATACTTGAAATGAG
* * *
2887717 AGTA-CTGATACATCACATAT-A-
1 AGTATC-AATACTTGA-A-ATGAG
2887738 AGTATCAATACTTGAAATGAG
1 AGTATCAATACTTGAAATGAG
*
2887759 AGTATCGATACT
1 AGTATCAATACT
2887771 CGCTTTATGT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
19 2 0.05
20 3 0.07
21 31 0.76
22 3 0.07
23 2 0.05
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.29
Consensus pattern (21 bp):
AGTATCAATACTTGAAATGAG
Found at i:2887722 original size:42 final size:42
Alignment explanation
Indices: 2887675--2887770 Score: 158
Period size: 42 Copynumber: 2.3 Consensus size: 42
2887665 AATGTGAATC
*
2887675 AGTACTGATACTTCCCATATAAGTATCAATACTTGAAATGAG
1 AGTACTGATACTTCACATATAAGTATCAATACTTGAAATGAG
*
2887717 AGTACTGATACATCACATATAAGTATCAATACTTGAAATGAG
1 AGTACTGATACTTCACATATAAGTATCAATACTTGAAATGAG
2887759 AGTA-TCGATACT
1 AGTACT-GATACT
2887771 CGCTTTATGT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
41 1 0.02
42 49 0.98
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.30
Consensus pattern (42 bp):
AGTACTGATACTTCACATATAAGTATCAATACTTGAAATGAG
Found at i:2887856 original size:21 final size:21
Alignment explanation
Indices: 2887830--2887908 Score: 113
Period size: 21 Copynumber: 3.7 Consensus size: 21
2887820 AATATTCCTA
*
2887830 TGAGTACCGACACTCCCTTGG
1 TGAGTACCGATACTCCCTTGG
2887851 TGAGTACCGATACTCCCTTGG
1 TGAGTACCGATACTCCCTTGG
* **
2887872 TGAATACCGATACTCTCCTTCA
1 TGAGTACCGATACTC-CCTTGG
2887894 TGAGTACCGATACTC
1 TGAGTACCGATACTC
2887909 TCTCTCCCCA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
21 34 0.65
22 18 0.35
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (21 bp):
TGAGTACCGATACTCCCTTGG
Found at i:2892603 original size:19 final size:19
Alignment explanation
Indices: 2892579--2892621 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
2892569 TTTTTAATTT
2892579 GATTTCTAAACTTATATTC
1 GATTTCTAAACTTATATTC
2892598 GATTTCTAAACTTATATTC
1 GATTTCTAAACTTATATTC
2892617 GATTT
1 GATTT
2892622 AAAAATTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.49
Consensus pattern (19 bp):
GATTTCTAAACTTATATTC
Found at i:2894415 original size:15 final size:16
Alignment explanation
Indices: 2894397--2894427 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2894387 GTGAAACTTC
2894397 AAAATAAGA-AAGAAG
1 AAAATAAGAGAAGAAG
2894412 AAAATAAGAGAAGAAG
1 AAAATAAGAGAAGAAG
2894428 GTGGAGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (16 bp):
AAAATAAGAGAAGAAG
Found at i:2894924 original size:18 final size:20
Alignment explanation
Indices: 2894887--2894926 Score: 57
Period size: 18 Copynumber: 2.0 Consensus size: 20
2894877 TGAGATCATG
2894887 GTTTCAAAGAATAAGAAAAAT
1 GTTTCAAAGAAT-AGAAAAAT
2894908 GTTTCAAA-AAT-GAAAAAT
1 GTTTCAAAGAATAGAAAAAT
2894926 G
1 G
2894927 AAAATGATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
20 3 0.16
21 8 0.42
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (20 bp):
GTTTCAAAGAATAGAAAAAT
Found at i:2899559 original size:23 final size:23
Alignment explanation
Indices: 2899533--2899599 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 23
2899523 ATATTTTGTT
2899533 TACATTTTTTATATACTTATATA
1 TACATTTTTTATATACTTATATA
* *
2899556 TACAAAATTTTTAT-TTC-TATATA
1 TAC--ATTTTTTATATACTTATATA
2899579 TACATTTATATT-TATACTTAT
1 TACATTT-T-TTATATACTTAT
2899600 TTTTTCAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
21 3 0.09
22 2 0.06
23 16 0.47
24 5 0.15
25 8 0.24
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (23 bp):
TACATTTTTTATATACTTATATA
Found at i:2907524 original size:105 final size:105
Alignment explanation
Indices: 2907342--2907967 Score: 1094
Period size: 105 Copynumber: 6.0 Consensus size: 105
2907332 CTCGAGAGTA
2907342 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
2907407 GACCGCTGGTTGTCAACAA-ACATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAACA-ACTTCCCAATTTCAGAGCC
2907447 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
2907512 GACCGCTGGTTGTCAACAA-ACATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAACA-ACTTCCCAATTTCAGAGCC
*
2907552 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAAGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
2907617 GACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCC
* *
2907657 AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
2907722 GACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCC
*
2907762 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
2907827 GACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAACC
66 GACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCC
* * *
2907867 AATTTCAACTTCACAACGAAGGATATTGGACTCAAGATAACGCAAGTTTAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
2907932 GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
