Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004206.1 Hibiscus syriacus cultivar Beakdansim tig00009206_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: 110008
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:59 original size:40 final size:41
Alignment explanation
Indices: 4--84 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
1 AAA
4 ATGGCATTGGGAACGAT-AAGAAGGAAAGGAAGAAGGAATT
1 ATGGCATTGGGAACGATAAAGAAGGAAAGGAAGAAGGAATT
44 ATGGCATTGGGAACGATAAAGAAGGAAAGGAAGAAGGAATT
1 ATGGCATTGGGAACGATAAAGAAGGAAAGGAAGAAGGAATT
85 TGAACAAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 17 0.43
41 23 0.57
ACGTcount: A:0.46, C:0.05, G:0.35, T:0.15
Consensus pattern (41 bp):
ATGGCATTGGGAACGATAAAGAAGGAAAGGAAGAAGGAATT
Found at i:2895 original size:37 final size:36
Alignment explanation
Indices: 2837--3203 Score: 147
Period size: 38 Copynumber: 10.2 Consensus size: 36
2827 ATTAATATAG
* *
2837 TATAGTTTCTGAAAATATTTTTAAAAAAATATAATA
1 TATAGTTTTTGAAAACATTTTTAAAAAAATATAATA
* * **
2873 TATAGTTTTTAGAAAACGTTTTTTGAAAACGTATAATA
1 TATAGTTTTT-GAAAAC-ATTTTTAAAAAAATATAATA
* * *
2911 TATACTTTTTGAAAACAATTTTTGAAAATATATATATTA
1 TATAGTTTTTGAAAAC-ATTTTT-AAAA-AAATATAATA
* ** *
2950 TATAG-TTTTG-AAACATTTTTTGAAAGTATATATTA
1 TATAGTTTTTGAAAACA-TTTTTAAAAAAATATAATA
** * *
2985 TATAG--TTTGAAAACGGTTTT-AGAATATATATATA
1 TATAGTTTTTGAAAACATTTTTAAAAAAATATA-ATA
* ** *
3019 TAATATGGTTTTGAAAACATATTTT--TGAAA-AT-GTA
1 T-ATA-GTTTTTGAAAACAT-TTTTAAAAAAATATAATA
* * *
3054 TATAGTTTTT-AAAATATTTTT-GAAAACTAT-ATA
1 TATAGTTTTTGAAAACATTTTTAAAAAAATATAATA
*** *
3087 -ATAG-TTTTGAAAACATATTTTTTTGAAAACAT-ATA
1 TATAGTTTTTGAAAAC--ATTTTTAAAAAAATATAATA
*** *
3122 TATAG-TTTTGAAAACATATTTTTTTTGAAAACAT-ATA
1 TATAGTTTTTGAAAAC--A-TTTTTAAAAAAATATAATA
* * * *
3159 TATAGTTTTTTAAAATATTTTTGAAAACATATAATA
1 TATAGTTTTTGAAAACATTTTTAAAAAAATATAATA
*
3195 TAAAGTTTT
1 TATAGTTTT
3204 AAAATGATTT
Statistics
Matches: 263, Mismatches: 46, Indels: 44
0.75 0.13 0.12
Matches are distributed among these distances:
31 8 0.03
32 16 0.06
33 17 0.06
34 20 0.08
35 42 0.16
36 43 0.16
37 50 0.19
38 52 0.20
39 15 0.06
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (36 bp):
TATAGTTTTTGAAAACATTTTTAAAAAAATATAATA
Found at i:3014 original size:72 final size:75
Alignment explanation
Indices: 2865--3057 Score: 216
Period size: 72 Copynumber: 2.6 Consensus size: 75
2855 TTTTAAAAAA
* * *
2865 ATATAATATATAGTTTTTAGAAAACGTTTTTTGAAAACGTATA-ATATATACTTTTTGAAAACAA
1 ATATATTATATAG-TTTT-GAAAACATTTTTTGAAAACGTATATATATATAC-GTTTGAAAACAA
*
2929 TTTTTGAAAATAT
63 TTTTAGAAAATAT
**
2942 ATATATTATATAGTTTTG-AAACATTTTTTG-AAA-GTATATATTATATA-GTTTGAAAACGGTT
1 ATATATTATATAGTTTTGAAAACATTTTTTGAAAACGTATATA-TATATACGTTTGAAAACAATT
*
3003 TTAGAATATAT
65 TTAGAAAATAT
* * *
3014 ATATATAATATGGTTTTGAAAACATATTTTTGAAAATGTATATA
1 ATATATTATATAGTTTTGAAAACAT-TTTTTGAAAACGTATATA
3058 GTTTTTAAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
72 41 0.41
73 10 0.10
74 23 0.23
75 4 0.04
76 11 0.11
77 12 0.12
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (75 bp):
ATATATTATATAGTTTTGAAAACATTTTTTGAAAACGTATATATATATACGTTTGAAAACAATTT
TAGAAAATAT
Found at i:3113 original size:36 final size:33
Alignment explanation
Indices: 3016--3194 Score: 195
Period size: 36 Copynumber: 5.2 Consensus size: 33
3006 GAATATATAT
*
3016 ATATAATATGGTTTTGAAAACATATTTTTGAAAAT
1 ATATAATA--GTTTTGAAAACATATTTTTGAAAAC
* *
3051 GTAT-ATAGTTTT-TAAA-ATATTTTTGAAAAC
1 ATATAATAGTTTTGAAAACATATTTTTGAAAAC
3081 TATATAATAGTTTTGAAAACATATTTTTTTGAAAAC
1 -ATATAATAGTTTTGAAAACATA--TTTTTGAAAAC
3117 ATATATATAGTTTTGAAAACATATTTTTTTTGAAAAC
1 ATATA-ATAGTTTTGAAAACATA---TTTTTGAAAAC
**
3154 ATATATATAGTTTTTTAAA-ATATTTTTGAAAAC
1 ATATA-ATAGTTTTGAAAACATATTTTTGAAAAC
3187 ATATAATA
1 ATATAATA
3195 TAAAGTTTTA
Statistics
Matches: 129, Mismatches: 7, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
30 13 0.10
31 6 0.05
32 16 0.12
33 19 0.15
34 6 0.05
35 8 0.06
36 31 0.24
37 30 0.23
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (33 bp):
ATATAATAGTTTTGAAAACATATTTTTGAAAAC
Found at i:3145 original size:35 final size:33
Alignment explanation
Indices: 2831--3226 Score: 220
Period size: 37 Copynumber: 11.2 Consensus size: 33
2821 ATATGTATTA
* *
2831 ATATAGTATAGTTTCTG-AAAATATTTTTAAAAAAAT
1 ATATA-TATAGTTT-TGAAAAATATTTTT--GAAAAC
*
2867 ATAATATATAGTTTTTAGAAAACGT-TTTTTGAAAAC
1 AT-ATATATAG-TTTT-GAAAA-ATATTTTTGAAAAC
* *
2903 GTATAATATATACTTTTTGAAAACA-ATTTTTGAAAATATAT
1 --AT-ATATATA-GTTTTGAAAA-ATATTTTTG--AA-A-AC
* *
2944 ATATTATATAGTTTTGAAACAT-TTTTTGAAAGTAT
1 ATA-TATATAGTTTTGAAAAATATTTTTGAAA--AC
*** * *
2979 ATATTATATAG-TTTGAAAACGGTTTTAGAATATAT
1 ATA-TATATAGTTTTGAAAAATATTTTTGAA-A-AC
3014 ATATATAATATGGTTTTGAAAACATATTTTTG-AAA-
1 ATATAT-ATA--GTTTTGAAAA-ATATTTTTGAAAAC
* *
3049 ATGTATATAGTTTT-TAAAATATTTTTGAAAAC
1 ATATATATAGTTTTGAAAAATATTTTTGAAAAC
3081 -TATATAATAGTTTTGAAAACATATTTTTTTGAAAAC
1 ATATAT-ATAGTTTTGAAAA-ATA--TTTTTGAAAAC
3117 ATATATATAGTTTTGAAAACATATTTTTTTTGAAAAC
1 ATATATATAGTTTTGAAAA-ATA---TTTTTGAAAAC
**
3154 ATATATATAGTTTTTTAAAATATTTTTGAAAAC
1 ATATATATAGTTTTGAAAAATATTTTTGAAAAC
3187 ATATAATATAAAGTTTT--AAAATGATTTTTGAAAAC
1 ATAT-ATAT--AGTTTTGAAAAAT-ATTTTTGAAAAC
3222 ATATA
1 ATATA
3227 GTTTTTAAAA
Statistics
Matches: 302, Mismatches: 22, Indels: 74
0.76 0.06 0.19
Matches are distributed among these distances:
30 9 0.03
31 10 0.03
32 13 0.04
33 18 0.06
34 27 0.09
35 53 0.18
36 51 0.17
37 63 0.21
38 40 0.13
39 16 0.05
40 1 0.00
41 1 0.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (33 bp):
ATATATATAGTTTTGAAAAATATTTTTGAAAAC
Found at i:3271 original size:29 final size:28
Alignment explanation
Indices: 3198--3273 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 28
3188 TATAATATAA
3198 AGTTTTAAAATGA-TTTTTGAAAACATAT
1 AGTTTTAAAATGATTTTTTGAAAACA-AT
*
3226 AGTTTTTAAAATGATTTTTTGGAAAC-AT
1 AG-TTTTAAAATGATTTTTTGAAAACAAT
3254 AGTTTTAGAAATGCATTTTT
1 AGTTTTA-AAATG-ATTTTT
3274 CGACATATAC
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
27 5 0.12
28 11 0.26
29 17 0.40
30 10 0.23
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (28 bp):
AGTTTTAAAATGATTTTTTGAAAACAAT
Found at i:3328 original size:31 final size:29
Alignment explanation
Indices: 3293--3366 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 29
3283 CATATTATTA
3293 TTTTATTTTATTTTCTAATTTTCATTTTCAT