66 GACCGCTGGTTGTCAA-CAACAACTTCCCAATTTCA
2907968 TAGCGAAGGA
Statistics
Matches: 506, Mismatches: 13, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
105 487 0.96
106 19 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCC
Found at i:2908032 original size:88 final size:87
Alignment explanation
Indices: 2907883--2908054 Score: 272
Period size: 88 Copynumber: 2.0 Consensus size: 87
2907873 AACTTCACAA
* * *
2907883 CGAAGGATATTGGACTCAAGATAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAA
*
2907948 TAAACAACTTCCCAATTTCATAG
66 CAAAC-ACTTCCCAATTTCATAG
*
2907971 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAA
1 CGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAA
* *
2908036 CAAACATTTCTCAATTTCA
66 CAAACACTTCCCAATTTCA
2908055 GAGCCAATTT
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
87 12 0.16
88 65 0.84
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (87 bp):
CGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAA
CAAACACTTCCCAATTTCATAG
Found at i:2908153 original size:105 final size:105
Alignment explanation
Indices: 2907971--2908580 Score: 1053
Period size: 105 Copynumber: 5.8 Consensus size: 105
2907961 AATTTCATAG
*
2907971 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* *
2908036 CAA-ACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAA
66 CAACA-ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAA
2908076 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* *
2908141 CAA-ACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAA
66 CAACA-ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAA
*
2908181 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
2908246 CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
66 CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAA
*
2908286 CGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
2908351 CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
66 CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAA
2908391 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
2908456 CAACAACTTCCCAATTTCAGAACCAATTTCAACTTCACAA
66 CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAA
* * *
2908496 CGAAGGATATTGGACTCAAGATAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
2908561 TAAACAACTTCCCAATTTCA
66 -CAACAACTTCCCAATTTCA
2908581 TAGCGAAGGA
Statistics
Matches: 489, Mismatches: 14, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
105 470 0.96
106 19 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAA
Found at i:2908523 original size:613 final size:613
Alignment explanation
Indices: 2907358--2909024 Score: 3041
Period size: 613 Copynumber: 2.7 Consensus size: 613
2907348 AACTTCACAA
*
2907358 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAA
2907423 CAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
66 CAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
2907488 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCA
131 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCA
2907553 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAAGAAGGG
196 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAAGAAGGG
2907618 ACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
261 ACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
2907683 TGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTC
326 TGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTC
2907748 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
391 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
2907813 CTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAACCAATTTCAACTT
456 CTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAACCAATTTCAACTT
2907878 CACAACGAAGGATATTGGACTCAAGATAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTT
521 CACAACGAAGGATATTGGACTCAAGATAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTT
2907943 GTCAATAAACAACTTCCCAATTTCATAG
586 GTCAATAAACAACTTCCCAATTTCATAG
2907971 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAA
2908036 CAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
66 CAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
2908101 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCA
131 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCA
2908166 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAAGAAGGG
196 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAAGAAGGG
2908231 ACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
261 ACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
2908296 TGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTC
326 TGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTC
2908361 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