1 TTTTATTTTATTTTCTAA-TTT-ATTTTCAT
* * *
3324 TTTTATTTTATTTACTTATTTATTTTTAT
1 TTTTATTTTATTTTCTAATTTATTTTCAT
*
3353 TTTT-TCTTATTTTC
1 TTTTATTTTATTTTC
3367 AGTCCAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
28 8 0.21
29 11 0.29
30 3 0.08
31 16 0.42
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (29 bp):
TTTTATTTTATTTTCTAATTTATTTTCAT
Found at i:4445 original size:5 final size:5
Alignment explanation
Indices: 4426--4463 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
4416 TATTTCCTTA
*
4426 ATTTT ATTTT -TATTT AATTT ATTTT ATTTT ATTTT ATT
1 ATTTT ATTTT AT-TTT ATTTT ATTTT ATTTT ATTTT ATT
4464 GCTTTTCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 1 0.03
5 28 0.97
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:4609 original size:12 final size:12
Alignment explanation
Indices: 4594--4618 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4584 GAATCGAAAT
4594 TTTAAATTTCAA
1 TTTAAATTTCAA
4606 TTTAAATTTCAA
1 TTTAAATTTCAA
4618 T
1 T
4619 GTTTTGCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAAATTTCAA
Found at i:7374 original size:99 final size:97
Alignment explanation
Indices: 7190--7384 Score: 309
Period size: 99 Copynumber: 2.0 Consensus size: 97
7180 CGTATACTAA
* *
7190 GATTATAATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACAACTCGGCTT
1 GATTATAATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTAGTTAAACAACCCGGCTT
*
7255 TATGGATAAGATTCAACTAGCTTGATAAAGGT
66 TATGGATAAGATTCAACTAGCCTGATAAAGGT
* **
7287 GATTATAATGTATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTAGTTAATCGCCCCGGC
1 GATTATAA--TATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTAGTTAAACAACCCGGC
*
7352 TTTATGGATAAGATTCAGCTAGCCTGATAAAGG
64 TTTATGGATAAGATTCAACTAGCCTGATAAAGG
7385 CAAATTACAA
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
97 8 0.09
99 81 0.91
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Consensus pattern (97 bp):
GATTATAATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTAGTTAAACAACCCGGCTT
TATGGATAAGATTCAACTAGCCTGATAAAGGT
Found at i:8814 original size:85 final size:85
Alignment explanation
Indices: 8666--9435 Score: 1051
Period size: 85 Copynumber: 9.1 Consensus size: 85
8656 AAACTATTCG
* *
8666 CAGCTTAGCTCAAGGC-AGCAAGGGCTATCTGTCAACAAAAACCTTCGAGTTTGATTACATTCAG
1 CAGCATAGCTCAAGGCGAG-AAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAG
* *
8730 CTCAAGGGTATATCAAACTTA
65 CTCAAGGGCATATCAAATTTA
** * ** * *
8751 CAATATAGCTCAAGGCGAGAAGGGTTATCTGTCAATGAAAACCTTCAAGTTCAATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
* *
8816 TCAAAGGCATGTCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * *
8836 CAGCATAGCTCAAGGCTAGAAGAGCTATCTGTCAACAAAAACCTTTGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
8901 TCAAGGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * * * **
8921 CAGCATAGCTCAAGGTGAGGAGGGCTATCTATC-A-AAAAACCTTCAAGTTCGATTACATTTTGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
8984 TCAAGGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * * * * * **
9004 CAGCATAGATCAATGCGAGAAGGGTTATCTGTCAATAAAAACCTTCAAGTTTGATTACATTTTGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
9069 TCAAGGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * * * * * * * *
9089 CAGCATAGATCAATGCGAAAAGGGTTACCTGCCAATAAAAACCTTCAAGTTCGATTACATTCGGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
*
9154 TCAATGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * *
9174 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTTAACAAAAACCTTCGAGGTCGATTATATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
*
9239 TCGAGGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * * *
9259 CATCATAGCTTAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCACC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
*
9324 TCAATGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
**
9344 CATAATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
9409 TCAAGGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
9429 CAGCATA
1 CAGCATA
9436 TCAAATTTAC
Statistics
Matches: 604, Mismatches: 78, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
83 72 0.12
84 2 0.00
85 528 0.87
86 2 0.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (85 bp):
CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
TCAAGGGCATATCAAATTTA
Found at i:9197 original size:170 final size:170
Alignment explanation
Indices: 8666--9596 Score: 1141
Period size: 170 Copynumber: 5.4 Consensus size: 170
8656 AAACTATTCG
* *
8666 CAGCTTAGCTCAAGGC-AGCAAGGGCTATCTGTCAACAAAAACCTTCGAGTTTGATTACATTCAG
1 CAGCATAGCTCAAGGCGAG-AAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAG
* * ** *
8730 CTCAAGGGTATATCAAACTTACAATATAGCTCAAGGCGAGAAGGGTTATCTGTCAATGAAAACCT
65 CTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATAAAAACCT
* * *
8795 TCAAGTTCAATTACATTCAGCTCAAAGGCATGTCAAATTTA
130 TCAAGTTCGATTACATTCAGCTCAATGGCATATCAAATTTA
* * *
8836 CAGCATAGCTCAAGGCTAGAAGAGCTATCTGTCAACAAAAACCTTTGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
* * * *
8901 TCAAGGGCATATCAAATTTACAGCATAGCTCAAGGTGAGGAGGGCTATCTATC-A-AAAAACCTT
66 TCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATAAAAACCTT
** *
8964 CAAGTTCGATTACATTTTGCTCAAGGGCATATCAAATTTA
131 CAAGTTCGATTACATTCAGCTCAATGGCATATCAAATTTA
* * * * * * **
9004 CAGCATAGATCAATGCGAGAAGGGTTATCTGTCAATAAAAACCTTCAAGTTTGATTACATTTTGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
* * * * *
9069 TCAAGGGCATATCAAATTTACAGCATAGATCAATGCGAAAAGGGTTACCTGCCAATAAAAACCTT
66 TCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATAAAAACCTT
*
9134 CAAGTTCGATTACATTCGGCTCAATGGCATATCAAATTTA
131 CAAGTTCGATTACATTCAGCTCAATGGCATATCAAATTTA
* * *
9174 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTTAACAAAAACCTTCGAGGTCGATTATATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
* * * *
9239 TCGAGGGCATATCAAATTTACATCATAGCTTAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTT
66 TCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATAAAAACCTT
* *
9304 CGAGTTCGATTACATTCACCTCAATGGCATATCAAATTTA
131 CAAGTTCGATTACATTCAGCTCAATGGCATATCAAATTTA
**
9344 CATAATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
* * * **
9409 TCAAGGGCATATCAAATTTACAGCATATCAAATTTACAACATATCTCAAGGTGATAAGGCCTATC
66 TCAAGGGCATATCAAATTTACAG----------------CATAGCTCAAGGCGAGAAGGGTTATC
*** *
9474 TGTCAGCGAAAACCTTCGAGTTCGATTACATTCAGCTCAA-GAGCATATCAAATTTA
115 TGTCAATAAAAACCTTCAAGTTCGATTACATTCAGCTCAATG-GCATATCAAATTTA
* * * * *
9530 CATCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGATTTTGATTCCATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
9595 TC
66 TC
9597 GATGACAACA
Statistics
Matches: 656, Mismatches: 85, Indels: 24
0.86 0.11 0.03
Matches are distributed among these distances:
168 141 0.21
169 2 0.00
170 377 0.57
171 2 0.00
185 1 0.00
186 133 0.20
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (170 bp):
CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
TCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATAAAAACCTT
CAAGTTCGATTACATTCAGCTCAATGGCATATCAAATTTA
Found at i:9436 original size:16 final size:16
Alignment explanation
Indices: 9415--9453 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
9405 CAGCTCAAGG
9415 GCATATCAAATTTACA
1 GCATATCAAATTTACA
9431 GCATATCAAATTTACA
1 GCATATCAAATTTACA
*
9447 ACATATC
1 GCATATC
9454 TCAAGGTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (16 bp):
GCATATCAAATTTACA
Found at i:9505 original size:101 final size:101
Alignment explanation
Indices: 9330--9536 Score: 326
Period size: 101 Copynumber: 2.0 Consensus size: 101
9320 CACCTCAATG
*
9330 GCATATCAAATTTACATAATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTT
1 GCATATCAAATTTACATAATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGTT
*
9395 CGATTACATTCAGCTCAAGGGCATATCAAATTTACA
66 CGATTACATTCAGCTCAAGAGCATATCAAATTTACA
* * * * *
9431 GCATATCAAATTTACA-ACATATCTCAAGGTGATAAGGCCTATCTGTCAGCGAAAACCTTCGAGT
1 GCATATCAAATTTACATA-ATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGT
9495 TCGATTACATTCAGCTCAAGAGCATATCAAATTTACA
65 TCGATTACATTCAGCTCAAGAGCATATCAAATTTACA
*
9532 TCATA
1 GCATA
9537 GCTCAAGGCG
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
100 1 0.01
101 96 0.99
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.27
Consensus pattern (101 bp):
GCATATCAAATTTACATAATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGTT
CGATTACATTCAGCTCAAGAGCATATCAAATTTACA
Found at i:9561 original size:186 final size:186
Alignment explanation
Indices: 9245--9596 Score: 553
Period size: 186 Copynumber: 1.9 Consensus size: 186
9235 CAGCTCGAGG
* * **
9245 GCATATCAAATTTACATCATAGCTTAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTT
1 GCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGTT
9310 CGATTACATTCACCTCAATGGCATATCAAATTTACATAATAGCTCAAGGCGAGAAGGGCTATCTG
66 CGATTACATTCACCTCAATGGCATATCAAATTTACATAATAGCTCAAGGCGAGAAGGGCTATCTG
9375 TCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACA
131 TCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACA
* * * * *
9431 GCATATCAAATTTACAACATATCTCAAGGTGATAAGGCCTATCTGTCAGCGAAAACCTTCGAGTT
1 GCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGTT
* * *
9496 CGATTACATTCAGCTCAA-GAGCATATCAAATTTACATCATAGCTCAAGGCGAGAAGGGTTATCT
66 CGATTACATTCACCTCAATG-GCATATCAAATTTACATAATAGCTCAAGGCGAGAAGGGCTATCT
* * *
9560 GTCAACAAAAACCTTCGATTTTGATTCCATTCAGCTC
130 GTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTC
9597 GATGACAACA
Statistics
Matches: 150, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
185 1 0.01
186 149 0.99
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (186 bp):
GCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGTT
CGATTACATTCACCTCAATGGCATATCAAATTTACATAATAGCTCAAGGCGAGAAGGGCTATCTG
TCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACA
Found at i:9573 original size:85 final size:85
Alignment explanation
Indices: 9430--9596 Score: 235
Period size: 85 Copynumber: 2.0 Consensus size: 85
9420 TCAAATTTAC
* * * * *
9430 AGCATATCAAATTTACAACATATCTCAAGGTGATAAGGCCTATCTGTCAGCGAAAACCTTCGAGT
1 AGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGT
9495 TCGATTACATTCAGCTCAAG
66 TCGATTACATTCAGCTCAAG
* ** *
9515 AGCATATCAAATTTACATCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGATT
1 AGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGT
* *
9580 TTGATTCCATTCAGCTC
66 TCGATTACATTCAGCTC
9597 GATGACAACA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 71 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (85 bp):
AGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGT
TCGATTACATTCAGCTCAAG
Found at i:10290 original size:37 final size:37
Alignment explanation
Indices: 10177--10475 Score: 200
Period size: 37 Copynumber: 7.9 Consensus size: 37
10167 ATTAATATAG
* * *
10177 TATAGTTTTTG-AAA-ATGTTTTTGAAAAAATATAATA
1 TATAG-TTTTGAAAACATATTTTTGAAAATATATATTA
** ** *
10213 TATAGTTTTTAGAAAAC-GGTTTTTGAAAACGTATAATA
1 TATAG-TTTT-GAAAACATATTTTTGAAAATATATATTA
*
10251 TATACTTTTTGAAAACA-ATTTTTGAAAATATATATTA
1 TATA-GTTTTGAAAACATATTTTTGAAAATATATATTA
* *
10288 TATAGTTTTGAAAACATTTTTTTGAAAGTATATATTA
1 TATAGTTTTGAAAACATATTTTTGAAAATATATATTA
* ** *
10325 TATAGTTCTGAAAAC-GGTTTTAGAATATATATATATATATA
1 TATAGTTTTGAAAACATATTTTTG-A-A-A-ATATATAT-TA
* *
10366 TAATATGGTTTTAAAAAACATATTTTTGAAAATGTATATAATA
1 T-ATA--GTTTT-GAAAACATATTTTTGAAAA--TATATATTA
* * * *
10409 TATAGTTTT-TAAA-ATATATTTGAAAACATATATAA
1 TATAGTTTTGAAAACATATTTTTGAAAATATATATTA
* *
10444 TATAGTTTTAAAAACATATTTTTTAAAA-ATAT
1 TATAGTTTTGAAAACATATTTTTGAAAATATAT
10476 TTTTGAAAAC
Statistics
Matches: 213, Mismatches: 30, Indels: 40
0.75 0.11 0.14
Matches are distributed among these distances:
35 15 0.07
36 33 0.15
37 83 0.39
38 33 0.15
39 1 0.00
40 12 0.06
41 3 0.01
42 7 0.03
43 4 0.02
44 11 0.05
45 6 0.03
46 5 0.02
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.44
Consensus pattern (37 bp):
TATAGTTTTGAAAACATATTTTTGAAAATATATATTA
Found at i:10445 original size:21 final size:22
Alignment explanation
Indices: 10421--10462 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
10411 TAGTTTTTAA
*
10421 AATATA-TTTGAAAACATATAT
1 AATATAGTTTAAAAACATATAT
10442 AATATAGTTTTAAAAACATAT
1 AATATAG-TTTAAAAACATAT
10463 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
23 12 0.67
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (22 bp):
AATATAGTTTAAAAACATATAT
Found at i:10475 original size:13 final size:14
Alignment explanation
Indices: 10449--10489 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
10439 TATAATATAG
10449 TTTTAAAAACATAT
1 TTTTAAAAACATAT
*
10463 TTTTTAAAA-ATAT
1 TTTTAAAAACATAT
*
10476 TTTTGAAAACATAT
1 TTTTAAAAACATAT