391 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
2908426 CTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAACCAATTTCAACTT
456 CTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAACCAATTTCAACTT
2908491 CACAACGAAGGATATTGGACTCAAGATAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTT
521 CACAACGAAGGATATTGGACTCAAGATAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTT
2908556 GTCAATAAACAACTTCCCAATTTCATAG
586 GTCAATAAACAACTTCCCAATTTCATAG
*
2908584 CGAAGGATATTGGACTCCATACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAA
* * * ** *
2908649 TAAACAACTTCCCAATTTTGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAA
66 CAAAC-ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA
* *
2908714 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAGAGC
130 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGC
* * *
2908779 CAATTTCAACTTCACGACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGACGAAG
194 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAAGAAG
* *
2908844 GGACCCCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGA
259 GGACCGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGA
* * * * *
2908909 TATTGGACTCGAGACAACACAAGTTCAACTTCACAACGTAA-GGACGGCTGGTTGTCAATAAACA
323 TATTGGACTCAAGACAACGCAAGTTCAACTTCACGACG-AAGGGACCGCTGGTTGTCAA-CAACA
* ** * *
2908973 ATTTCCCGGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
386 ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
2909025 GGAACAATAC
Statistics
Matches: 1023, Mismatches: 25, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
613 680 0.66
614 100 0.10
615 95 0.09
616 97 0.09
617 51 0.05
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (613 bp):
CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAA
CAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCA
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAAGAAGGG
ACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
TGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTC
CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
CTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAACCAATTTCAACTT
CACAACGAAGGATATTGGACTCAAGATAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTT
GTCAATAAACAACTTCCCAATTTCATAG
Found at i:2908645 original size:88 final size:88
Alignment explanation
Indices: 2908496--2908666 Score: 297
Period size: 88 Copynumber: 1.9 Consensus size: 88
2908486 AACTTCACAA
* * *
2908496 CGAAGGATATTGGACTCAAGATAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAA
2908561 TAAACAACTTCCCAATTTCATAG
66 TAAACAACTTCCCAATTTCATAG
* *
2908584 CGAAGGATATTGGACTCCATACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAA
1 CGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAA
2908649 TAAACAACTTCCCAATTT
66 TAAACAACTTCCCAATTT
2908667 TGGAGCCAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 78 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (88 bp):
CGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAA
TAAACAACTTCCCAATTTCATAG
Found at i:2909025 original size:106 final size:106
Alignment explanation
Indices: 2908577--2909024 Score: 659
Period size: 106 Copynumber: 4.2 Consensus size: 106
2908567 ACTTCCCAAT
* * *
2908577 TTCATAGCGAAGGATATTGGACTCCATACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGG
1 TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* **
2908642 TTGTCAATAAACAACTTCCCAATTTTGGAGCCAATTTCAAC
66 TTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAAC
2908683 TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
1 TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* *
2908748 TTGTCAACAAACAACTTCTCAATTTTAGAGCCAATTTCAAC
66 TTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAAC
* *
2908789 TTCAC-GACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGACGAAGGGACCCCTG
1 TTCACAG-CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
*
2908853 GTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAAC
65 GTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAAC
* * * *
2908895 TTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGTAA-GGACGGCTG
1 TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG-AAGGGACCGCTG
* * ** *
2908959 GTTGTCAATAAACAATTTCCCGGTTCCAGAGCCAATTTCAAC
65 GTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAAC
*
2909001 TTCAC-GACGGAGGATATTGGACTC
1 TTCACAG-CGAAGGATATTGGACTC
2909025 GGAACAATAC
Statistics
Matches: 316, Mismatches: 22, Indels: 8
0.91 0.06 0.02
Matches are distributed among these distances:
105 2 0.01
106 311 0.98
107 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
TTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAAC
Found at i:2914676 original size:15 final size:15
Alignment explanation