10490 AATAAGGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (14 bp):
TTTTAAAAACATAT
Found at i:10546 original size:31 final size:30
Alignment explanation
Indices: 10449--10559 Score: 120
Period size: 31 Copynumber: 3.7 Consensus size: 30
10439 TATAATATAG
* *
10449 TTTTAAAAACATAT--TTTTTAAAAAT-AT
1 TTTTGAAAACATATAGTTTTTTAAAATGAT
* *
10476 TTTTGAAAACATATAATAAGGTTTTAAAATGAT
1 TTTTGAAAACATATAGT---TTTTTAAAATGAT
*
10509 TTTTGAAAACATGTAGTTTTTTAAAATGATT
1 TTTTGAAAACATATAGTTTTTTAAAATGA-T
10540 TTTTGAAAACATATAGTTTT
1 TTTTGAAAACATATAGTTTT
10560 GGAAATGCAT
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
27 13 0.19
29 1 0.01
30 11 0.16
31 20 0.29
32 8 0.11
33 17 0.24
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (30 bp):
TTTTGAAAACATATAGTTTTTTAAAATGAT
Found at i:10572 original size:31 final size:31
Alignment explanation
Indices: 10449--10573 Score: 102
Period size: 31 Copynumber: 4.1 Consensus size: 31
10439 TATAATATAG
* *
10449 TTTTAAAAACATAT--TTTTTAAAAAT-A-T
1 TTTTGAAAACATATAGTTTTTGAAAATGATT
*
10476 TTTTGAAAACATATAATAAGGTTTT-AAAATGA-T
1 TTTTGAAAAC--AT-AT-AGTTTTTGAAAATGATT
* *
10509 TTTTGAAAACATGTAGTTTTTTAAAATGATT
1 TTTTGAAAACATATAGTTTTTGAAAATGATT
*
10540 TTTTGAAAACATATAG-TTTTGGAAATGCATT
1 TTTTGAAAACATATAGTTTTTGAAAATG-ATT
10571 TTT
1 TTT
10574 CGACATATAT
Statistics
Matches: 81, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
27 9 0.11
29 8 0.10
30 19 0.23
31 24 0.30
32 5 0.06
33 16 0.20
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (31 bp):
TTTTGAAAACATATAGTTTTTGAAAATGATT
Found at i:10622 original size:23 final size:21
Alignment explanation
Indices: 10595--10659 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 21
10585 CATATTATTA
10595 TTTTATTTTTTTCTATTTTCCAT
1 TTTTATTTTTTTCTATTTT--AT
10618 TTTTATTTTATTTACT-TGTTTAT
1 TTTTATTTT-TTT-CTAT-TTTAT
10641 TTTTA-TTTTTTCTTATTTT
1 TTTTATTTTTTTC-TATTTT
10660 TAGTCCAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
20 1 0.03
21 7 0.19
22 4 0.11
23 16 0.43
24 4 0.11
25 5 0.14
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTATTTTTTTCTATTTTAT
Found at i:11661 original size:19 final size:19
Alignment explanation
Indices: 11619--11661 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
11609 TTTTTAGCAT
11619 TTTTTAAACATTTTTCTTC
1 TTTTTAAACATTTTTCTTC
*
11638 CTTTTAATAC-TTTTTCTTC
1 TTTTTAA-ACATTTTTCTTC
11657 TTTTT
1 TTTTT
11662 TTCTCTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTAAACATTTTTCTTC
Found at i:12530 original size:22 final size:21
Alignment explanation
Indices: 12505--12550 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
12495 GCATAAATGT
* *
12505 TAAAAAGCATAAATGTTTTAAG
1 TAAAAAGAAT-AATATTTTAAG
*
12527 TAAAAATAATAATATTTTAAG
1 TAAAAAGAATAATATTTTAAG
12548 TAA
1 TAA
12551 TTTTTTACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.35
Consensus pattern (21 bp):
TAAAAAGAATAATATTTTAAG
Found at i:13476 original size:30 final size:30
Alignment explanation
Indices: 13442--13499 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
13432 AGTGAACCGA
* *
13442 CGGTTCAAATCGATTTTGCCGGTTTTCAAC
1 CGGTTCAAACCGATTTTCCCGGTTTTCAAC
**
13472 CGGTTCACCCCGATTTTCCCGGTTTTCA
1 CGGTTCAAACCGATTTTCCCGGTTTTCA
13500 GCCGATTCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.19, T:0.36
Consensus pattern (30 bp):
CGGTTCAAACCGATTTTCCCGGTTTTCAAC
Found at i:19265 original size:6 final size:6
Alignment explanation
Indices: 19254--19293 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
19244 CAAAAATATA
* *
19254 ATAATT ATAATT ATAATT ATTATC ATAATT ATAATT ATAA
1 ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT ATAA
19294 GAAATCATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (6 bp):
ATAATT
Found at i:21328 original size:31 final size:31
Alignment explanation
Indices: 21293--21351 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
21283 TTGTCTCCTG
* * *
21293 AAATTTTATAAGTTCAAGTTTGTTCTCTCTA
1 AAATTTTAAAAATTCAAGTTCGTTCTCTCTA
21324 AAATTTTAAAAATTCAAGTTCGTTCTCT
1 AAATTTTAAAAATTCAAGTTCGTTCTCT
21352 AACATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (31 bp):
AAATTTTAAAAATTCAAGTTCGTTCTCTCTA
Found at i:23315 original size:2 final size:2
Alignment explanation
Indices: 23308--23336 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23298 GAAGTAAATA
23308 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
23337 AAAGCAGGAT
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:23368 original size:168 final size:159
Alignment explanation
Indices: 23175--23592 Score: 447
Period size: 158 Copynumber: 2.6 Consensus size: 159
23165 TTTTGTAAAT
* * *
23175 AGGACATTTATTTA--TTTACAAATATCAGAAAATGACATCTAGTTGCTTTAA-AATTTCATTTT
1 AGGATATTTATTTATTTTTA-AAATATCAGAAAA-GACATCTAGTTGCTTTAAGACTGTCATTTT
23237 CTTTGATATTAATAAATAAATAAATATTAATAAGAATATAATAATTTTCCTAA-AAAATAATGAA
64 CTTTGATATTAA-AAATAAATAAATATT-ATAA-AA-ATAATAATTTTCCTAAGAAAATAAT---
* * *
23301 GTAAATAATATATATATATATATATATATATATATAAAAGC
122 GTAAATAAAACA-ATATATAT-TATATAGAT-TATAAAAGC
*
23342 AGGATATTTATTTATTTTTAAAATATCAGAATAAGACATCTAGTTGCTTTAAGACTGTC-CTTTC
1 AGGATATTTATTTATTTTTAAAATATCAGAA-AAGACATCTAGTTGCTTTAAGACTGTCATTTTC
* *
23406 -TTAATATTTGAAAAATAAATAAATA-T-TAAAAATAATAATTTTCCTAAGAAAATAATTTAAAT
65 TTTGATA-TT-AAAAATAAATAAATATTATAAAAATAATAATTTTCCTAAGAAAATAATGTAAAT
* * * * * * *
23468 AAAACAATATGTATTTTCTGGATTTTATAAGT
128 AAAACAATATATATTATATAGATTATAAAAGC
* * * * *
23500 AGTATATTTATTTATTTTTAAAATACCATAATAGGACATCTAGTTGCTTTAAGACTGCCATTTTC
1 AGGATATTTATTTATTTTTAAAATATCAGAA-AAGACATCTAGTTGCTTTAAGACTGTCATTTTC
23565 TTTGATATTAAAAATAAATAAATATTAT
65 TTTGATATTAAAAATAAATAAATATTAT
23593 TATCTAATCA
Statistics
Matches: 217, Mismatches: 23, Indels: 29
0.81 0.09 0.11
Matches are distributed among these distances:
158 75 0.35
159 12 0.06
160 13 0.06
161 9 0.04
163 16 0.07
164 10 0.05
165 3 0.01
167 19 0.09
168 48 0.22
169 12 0.06
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (159 bp):
AGGATATTTATTTATTTTTAAAATATCAGAAAAGACATCTAGTTGCTTTAAGACTGTCATTTTCT
TTGATATTAAAAATAAATAAATATTATAAAAATAATAATTTTCCTAAGAAAATAATGTAAATAAA
ACAATATATATTATATAGATTATAAAAGC
Found at i:23667 original size:4 final size:4
Alignment explanation
Indices: 23653--23684 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
23643 TGAATAAAAC
23653 ATAA A-AA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