Indices: 2914656--2914688 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2914646 TATATGTTTT
2914656 GATATGTTTTAACTA
1 GATATGTTTTAACTA
2914671 GATATGTTTTAACTA
1 GATATGTTTTAACTA
2914686 GAT
1 GAT
2914689 TAAGTATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.45
Consensus pattern (15 bp):
GATATGTTTTAACTA
Found at i:2914874 original size:21 final size:21
Alignment explanation
Indices: 2914810--2914866 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
2914800 CCCTTGACTG
* *
2914810 AAAGGATTGATTCCTTCTAAA
1 AAAGGATCGATCCCTTCTAAA
2914831 AAAGGATCGATCCCTTCTAAA
1 AAAGGATCGATCCCTTCTAAA
2914852 AAAGGA-CGATCCCTT
1 AAAGGATCGATCCCTT
2914867 ACCTAAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (21 bp):
AAAGGATCGATCCCTTCTAAA
Found at i:2914875 original size:20 final size:20
Alignment explanation
Indices: 2914787--2914866 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 20
2914777 CATTTTCCAG
*
2914787 AAAAAAGATCGATCCCTTGACT
1 AAAAAGGATCGATCCCTT--CT
* * *
2914809 -GAAAGGATTGATTCCTTCT
1 AAAAAGGATCGATCCCTTCT
2914828 AAAAAAGGATCGATCCCTTCT
1 -AAAAAGGATCGATCCCTTCT
2914849 AAAAAAGGA-CGATCCCTT
1 -AAAAAGGATCGATCCCTT
2914867 ACCTAAAAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
19 2 0.04
20 9 0.18
21 38 0.78
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (20 bp):
AAAAAGGATCGATCCCTTCT
Found at i:2920081 original size:32 final size:32
Alignment explanation
Indices: 2920039--2920139 Score: 175
Period size: 32 Copynumber: 3.2 Consensus size: 32
2920029 TAAGGTGACT
2920039 CTTGGGTAGGCTCTTAGGCCCCAAGATGCTCC
1 CTTGGGTAGGCTCTTAGGCCCCAAGATGCTCC
*
2920071 CTTGGTTAGGCTCTTAGGCCCCAAGATGCTCC
1 CTTGGGTAGGCTCTTAGGCCCCAAGATGCTCC
* *
2920103 CTTGGGTAGGCTCTTAGTCCCCAAGATACTCC
1 CTTGGGTAGGCTCTTAGGCCCCAAGATGCTCC
2920135 CTTGG
1 CTTGG
2920140 TTGGGTAGAC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.16, C:0.31, G:0.26, T:0.28
Consensus pattern (32 bp):
CTTGGGTAGGCTCTTAGGCCCCAAGATGCTCC
Found at i:2920176 original size:31 final size:31
Alignment explanation
Indices: 2920140--2920201 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2920130 ACTCCCTTGG
* *
2920140 TTGGGTAGACTTTAAGGCTCCAAGGTATTCC
1 TTGGGTAGACTCTAAGGCCCCAAGGTATTCC
* *
2920171 TTGGGTAGGCTCTAAGTCCCCAAGGTATTCC
1 TTGGGTAGACTCTAAGGCCCCAAGGTATTCC
2920202 CTTAAGTTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.31
Consensus pattern (31 bp):
TTGGGTAGACTCTAAGGCCCCAAGGTATTCC
Found at i:2921804 original size:23 final size:23
Alignment explanation
Indices: 2921772--2921815 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
2921762 TGTTAAAGAA
2921772 GTTTTAAGATTAT-TTTGATTTG
1 GTTTTAAGATTATATTTGATTTG
2921794 GTTTTCAAGATTATATTTGATT
1 GTTTT-AAGATTATATTTGATT
2921816 CAATCGTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 8 0.40
24 7 0.35
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.57
Consensus pattern (23 bp):
GTTTTAAGATTATATTTGATTTG
Found at i:2928529 original size:2 final size:2
Alignment explanation
Indices: 2928524--2928585 Score: 67
Period size: 2 Copynumber: 32.0 Consensus size: 2
2928514 AAAAAATTGA
*
2928524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2928564 -T AT AT AT AA ACT AT AT TT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT
2928586 TGTAAACTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
1 3 0.06
2 47 0.92
3 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2928593 original size:18 final size:18
Alignment explanation
Indices: 2928563--2928718 Score: 77
Period size: 18 Copynumber: 8.3 Consensus size: 18
2928553 TAATATAAAA
2928563 TTATA-TATAAACTATAT
1 TTATATTATAAACTATAT
*
2928580 TTATATTGTAAACTATA-
1 TTATATTATAAACTATAT
*
2928597 TAATTATTATAAACTATAT
1 TTA-TATTATAAACTATAT
* * * *
2928616 ATATAAATTATATTTA-TGTGAA
1 -T-TATATTATA--AACTAT-AT
*
2928638 CTATATATATAAACTATGTAT
1 TTATAT-TATAAACTA--TAT
* *
2928659 ATAAAATTATAAACTATAT
1 -TTATATTATAAACTATAT
2928678 TTATATTATAAACTATA-
1 TTATATTATAAACTATAT
* *
2928695 TAATTATTATAAGCTATAT
1 TTA-TATTATAAACTATAT
*
2928714 ATATA
1 TTATA
2928719 AATTATGTTT
Statistics
Matches: 102, Mismatches: 22, Indels: 29
0.67 0.14 0.19
Matches are distributed among these distances:
17 9 0.09
18 53 0.52
19 5 0.05
20 12 0.12
21 17 0.17
22 6 0.06
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (18 bp):
TTATATTATAAACTATAT
Found at i:2928620 original size:80 final size:79
Alignment explanation
Indices: 2928533--2928696 Score: 183
Period size: 80 Copynumber: 2.1 Consensus size: 79
2928523 AATATATATA
* * * *
2928533 TATATATATATATATATATATAATATAAAAT-TATATATAAACTA-TAT-TTATATTGTAAACTA
1 TATATATATAAAT-TATAT-TAATATAAAATATATATATAAACTAGTATATAAAATTATAAACTA
2928595 TATA-ATTATTATAAAC
64 TATATA-TATTATAAAC
* * * *