23685 ATACTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:25047 original size:39 final size:39
Alignment explanation
Indices: 24996--25077 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
24986 GTTGAATAAG
*
24996 TTCTTCTCCTTCAGATGAATTCTTCTCATTATGAACTTC
1 TTCTTCTCCTTCAGATGAATTCTTCTCATTACGAACTTC
* * *
25035 TTCTTC-CTCTTCAGGTGAGTTCTTCTTATTACGAACTTC
1 TTCTTCTC-CTTCAGATGAATTCTTCTCATTACGAACTTC
25074 TTCT
1 TTCT
25078 GGAAATGTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 1 0.03
39 37 0.97
ACGTcount: A:0.17, C:0.26, G:0.10, T:0.48
Consensus pattern (39 bp):
TTCTTCTCCTTCAGATGAATTCTTCTCATTACGAACTTC
Found at i:25260 original size:73 final size:73
Alignment explanation
Indices: 25111--25472 Score: 604
Period size: 73 Copynumber: 5.0 Consensus size: 73
25101 TGGAAATTTA
* * * *
25111 TGTTTCTAGTGAAACTGTCTCAAGCGAGACGAATCTTATTTTAA-AAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
25175 TAAATTGT
66 TAAATTGT
*
25183 TGTTTCGAGTGAAACTGTCTTAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
25248 TAAATTGT
66 TAAATTGT
*
25256 TGTTTCGAGTGAAACTGTCTCAAGCGAGACACATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
25321 TAAATTGT
66 TAAATTGT
* *
25329 TGTTTCGAGTGAAACTGTCTCAAGCGAGACACAA-TTTCTTTTAAGAAAAATAATCTCAAGTGAG
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACA-AATTTTGTTTTAAGAAAAACAATCTCAAGTGAG
*
25393 ATAAATTTT
65 ATAAATTGT
25402 TGTTTCGAGTGAAACTGTCTCAAGCGAGACACAA-TTTGTTTTAAGAAAAACAATCTCAAGTGAG
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACA-AATTTTGTTTTAAGAAAAACAATCTCAAGTGAG
25466 ATAAATT
65 ATAAATT
25473 ACTATTTGAA
Statistics
Matches: 275, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
72 39 0.14
73 235 0.85
74 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (73 bp):
TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
TAAATTGT
Found at i:26250 original size:22 final size:22
Alignment explanation
Indices: 26190--26251 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
26180 GGAATCCAAT
*
26190 AAATCT-T-ATCTTTGAAAAGA
1 AAATCTATCATCTTTGAAGAGA
*
26210 AAATCTATCATTTTTGAAGAGA
1 AAATCTATCATCTTTGAAGAGA
26232 AAATCTATCATCTTTGAAGA
1 AAATCTATCATCTTTGAAGA
26252 ATGTAGATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 6 0.16
21 1 0.03
22 30 0.81
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.35
Consensus pattern (22 bp):
AAATCTATCATCTTTGAAGAGA
Found at i:26701 original size:54 final size:53
Alignment explanation
Indices: 26619--26780 Score: 218
Period size: 54 Copynumber: 3.0 Consensus size: 53
26609 ATAATCACTG
* * *
26619 GTTCGTAAAACATGTGACAATACATTCATCTTTTCTCGTGGTTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCTTTTCT-ATGGTTTCTGCACAGAT
* *
26673 GTTCGTAAAACATTTGATAACACATTCATCTTTTCTTATGGCTTCTGGC-CAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCTTTTC-TATGGTTTCT-GCACAGAT
* *
26727 GTTCGTAAAGCATTTGACAACACATTCATCATTTTATATGGTTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATC-TTTTCTATGGTTTCTGCACAGAT
26781 TTATGATCAA
Statistics
Matches: 95, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
53 2 0.02
54 86 0.91
55 7 0.07
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCTTTTCTATGGTTTCTGCACAGAT
Found at i:30154 original size:7 final size:8
Alignment explanation
Indices: 30135--30165 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
30125 CTTGATTCAA
30135 TTTTTTCC
1 TTTTTTCC
30143 TTTTTTCC
1 TTTTTTCC
30151 TTTTTTCC
1 TTTTTTCC
30159 TTATTTT
1 TT-TTTT
30166 TGGATGAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCC
Found at i:34281 original size:25 final size:26
Alignment explanation
Indices: 34231--34294 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 26
34221 TTAATACATG
34231 AAAATAA-A-ATAAAGATATTAATAA
1 AAAATAATATATAAAGATATTAATAA
34255 AAAATAATATATAAA-ATATT-ATGAA
1 AAAATAATATATAAAGATATTAAT-AA
34280 AATAATAAATATATA
1 AA-AAT-AATATATA
34295 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
24 9 0.26
25 10 0.29
26 8 0.23
27 8 0.23
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (26 bp):
AAAATAATATATAAAGATATTAATAA
Found at i:34285 original size:23 final size:24
Alignment explanation
Indices: 34228--34287 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 24
34218 AATTTAATAC
34228 ATGAAAATAA-AATAAAGATATTA
1 ATGAAAATAATAATAAAGATATTA
*
34251 ATAAAAAATAATATATAAA-ATATT-
1 AT-GAAAATAATA-ATAAAGATATTA
34275 ATGAAAATAATAA
1 ATGAAAATAATAA
34288 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 1 0.03
23 11 0.34
24 9 0.28
25 6 0.19
26 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (24 bp):
ATGAAAATAATAATAAAGATATTA
Found at i:34295 original size:2 final size:2
Alignment explanation
Indices: 34288--34324 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
34278 AAAATAATAA
34288 AT AT AT AT 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 AT AT AT AT A
34325 ATTGAAAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34835 original size:2 final size:2
Alignment explanation
Indices: 34824--34857 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
34814 CTAAGGAAAA
34824 AT AT -T 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 AT AT AT A
34858 GGGTTTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35162 original size:157 final size:152
Alignment explanation
Indices: 34877--35276 Score: 389
Period size: 157 Copynumber: 2.6 Consensus size: 152
34867 TAAATAGAAC
* * * * *
34877 ATTTATTTATTTAT-AAATATCAGAA-AATGATATCTAGTTGTTTTAAGAATACCTTTTCTTTAA
1 ATTTATTTATTTTTAAAATATCAGAATAA-GACATCTAGTTGCTTTAAGACTGCCTTTTC-TTAA
* *
34940 TATTAATTAATAAATAAATATTAATAAGAATATAATAATTTTCCTAAAAAATAATGAAGTAAATA
64 TATTAA-AAATAAATAAATA-T--TAAGAATATAATAATTTTCCTAAAAAATAATGAAATAAATA
*
35005 TATATATATATA-TATATATAAGCAGGAT
125 TATAT-TATATAGTATATATAAGCAAGAT
* * *
35033 ATTTATTTATTTTTAAAATATCAGAATAAAACATCTAGTTGCTTTAAGACTGTCATTTCTTAATA
1 ATTTATTTATTTTTAAAATATCAGAATAAGACATCTAGTTGCTTTAAGACTGCCTTTTCTTAATA
* *
35098 TTTGAAAAATAAATAAATATTAA-AA-ATAATAATTTTCCTAAGAAAATATTTAAATAAAACAAT
66 -TT-AAAAATAAATAAATATTAAGAATATAATAATTTTCCTAA-AAAATAATGAAAT---A-AAT
* * * * * * *
35161 ATGTATTTTCTAGTTTTTATAAGTAATAT
124 ATATATTATATAGTATATATAAGCAAGAT
* * * *
35190 ATTTATTTATTTTTAAAATA-CTATAATAAGACATCTAGTTGCTTTAAAACTGCCCTTTTATTTG
1 ATTTATTTATTTTTAAAATATC-AGAATAAGACATCTAGTTGCTTTAAGACTG-CCTTTT-CTTA
35254 ATATTAAAAATAAATAAATATTA