2928611 TATATATATAAATTATATTTATGTGAACTATATATATAAACTATGTATATAAAATTATAAACTAT
1 TATATATATAAATTATATTAATATAAAATATATATATAAACTA-GTATATAAAATTATAAACTAT
*
2928676 ATTTATATTATAAAC
65 ATATATATTATAAAC
2928691 TATATA
1 TATATA
2928697 ATTATTATAA
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
76 7 0.10
77 18 0.25
78 12 0.17
79 3 0.04
80 31 0.43
81 1 0.01
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (79 bp):
TATATATATAAATTATATTAATATAAAATATATATATAAACTAGTATATAAAATTATAAACTATA
TATATATTATAAAC
Found at i:2928622 original size:13 final size:13
Alignment explanation
Indices: 2928525--2928781 Score: 127
Period size: 13 Copynumber: 19.3 Consensus size: 13
2928515 AAAAATTGAA
*
2928525 TATATATATATA-
1 TATATATATAAAC
*
2928537 TATATATATATA-
1 TATATATATAAAC
*
2928549 TATATAATATAAAA
1 TATAT-ATATAAAC
2928563 T-TATATATAAAC
1 TATATATATAAAC
* ***
2928575 TATATTTATATTG
1 TATATATATAAAC
*
2928588 TAAACTATAT-AA-
1 TATA-TATATAAAC
2928600 T-TAT-TATAAAC
1 TATATATATAAAC
*
2928611 TATATATATAAAT
1 TATATATATAAAC
* *
2928624 TATATTTATGTGAAC
1 TATA--TATATAAAC
2928639 TATATATATAAAC
1 TATATATATAAAC
* *
2928652 TATGTATATAAAA
1 TATATATATAAAC
* *
2928665 T-TATAAACTATA-
1 TATATATA-TAAAC
*
2928677 TTTATATTATAAAC
1 TATATA-TATAAAC
2928691 TATATAATTATTATAAGC
1 TATAT-A-TA-TA-AA-C
*
2928709 TATATATATAAAT
1 TATATATATAAAC
* * *
2928722 TATGTTTATGTGAAC
1 TA--TATATATAAAC
2928737 TATATATATAAAC
1 TATATATATAAAC
*
2928750 TATGTATATAAAC
1 TATATATATAAAC
2928763 TATATATGTATAAAC
1 TATATA--TATAAAC
2928778 TATA
1 TATA
2928782 AAAGTATATA
Statistics
Matches: 188, Mismatches: 35, Indels: 41
0.71 0.13 0.16
Matches are distributed among these distances:
9 3 0.02
10 3 0.02
11 2 0.01
12 34 0.18
13 85 0.45
14 12 0.06
15 36 0.19
16 4 0.02
17 3 0.02
18 6 0.03
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:2928682 original size:21 final size:18
Alignment explanation
Indices: 2928639--2928718 Score: 83
Period size: 18 Copynumber: 4.3 Consensus size: 18
2928629 TTATGTGAAC
2928639 TATATA-TATAAACTATGTA
1 TATATATTATAAACTA--TA
*
2928658 TATAAAATTATAAACTATA
1 TAT-ATATTATAAACTATA
*
2928677 TTTATATTATAAACTATA
1 TATATATTATAAACTATA
*
2928695 TA-ATTATTATAAGCTATA
1 TATA-TATTATAAACTATA
2928713 TATATA
1 TATATA
2928719 AATTATGTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
17 1 0.02
18 32 0.62
19 8 0.15
20 2 0.04
21 9 0.17
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (18 bp):
TATATATTATAAACTATA
Found at i:2928683 original size:98 final size:98
Alignment explanation
Indices: 2928568--2928761 Score: 361
Period size: 98 Copynumber: 2.0 Consensus size: 98
2928558 TAAAATTATA
*
2928568 TATAAACTATATTTATATTGTAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
1 TATAAACTATATTTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
2928633 GTGAACTATATATATAAACTATGTATATAAAAT
66 GTGAACTATATATATAAACTATGTATATAAAAT
* *
2928666 TATAAACTATATTTATATTATAAACTATATAATTATTATAAGCTATATATATAAATTATGTTTAT
1 TATAAACTATATTTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
2928731 GTGAACTATATATATAAACTATGTATATAAA
66 GTGAACTATATATATAAACTATGTATATAAA
2928762 CTATATATGT
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (98 bp):
TATAAACTATATTTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
GTGAACTATATATATAAACTATGTATATAAAAT
Found at i:2928770 original size:17 final size:17
Alignment explanation
Indices: 2928750--2928798 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
2928740 ATATATAAAC
2928750 TATGTATATAAACTATA
1 TATGTATATAAACTATA
2928767 TATG--TATAAACTATA
1 TATGTATATAAACTATA
* *
2928782 AAAGTATATAAACTATA
1 TATGTATATAAACTATA
2928799 AAAAGTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (17 bp):
TATGTATATAAACTATA
Found at i:2928804 original size:18 final size:17
Alignment explanation
Indices: 2928753--2928809 Score: 73
Period size: 15 Copynumber: 3.4 Consensus size: 17
2928743 TATAAACTAT
*
2928753 GTATATAAACTAT-ATA
1 GTATATAAACTATAAAA
*
2928769 -TGTATAAACTATAAAA
1 GTATATAAACTATAAAA
2928785 GTATATAAACTATAAAAA
1 GTATATAAACTAT-AAAA
2928803 GTATATA
1 GTATATA
2928810 GTTTATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 11 0.31
16 2 0.06
17 11 0.31
18 11 0.31
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.33
Consensus pattern (17 bp):
GTATATAAACTATAAAA
Found at i:2928819 original size:18 final size:18
Alignment explanation
Indices: 2928771--2928809 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2928761 ACTATATATG
2928771 TATAAACTAT-AAAAGTA
1 TATAAACTATAAAAAGTA
2928788 TATAAACTATAAAAAGTA
1 TATAAACTATAAAAAGTA
2928806 TATA
1 TATA
2928810 GTTTATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (18 bp):
TATAAACTATAAAAAGTA
Found at i:2928847 original size:2 final size:2
Alignment explanation
Indices: 2928834--2928916 Score: 50