63 ATATTAAAAATAAATAAATATTA
35277 TTATCTAATC
Statistics
Matches: 204, Mismatches: 27, Indels: 25
0.80 0.11 0.10
Matches are distributed among these distances:
152 16 0.08
153 12 0.06
154 3 0.01
156 26 0.13
157 132 0.65
158 10 0.05
159 5 0.02
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (152 bp):
ATTTATTTATTTTTAAAATATCAGAATAAGACATCTAGTTGCTTTAAGACTGCCTTTTCTTAATA
TTAAAAATAAATAAATATTAAGAATATAATAATTTTCCTAAAAAATAATGAAATAAATATATATT
ATATAGTATATATAAGCAAGAT
Found at i:35343 original size:7 final size:7
Alignment explanation
Indices: 35330--35372 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 7
35320 AATATTAGTG
35330 AATAAAA
1 AATAAAA
*
35337 CATAAAA
1 AATAAAA
35344 AATAAATA
1 AATAAA-A
35352 AATAAATA
1 AATAAA-A
35360 AATAAATA
1 AATAAA-A
35368 AATAA
1 AATAA
35373 CTATATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
7 11 0.33
8 22 0.67
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (7 bp):
AATAAAA
Found at i:35352 original size:4 final size:4
Alignment explanation
Indices: 35338--35372 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
35328 TGAATAAAAC
35338 ATAA A-AA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
35373 CTATATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:49250 original size:18 final size:18
Alignment explanation
Indices: 49229--49266 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
49219 GTGCTGATGT
*
49229 TGTTGTTGTTGCTGCTGC
1 TGTTGTTGATGCTGCTGC
*
49247 TGTTGTTGATGCTGTTGC
1 TGTTGTTGATGCTGCTGC
49265 TG
1 TG
49267 GTGCATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.13, G:0.34, T:0.50
Consensus pattern (18 bp):
TGTTGTTGATGCTGCTGC
Found at i:49252 original size:15 final size:15
Alignment explanation
Indices: 49213--49260 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
49203 AATGTTGCTC
* *
49213 CTGCTGGTGCTGATG
1 CTGCTGTTGTTGATG
* * *
49228 TTGTTGTTGTTGCTG
1 CTGCTGTTGTTGATG
49243 CTGCTGTTGTTGATG
1 CTGCTGTTGTTGATG
49258 CTG
1 CTG
49261 TTGCTGGTGC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.04, C:0.15, G:0.35, T:0.46
Consensus pattern (15 bp):
CTGCTGTTGTTGATG
Found at i:51949 original size:2 final size:2
Alignment explanation
Indices: 51942--51973 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
51932 TTGTTTATTT
51942 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51974 GGTGATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55094 original size:31 final size:28
Alignment explanation
Indices: 55032--55097 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 28
55022 GTGTTGGAAT
*
55032 ATTAAAGGACTAAAATAAAATACATGTA
1 ATTAAAGGACTAAAATAAAATACATGAA
55060 ATTAAAGGAACATAAAAATAAAATAC-TGAAA
1 ATTAAAGG-AC-T-AAAATAAAATACATG-AA
55091 ATTAAAG
1 ATTAAAG
55098 TGTTGAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 8 0.24
29 2 0.06
30 3 0.09
31 20 0.61
ACGTcount: A:0.61, C:0.06, G:0.11, T:0.23
Consensus pattern (28 bp):
ATTAAAGGACTAAAATAAAATACATGAA
Found at i:55112 original size:4 final size:4
Alignment explanation
Indices: 55103--55129 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
55093 TAAAGTGTTG
55103 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
55130 GGAATATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:55544 original size:100 final size:102
Alignment explanation
Indices: 55352--55606 Score: 266
Period size: 100 Copynumber: 2.5 Consensus size: 102
55342 GTTAGTAGAG
** * * *
55352 TAATAATGTTCATTGTACCCCGGATTGGGTCACCACAAGGTCAAATAATAATTCAAACAAATTAA
1 TAATAATGTGGATCGTACCCCGGATTGGGTCACCACAAGGTCGAATAATAAATCAAACAAATTAA
*** ** * *
55417 TAAAAAAAAGTTAGTGGTTAGCAGAGTT-C-GA-ACTA
66 TAAAAAAAAAAAAACGGATAG-AGAGTTACAGATACCA
* * *
55452 TAATAATGTGGATCGTACCCCAGATCGGATCACCACAAGGTCGAATAATAAATCAAACAAATTAA
1 TAATAATGTGGATCGTACCCCGGATTGGGTCACCACAAGGTCGAATAATAAATCAAACAAATTAA
55517 TAAAAATAATAAAAAACGGATAG-GAGTTACTAGAGTCTGTACCA
66 TAAAAA-AA-AAAAAACGGATAGAGAGTTAC-AGA-----TACCA
55561 TAATAATGTGGATCGTACCCCGGATTGGGTCACCACAAGGTCGAAT
1 TAATAATGTGGATCGTACCCCGGATTGGGTCACCACAAGGTCGAAT
55607 TAAATATGAG
Statistics
Matches: 126, Mismatches: 18, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
100 68 0.54
101 3 0.02
102 7 0.06
103 2 0.02
109 46 0.37
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.24
Consensus pattern (102 bp):
TAATAATGTGGATCGTACCCCGGATTGGGTCACCACAAGGTCGAATAATAAATCAAACAAATTAA
TAAAAAAAAAAAAACGGATAGAGAGTTACAGATACCA
Found at i:55711 original size:29 final size:29
Alignment explanation
Indices: 55655--55711 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
55645 ATAGTTAGAA
***
55655 TGCAAGAAAATAAAAGTCAGTTGTTAATG
1 TGCAAGAAAATAAAAGTCAGTAAATAATG
* *
55684 TGCAATAAAATAAAAGTTAGTAAATAAT
1 TGCAAGAAAATAAAAGTCAGTAAATAAT
55712 ACTAAACATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.28
Consensus pattern (29 bp):
TGCAAGAAAATAAAAGTCAGTAAATAATG
Found at i:56401 original size:12 final size:12
Alignment explanation
Indices: 56384--56415 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
56374 AGACTTAAAG
*
56384 AAAACAAGTATA
1 AAAACAAGGATA
56396 AAAACAAGGATA
1 AAAACAAGGATA
56408 AAAACAAG
1 AAAACAAG
56416 AAGACCAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.69, C:0.09, G:0.12, T:0.09
Consensus pattern (12 bp):
AAAACAAGGATA
Found at i:56597 original size:3 final size:3
Alignment explanation
Indices: 56589--56627 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
56579 AGGGTATTAC
* *
56589 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
56628 GATGTCAGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:57077 original size:134 final size:134
Alignment explanation
Indices: 56807--57245 Score: 542
Period size: 134 Copynumber: 3.3 Consensus size: 134
56797 AAACGTCGAC
* * * * * * * * * *
56807 TCATCCCATTGTTCTCCACGGAAGATTGAATCAAGGAAGACTTGTTTCATTGTTCCTCAGGGAAG
1 TCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAAT
* * * * *
56872 ATCAAATCTGGAAAAAAAAGAGGGATATGTTTCACTTTTTCTTGAGGGAAAATCAGATCTGGGGA
66 ATCAAATCTTG---AAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCATATCTGGGGA
56937 CGTTGAT
128 CGTTGAT
* *
56944 TCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCTACTGTTAC-CTAGGGAA
1 TCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTC-AGGGAA
* * * * * *
57008 TATTAAATCTTGAACGAGAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCATATCTGGGAACA
65 TATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCATATCTGGGGACG
57073 TTGAT
130 TTGAT
** *
57078 TCATTCCACTGTTACTT-AGGGAAGATTGAATCGAGGTTGATTTGTTCCACTGTTACTCAGGGAA
1 TCATTCCACTGTT-CTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAA
* *
57142 TATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTT-TCTGAGGGAAAATCATATATGGGGAT
65 TATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCT-TGAGGGAAAATCATATCTGGGGAC
57206 GTTGAT
129 GTTGAT
*
57212 TCATTCCACTGTTCTTCAAGGAAGATTGAATCGA
1 TCATTCCACTGTTCTTCAGGGAAGATTGAATCGA
57246 ATTCGATTTT
Statistics
Matches: 260, Mismatches: 37, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
133 4 0.02
134 191 0.73
135 4 0.02
136 1 0.00
137 60 0.23
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (134 bp):
TCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAAT
ATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCATATCTGGGGACGT
TGAT
Found at i:58992 original size:13 final size:13
Alignment explanation
Indices: 58974--59002 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
58964 ACTCACCTAG
58974 TATGCCTCACTAT
1 TATGCCTCACTAT
58987 TATGCCTCACTAT
1 TATGCCTCACTAT
59000 TAT
1 TAT
59003 CCCTTACTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.28, G:0.07, T:0.41
Consensus pattern (13 bp):
TATGCCTCACTAT
Found at i:60463 original size:42 final size:41
Alignment explanation
Indices: 60373--60465 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 41
60363 ATCCTACCCG
* * ** *
60373 AAGATCTTATAGATGCCCCGAAGGACTTATTATCTTGCTCAA
1 AAGA-CTTACAGATGACCCGAAGGACTTAGCATCATGCTCAA
*
60415 AAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAA
1 AAGACTTACAGATGACCCGAAGGACTT-AGCATCATGCTCAA
60457 AAGACTTAC
1 AAGACTTAC
60466 TGATTGTCCG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
41 20 0.45
42 24 0.55
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (41 bp):
AAGACTTACAGATGACCCGAAGGACTTAGCATCATGCTCAA
Found at i:60816 original size:232 final size:233
Alignment explanation
Indices: 60204--61366 Score: 1559
Period size: 233 Copynumber: 5.0 Consensus size: 233
60194 CAACCTGAAA
* *
60204 GATTTAAGCATAAT-CTTCGAAAGACTTACTGATGACCCGAAGGACTTACCAATTTTGGAAATAG
1 GATTTAAGCATCATGC-TCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAG
* * * *
60268 TTTACTAGG-ATAGAAACTTTTCATACTATTCAAAAAATTT-AAATTTCAGATTCAAATGAGAAA
65 TTTACTAGGCA-AGAAACTTTTCTTACTTTTC-AAAAATTTCAATTTTCAGATTTAAATGAGAAA
* * * * * *
60331 TTTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTACCCGAAGATCTTATAGATGCCCCGAAG
128 ATTTTCTCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAG
* *
60396 GACTTATTATCTTGCTCAAAAGACTTACAGATGACCCGAAG
193 GACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAG
* * * *
60437 GATTTAAGCATCATGCTCAAAAGACTTACTGATTGTCCGAATGACTTACCAATTTTGGAAATAGT
1 GATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGT
* * * * *
60502 TTACTAGGTAAGAAACTTTTTTTACTTTTTAAAAATTTCAATTTTCAAATTTAAATGAGAAACTT
66 TTACTAGGCAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAATT
** *
60567 TTCTCATTTTTCGAAAAACATGTGAAAACATCCTGCTTGAAGGTCTTATGGATGGCCCGAATGAC
131 TTCTCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGAC
* **
60632 TTATTATCTTGCTCGAAAGACTTACAGATGACCTTAAG
196 TTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAG
*
60670 GATTTAAGCATCATGCGCGAAAGACTTA-TGATGGCCCGAAGGACTTACCAATTTTGGAAATAGT
1 GATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGT
* *
60734 TTACTAGGCAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAAAGT
66 TTACTAGGCAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAATT
* * * *
60799 TTCACACTTTTCGAAAAACATGTGAAAACATCTTGCCCGAAGGTCTTATAGATGGCCCGAAGGAC
131 TTCTCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGAC
* * *
60864 TTATCATATTACTCGAAAGACTTACAGATGACCCGAAA
196 TTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAG
* * * ** * * *
60902 GATTTAAGAATCATACTCGAAAGACTTACAGATGTACCTAAGGACTTATCAATTTTGGAAATAAT
1 GATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGT
* * * *
60967 TTAATAGGCAAGAAACTTTTTTTACTTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAATTT
66 TTACTAGGCAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAATT
* * * * *
61032 TTCTCATTTTTTGAAAAACAT-TTAAAAGCATTCTGCCCGAAGGTCTTGTGGATGGCCCAAAGGA
131 TTCTCATTTTTCGAAAAACATGTGAAAA-CATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGA
* *
61096 CTCATCATCTTGCTCGAAAGACTTACAGATGGCCCGAAG
195 CTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAG
* * * * * *
61135 GATTTAAGCATCAAGCTCGAAAGACTTACTGATGGCTCGAATGACTTACAAATTGTGGAAATTGT
1 GATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGT
* * *
61200 TTACTAGGTAAGAAACTTTTCTTATTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACA-
66 TTACTAGGCAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAA-AT
* * * *
61264 TTTCTCA-TTTTCGAAAAACATAT-ATAAACATCCTTCTCGAAGGTCTTATGGATGGCCCGAATG
130 TTTCTCATTTTTCGAAAAACATGTGA-AAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGG
* *
61327 ACTTATCATCTTGCTCGAAAGACTTACTGATGGCCCGAAG
194 ACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAG
61367 AACTTACCAA
Statistics
Matches: 814, Mismatches: 108, Indels: 17
0.87 0.12 0.02
Matches are distributed among these distances:
232 301 0.37
233 511 0.63
234 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (233 bp):
GATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGT
TTACTAGGCAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAATT
TTCTCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGAC
TTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAG
Found at i:60902 original size:20 final size:20
Alignment explanation
Indices: 60843--60935 Score: 62
Period size: 20 Copynumber: 4.5 Consensus size: 20
60833 GCCCGAAGGT
* * *
60843 CTTATAGATGGCCCGAAGGA
1 CTTACAGATGACCCGAAAGA
* * *
60863 CTTATCATATTACTCGAAAGA
1 CTTA-CAGATGACCCGAAAGA
60884 CTTACAGATGACCCGAAAGA
1 CTTACAGATGACCCGAAAGA
* * *
60904 TTTA-AGAATCATACTCGAAAGA
1 CTTACAG-AT--GACCCGAAAGA
60926 CTTACAGATG
1 CTTACAGATG
60936 TACCTAAGGA
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
19 2 0.04
20 22 0.41
21 14 0.26
22 14 0.26
23 2 0.04
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (20 bp):
CTTACAGATGACCCGAAAGA
Found at i:61110 original size:465 final size:462
Alignment explanation
Indices: 60204--61365 Score: 1607
Period size: 465 Copynumber: 2.5 Consensus size: 462