Period size: 2 Copynumber: 42.0 Consensus size: 2
2928824 ATTTATATTA
* *
2928834 AT AT AGT AT AT AT AT AT AT AT AT AT AA ACT AT AT A- AA AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * *
2928877 AGT TT AT AT GT -T AT A- AT TT AT AT -T A- AT AT AGT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
2928917 GTATGCATTA
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
1 5 0.08
2 53 0.83
3 6 0.09
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2928866 original size:68 final size:68
Alignment explanation
Indices: 2928786--2928916 Score: 210
Period size: 68 Copynumber: 1.9 Consensus size: 68
2928776 ACTATAAAAG
*
2928786 TATATAAACTATA-AAAAGTATATAGTTTATAAAATATTATTTATATTAATATAGTATATATATA
1 TATATAAACTATATAAAA-TATATAGTTTATAAAATATAATTTATATTAATATAGTATATATATA
2928850 TATA
65 TATA
***
2928854 TATATAAACTATATAAAATATATAGTTTATATGTTATAATTTATATTAATATAGTATATATAT
1 TATATAAACTATATAAAATATATAGTTTATAAAATATAATTTATATTAATATAGTATATATAT
2928917 GTATGCATTA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 54 0.93
69 4 0.07
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.46
Consensus pattern (68 bp):
TATATAAACTATATAAAATATATAGTTTATAAAATATAATTTATATTAATATAGTATATATATAT
ATA
Found at i:2929075 original size:20 final size:20
Alignment explanation
Indices: 2929052--2929090 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2929042 TATATAGAGG
* *
2929052 TATATATAGTTTATATATAC
1 TATACATAGTCTATATATAC
*
2929072 TATACATGGTCTATATATA
1 TATACATAGTCTATATATA
2929091 TATTAGGGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (20 bp):
TATACATAGTCTATATATAC
Found at i:2929087 original size:31 final size:31
Alignment explanation
Indices: 2929023--2929090 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
2929013 TAATTTACTT
* *
2929023 TATATAGTTTATATATATATATATAGAGGTA
1 TATATAGTTTATATATATATACATAGAGCTA
2929054 TATATAGTTTATATATACTATACAT-G-GTCTA
1 TATATAGTTTATATATA-TATACATAGAG-CTA
2929085 TATATA
1 TATATA
2929091 TATTAGGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 1 0.03
31 26 0.79
32 6 0.18
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (31 bp):
TATATAGTTTATATATATATACATAGAGCTA
Found at i:2929112 original size:14 final size:14
Alignment explanation
Indices: 2929093--2929144 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
2929083 TATATATATA
2929093 TTAGGGTTTATGAT
1 TTAGGGTTTATGAT
* * *
2929107 TTAGGGTTGAAGGT
1 TTAGGGTTTATGAT
*
2929121 TTAGGGTTTTTGAT
1 TTAGGGTTTATGAT
*
2929135 TTAAGGTTTA
1 TTAGGGTTTA
2929145 AGGTTTATAT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (14 bp):
TTAGGGTTTATGAT
Found at i:2929134 original size:28 final size:28
Alignment explanation
Indices: 2929093--2929151 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
2929083 TATATATATA
*
2929093 TTAGGGTTTATGATTTAGGGTTGAAGGT
1 TTAGGGTTTATGATTTAAGGTTGAAGGT
* *
2929121 TTAGGGTTTTTGATTTAAGGTTTAAGGT
1 TTAGGGTTTATGATTTAAGGTTGAAGGT
2929149 TTA
1 TTA
2929152 TATAAACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (28 bp):
TTAGGGTTTATGATTTAAGGTTGAAGGT
Found at i:2929151 original size:14 final size:14
Alignment explanation
Indices: 2929093--2929151 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 14
2929083 TATATATATA
* *
2929093 TTAGGGTTTATGAT
1 TTAGGGTTTAAGGT
*
2929107 TTAGGGTTGAAGGT
1 TTAGGGTTTAAGGT
** *
2929121 TTAGGGTTTTTGAT
1 TTAGGGTTTAAGGT
*
2929135 TTAAGGTTTAAGGT
1 TTAGGGTTTAAGGT
2929149 TTA
1 TTA
2929152 TATAAACTAT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (14 bp):
TTAGGGTTTAAGGT
Found at i:2929422 original size:20 final size:20
Alignment explanation
Indices: 2929378--2929419 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
2929368 AAATTTTTCT
2929378 ATTT-CCTCTAAATTTCCCA
1 ATTTCCCTCTAAATTTCCCA
2929397 ATTTCCCTCTAAA-TTCCCA
1 ATTTCCCTCTAAATTTCCCA
2929416 ATTT
1 ATTT
2929420 TCCTATATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTTCCCTCTAAATTTCCCA
Found at i:2929437 original size:46 final size:47
Alignment explanation
Indices: 2929363--2929457 Score: 140
Period size: 46 Copynumber: 2.0 Consensus size: 47
2929353 TGGCCCCAAC
* *
2929363 TTCCCAAATTTTTCTATTTCCTCTAAATTTCCCAATTTCCCTCTAAA
1 TTCCCAAATTTTCCTATTTCCTCAAAATTTCCCAATTTCCCTCTAAA
*
2929410 TTCCC-AATTTTCCTATATT-CTCAAAATTTCCTAATTTCCCTCTAAA
1 TTCCCAAATTTTCCTAT-TTCCTCAAAATTTCCCAATTTCCCTCTAAA
2929456 TT
1 TT
2929458 GTCAAATAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 37 0.84
47 7 0.16
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.45
Consensus pattern (47 bp):
TTCCCAAATTTTCCTATTTCCTCAAAATTTCCCAATTTCCCTCTAAA
Found at i:2929539 original size:2 final size:2
Alignment explanation
Indices: 2929532--2929561 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2929522 ACTTTGAATA
2929532 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
2929562 TAAACATAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2930010 original size:2 final size:2
Alignment explanation
Indices: 2930003--2930057 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
2929993 TATGTTTAAT
* *
2930003 TA TA TA TA TA TA TA TA TT TA TG 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
2930045 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
2930058 TATTCAAAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2930189 original size:18 final size:20
Alignment explanation
Indices: 2930166--2930205 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
2930156 TTGAGAATAA
2930166 AGGGAAATT-GG-AATTTAG
1 AGGGAAATTGGGAAATTTAG
2930184 AGGGAAATTGGGAAATTTAG
1 AGGGAAATTGGGAAATTTAG
2930204 AG
1 AG
2930206 AGAATAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.35, T:0.25
Consensus pattern (20 bp):
AGGGAAATTGGGAAATTTAG
Found at i:2930704 original size:14 final size:14
Alignment explanation
Indices: 2930685--2930731 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
2930675 TTTTTTCTTT
2930685 TATATAAATTAAAC
1 TATATAAATTAAAC
2930699 TATAT-AATT----
1 TATATAAATTAAAC
2930708 TATATAAATTAAAC
1 TATATAAATTAAAC
*
2930722 TATATTAATT
1 TATATAAATT
2930732 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:2930711 original size:23 final size:24
Alignment explanation
Indices: 2930683--2930732 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
2930673 ATTTTTTTCT
2930683 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
2930706 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
2930730 TTT
1 TTT
2930733 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:2931014 original size:16 final size:16
Alignment explanation
Indices: 2930993--2931023 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2930983 TCATTTACAT
2930993 GTCAGGTTGAAAACAA
1 GTCAGGTTGAAAACAA
2931009 GTCAGGTTGAAAACA
1 GTCAGGTTGAAAACA
2931024 GGTCGGGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.26, T:0.19
Consensus pattern (16 bp):
GTCAGGTTGAAAACAA
Found at i:2931720 original size:24 final size:24
Alignment explanation
Indices: 2931693--2931742 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
2931683 ATAACTGCAC
* *
2931693 AACTACTCTAGCAAACTATCAACT
1 AACTAATCTAACAAACTATCAACT
* *
2931717 AACTAATGTAACAAACTATCCACT
1 AACTAATCTAACAAACTATCAACT
2931741 AA
1 AA
2931743 TTCACAGCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.26, G:0.04, T:0.24
Consensus pattern (24 bp):
AACTAATCTAACAAACTATCAACT
Found at i:2933227 original size:2 final size:2
Alignment explanation
Indices: 2933215--2933250 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
2933205 CTTAAAAACT
2933215 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2933251 TCAAGTTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2939075 original size:14 final size:14
Alignment explanation
Indices: 2939050--2939086 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2939040 GGTATTTTTA
2939050 AAAAAGTAAAATTAT
1 AAAAA-TAAAATTAT
*
2939065 CAAAATAAAATTAT
1 AAAAATAAAATTAT
2939079 AAAAATAA
1 AAAAATAA
2939087 TTGAATGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (14 bp):
AAAAATAAAATTAT
Found at i:2939298 original size:30 final size:29
Alignment explanation
Indices: 2939250--2939309 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
2939240 ATTTGATCCT
*
2939250 ATTACATAATACAGGCATGTTTCTGCTTAA
1 ATTACATAATACAAGCATGTTTCTG-TTAA
* * *
2939280 ATTATATAATAGAAGCATGTTTTTGTTAA
1 ATTACATAATACAAGCATGTTTCTGTTAA
2939309 A
1 A
2939310 GTTGTTTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (29 bp):
ATTACATAATACAAGCATGTTTCTGTTAA
Found at i:2953688 original size:24 final size:24
Alignment explanation
Indices: 2953661--2953719 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
2953651 TTCAATTATC
2953661 CGTTCGTTTATGATCATTTATGTT
1 CGTTCGTTTATGATCATTTATGTT
* * *
2953685 CGTTCGTATATGTTTATTTATGTT
1 CGTTCGTTTATGATCATTTATGTT
*
2953709 CGTTCATTTAT
1 CGTTCGTTTAT
2953720 ATTTAGCCTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.17, C:0.12, G:0.15, T:0.56
Consensus pattern (24 bp):
CGTTCGTTTATGATCATTTATGTT
Found at i:2953724 original size:24 final size:24
Alignment explanation
Indices: 2953676--2953724 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2953666 GTTTATGATC
* *
2953676 ATTTATGTTCGTTCGTATATGTTT
1 ATTTATGTTCGTTCATATATATTT
*
2953700 ATTTATGTTCGTTCATTTATATTT
1 ATTTATGTTCGTTCATATATATTT
2953724 A
1 A
2953725 GCCTAATCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.08, G:0.12, T:0.59
Consensus pattern (24 bp):
ATTTATGTTCGTTCATATATATTT
Found at i:2953920 original size:24 final size:24
Alignment explanation
Indices: 2953893--2953951 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
2953883 AATATAAACT
*
2953893 TGTTCGTTTATGTTCGTTCATTTG
1 TGTTCGTTTATGTTCGTCCATTTG
* **
2953917 TGTTTGTTTGCGTTCGTCCATTTG
1 TGTTCGTTTATGTTCGTCCATTTG
2953941 TGTTCGTTTAT
1 TGTTCGTTTAT
2953952 CATTTTAACG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.07, C:0.14, G:0.22, T:0.58
Consensus pattern (24 bp):
TGTTCGTTTATGTTCGTCCATTTG
Found at i:2956091 original size:13 final size:13
Alignment explanation
Indices: 2956073--2956116 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2956063 AATAATATTC
*
2956073 AATAAAATATTTA
1 AATAAAATAATTA
*
2956086 AATAAAAAAATTA
1 AATAAAATAATTA
*
2956099 AATTAACATAATTA
1 AA-TAAAATAATTA
2956113 AATA
1 AATA
2956117 TTTTTACCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAAAATAATTA
Found at i:2959485 original size:20 final size:22
Alignment explanation
Indices: 2959451--2959492 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
2959441 AGTAATATCA
2959451 ATTTTAAAGAATAA-TAGCATT
1 ATTTTAAAGAATAATTAGCATT
2959472 ATTTTAAA-AATAATTAGCATT
1 ATTTTAAAGAATAATTAGCATT
2959493 CTCTAACGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (22 bp):
ATTTTAAAGAATAATTAGCATT
Found at i:2960219 original size:19 final size:20
Alignment explanation
Indices: 2960181--2960220 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2960171 TATACATTCT
*
2960181 ATTAATTCAGTCCTAATTTAA
1 ATTAATTCAGT-CAAATTTAA
2960202 ATTAATTCAGT-AAATTTAA
1 ATTAATTCAGTCAAATTTAA
2960221 CCATCTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (20 bp):
ATTAATTCAGTCAAATTTAA
Found at i:2962054 original size:22 final size:22
Alignment explanation
Indices: 2962006--2962048 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2961996 ATTAGATTGT
*
2962006 CCAGGGGGTACAGATTCTCCCC
1 CCAGGGGGTACAAATTCTCCCC
2962028 CCAGGGGGTACAAATTC-CCCC
1 CCAGGGGGTACAAATTCTCCCC
2962049 TGCAGGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.21, C:0.37, G:0.26, T:0.16
Consensus pattern (22 bp):
CCAGGGGGTACAAATTCTCCCC
Found at i:2962106 original size:21 final size:21
Alignment explanation
Indices: 2962081--2962122 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2962071 AACAAAATGT
*
2962081 CCAGGGGGTACAAATTCCCCC
1 CCAGGGAGTACAAATTCCCCC
**
2962102 CCAGGGAGTACCGATTCCCCC
1 CCAGGGAGTACAAATTCCCCC
2962123 TTGTCTAACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.40, G:0.24, T:0.14
Consensus pattern (21 bp):
CCAGGGAGTACAAATTCCCCC
Found at i:2963432 original size:20 final size:19
Alignment explanation
Indices: 2963398--2963445 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
2963388 AACGATTTTC
* *
2963398 TTTTGAAAACAAAATTAGA
1 TTTTGAAAACAAAATGAAA
*
2963417 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAA-ACAAAATGAAA
2963437 TTTTGAAAA
1 TTTTGAAAA
2963446 GGATTTAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (19 bp):
TTTTGAAAACAAAATGAAA
Found at i:2964978 original size:20 final size:20
Alignment explanation
Indices: 2964955--2965003 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2964945 CAGGGGTATC
2964955 GATTCCCCCCA-AGGGAAACA
1 GATTCCCCCCAGAGGG-AACA
* *
2964975 GATTCCCCCCAGAGGGTACC
1 GATTCCCCCCAGAGGGAACA
2964995 GATTCCCCC
1 GATTCCCCC
2965004 ATGTCTAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.24, C:0.41, G:0.20, T:0.14
Consensus pattern (20 bp):
GATTCCCCCCAGAGGGAACA
Found at i:2966351 original size:169 final size:169
Alignment explanation
Indices: 2966058--2966393 Score: 437
Period size: 169 Copynumber: 2.0 Consensus size: 169
2966048 TAATCAAAGC
* * * * * *
2966058 CCCAAAGCAATTCGTGGATAGTCGTCGACGTTCACCGGAATTGAGCCCTTGAAGTTTCGTCGAAA
1 CCCAAAACAATTCATGGATAGTCGTCGACGTTCACCGAAATCGAGCCCTTAAAGTTTCGTCAAAA
* * * *
2966123 ACCCACCCCGACGCCTTAGATTTTGGACGATTTCGACCGCCTCGGACCTCTGCTCGCCTCACCGC
66 ACCCACCCCAACGCCTCAGATTTTGGACGATTCCGACCGCCTCGAACCTCTGCTCGCCTCACCGC
*
2966188 AATCATAGTTAGCTTCCTCATCGCCGTCAT-CTCAAAAAA
131 AACCATAGTTAGCTTCCTCATCGCCGTC-TGCTCAAAAAA
*
2966227 CCCAAAACAATTCATGGATAGTCGTC-ACCGTTCGCCGAAATCGAGCCCTTAAAGTTTCG-CTAA
1 CCCAAAACAATTCATGGATAGTCGTCGA-CGTTCACCGAAATCGAGCCCTTAAAGTTTCGTC-AA
* * *
2966290 AAACCCACCCCAATGTCTCAGATTTTGGACGATTCCGACCGCCTCGAACCT-TCGTTCGCCTCAC
64 AAACCCACCCCAACGCCTCAGATTTTGGACGATTCCGACCGCCTCGAACCTCT-GCTCGCCTCAC
* * * *
2966354 CGCCACCATATTTAGCTTCCTCCTCGTCGTCTGCTCAAAA
128 CGCAACCATAGTTAGCTTCCTCATCGCCGTCTGCTCAAAA
2966394 CCCAACCAGT
Statistics
Matches: 144, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
168 4 0.03
169 140 0.97
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.25
Consensus pattern (169 bp):
CCCAAAACAATTCATGGATAGTCGTCGACGTTCACCGAAATCGAGCCCTTAAAGTTTCGTCAAAA
ACCCACCCCAACGCCTCAGATTTTGGACGATTCCGACCGCCTCGAACCTCTGCTCGCCTCACCGC
AACCATAGTTAGCTTCCTCATCGCCGTCTGCTCAAAAAA
Done.