60194 CAACCTGAAA
* *
60204 GATTTAAGCATAAT-CTTCGAAAGACTTACTGATGACCCGAAGGACTTACCAATTTTGGAAATAG
1 GATTTAAGCATCATGC-TCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAG
* * * * *
60268 TTTACTAGGATAGAAACTTTTCATACTATTCAAAAAATTT-AAATTTCAGATTCAAATGAGAAAT
65 TTTACTAGGA-AGAAACTTTTCTTACTTTTC-AAAAATTTCAATTTTCATATTTAAATGAGAAA-
* * * * *
60332 TTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTACCCGAAGATCTTATAGATGCCCCGAAGG
127 ATTTCTCA-TTTTCGAAAAACATGTGAAAACAT-CTTCCCGAAGGTCTTATAGATGGCCCGAAGG
* * * * *
60397 ACTTATTATCTTGCTCAAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGAC
190 ACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAAGATTTAAGAATCATACTCAAAAGAC
* * * * *
60462 TTACTGATTGTCCGAATGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTTTTAC
255 TTACAGATTGTCCGAAGGACTTACCAATTTTGGAAATAATTTAATAGGCAAGAAACTTTTTTTAC
*
60527 TTTTTAAAAATTTCAATTTTCAAATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTGA
320 TTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTGA
** * * * *
60592 AAACATCCTGCTTGAAGGTCTTATGGATGGCCCGAATGACTTATTATCTTGCTCGAAAGACTTAC
385 AAACATCCTGCCCGAAGGTCTTATGGATGGCCCAAAGGACTCATCATCTTGCTCGAAAGACTTAC
**
60657 AGATGACCTTAAG
450 AGATGACCCGAAG
*
60670 GATTTAAGCATCATGCGCGAAAGACTTA-TGATGGCCCGAAGGACTTACCAATTTTGGAAATAGT
1 GATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGT
60734 TTACTAGGCAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAAAGT
66 TTACTAGG-AAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAAA-T
*
60799 TTCACACTTTTCGAAAAACATGTGAAAACATCTTGCCCGAAGGTCTTATAGATGGCCCGAAGGAC
129 TTCTCA-TTTTCGAAAAACATGTGAAAACATCTT-CCCGAAGGTCTTATAGATGGCCCGAAGGAC
* * *
60864 TTATCATATTACTCGAAAGACTTACAGATGACCCGAAAGATTTAAGAATCATACTCGAAAGACTT
192 TTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAAGATTTAAGAATCATACTCAAAAGACTT
* *
60929 ACAGA-TGTACCTAAGGACTTATCAATTTTGGAAATAATTTAATAGGCAAGAAACTTTTTTTACT
257 ACAGATTGT-CCGAAGGACTTACCAATTTTGGAAATAATTTAATAGGCAAGAAACTTTTTTTACT
* * * * *
60993 TTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAATTTTTCTCATTTTTTGAAAAACAT-TTAA
321 TTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTGAA
* *
61057 AAGCATTCTGCCCGAAGGTCTTGTGGATGGCCCAAAGGACTCATCATCTTGCTCGAAAGACTTAC
386 AA-CATCCTGCCCGAAGGTCTTATGGATGGCCCAAAGGACTCATCATCTTGCTCGAAAGACTTAC
*
61122 AGATGGCCCGAAG
450 AGATGACCCGAAG
* * * * * *
61135 GATTTAAGCATCAAGCTCGAAAGACTTACTGATGGCTCGAATGACTTACAAATTGTGGAAATTGT
1 GATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGT
*
61200 TTACTAGGTAAGAAACTTTTCTTATTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACAT
66 TTACTAGG-AAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAA-AT
* * * *
61265 TTCTCATTTTCGAAAAACATAT-ATAAACATCCTTCTCGAAGGTCTTATGGATGGCCCGAATGAC
129 TTCTCATTTTCGAAAAACATGTGA-AAACAT-CTTCCCGAAGGTCTTATAGATGGCCCGAAGGAC
* *
61329 TTATCATCTTGCTCGAAAGACTTACTGATGGCCCGAA
192 TTATCATCTTGCTCGAAAGACTTACAGATGACCCGAA
61366 GAACTTACCA
Statistics
Matches: 620, Mismatches: 65, Indels: 23
0.88 0.09 0.03
Matches are distributed among these distances:
464 19 0.03
465 474 0.76
466 125 0.20
467 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (462 bp):
GATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGT
TTACTAGGAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAAATTT
CTCATTTTCGAAAAACATGTGAAAACATCTTCCCGAAGGTCTTATAGATGGCCCGAAGGACTTAT
CATCTTGCTCGAAAGACTTACAGATGACCCGAAAGATTTAAGAATCATACTCAAAAGACTTACAG
ATTGTCCGAAGGACTTACCAATTTTGGAAATAATTTAATAGGCAAGAAACTTTTTTTACTTTTCA
AAAATTTCAATTTTCAAATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTGAAAACAT
CCTGCCCGAAGGTCTTATGGATGGCCCAAAGGACTCATCATCTTGCTCGAAAGACTTACAGATGA
CCCGAAG
Found at i:61512 original size:423 final size:424
Alignment explanation
Indices: 60917--61781 Score: 1191
Period size: 423 Copynumber: 2.0 Consensus size: 424
60907 AAGAATCATA
* * * *
60917 CTCGAAAGACTTACAGATGTACCTAAGGACTTATCAATTTTGGAAATAATTTAATAGGCAAGAAA
1 CTCGAAAGACTTACAGATGGACCGAAGAACTTACCAATTTTGGAAATAATTTAATAGGCAAGAAA
* * ** * **
60982 CTTTTTTTACTTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAATTTTTCTCATTTTTTGAA
66 CTTTTATTACTTTTCAAAAATTTAAATTTCCAGATTTAAATGAGAAATGTTTCTCATTTTTCAAA
* * ** *
61047 AAACATTTAAAAGCATTCTGCCCGAAGGTCTTGTGGATGGCCCAAAGGACTCATCATCTTGCTCG
131 AAACATTGAAAAGCATTCTGCCCGAAGGTCTTATAAATGGCCCAAAGAACTCATCATCTTGCTCG
* * * *
61112 AAAGACTTACAGATGGCCCGAAGGATTTAAGCATCAAGCTCGAAAGACTTACTGATGGCTCGAAT
196 AAAGACTTACAGATGACCCGAAGGATTTAAGCATCAAGCTCGAAAGACTTACTGATGGCCCAAAG
** * * *
61177 GACTTACAAATTGTGGAAATTGTTTACTAGGTAAGAAACTTTTCTTATTTTTCAAAAATTTCAAT
261 GACTTACAAATTGTGGAAACAGTTTACTAGGAAAGAAACTTTTCTTACTTTTAAAAAATTTCAAT
* *
61242 TTTCATATTTAAATGAGAAACATTTCTCA-TTTTCGAAAAACATAT-ATAAACATCCTTCTCGAA
326 TTTCAGATTTAAATGAGAAACATTTCTCATTTTTCGAAAAACATATGA-AAACATCCTGCTCGAA
*
61305 GGTCTTATGGATGGCCCGAATGACTTATCATCTTG
390 GGTCTTATGGATGGCCCGAAGGACTTATCATCTTG
* * * * * *
61340 CTCGAAAGACTTACTGATGGCCCGAAGAACTTACCAATTTTGGAAATAGTTTATTAGGTAATAAA
1 CTCGAAAGACTTACAGATGGACCGAAGAACTTACCAATTTTGGAAATAATTTAATAGGCAAGAAA
61405 CTTTTATTACTTTTCAAAAATTTAAATTTCCAGATTTAAATGAG-AATCGTTTCTCATTTTTCAA
66 CTTTTATTACTTTTCAAAAATTTAAATTTCCAGATTTAAATGAGAAAT-GTTTCTCATTTTTCAA
* * * *
61469 AAAATATGTGAAAA-CATT-TGGCCCGAAGGTCTTATAAATGGCCCGAATAACTTATCATCTTGC
130 AAAACAT-TGAAAAGCATTCT-GCCCGAAGGTCTTATAAATGGCCCAAAGAACTCATCATCTTGC
* * * * *
61532 TCGAGAGTCTTACAGATGACCCGAAGGATTTAAGTATCATGCTCGAAATACTTACTGATGGCCCA
193 TCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCAAGCTCGAAAGACTTACTGATGGCCCA
* *
61597 AAGGACTTACCAATTTTGGAAACAGTTTACTAGGAAAGAAACTTTTCTTACTTTTAAAAAATTTC
258 AAGGACTTACAAATTGTGGAAACAGTTTACTAGGAAAGAAACTTTTCTTACTTTTAAAAAATTTC
* ** * *
61662 AATTTTTAGATTTAAATGAGAAATTTTTCTCATTTTTCGAAAAACATGTGAAAACATCCTGCTTG
323 AATTTTCAGATTTAAATGAGAAACATTTCTCATTTTTCGAAAAACATATGAAAACATCCTGCTCG
*
61727 AAGGTCTTATGGATTGCCCGAAGGACTTATCATCTTG
388 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTG
*
61764 TTCGAAAGACTTACAGAT
1 CTCGAAAGACTTACAGAT
61782 AACTCGAAGG
Statistics
Matches: 384, Mismatches: 53, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
422 4 0.01
423 296 0.77
424 83 0.22
425 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (424 bp):
CTCGAAAGACTTACAGATGGACCGAAGAACTTACCAATTTTGGAAATAATTTAATAGGCAAGAAA
CTTTTATTACTTTTCAAAAATTTAAATTTCCAGATTTAAATGAGAAATGTTTCTCATTTTTCAAA
AAACATTGAAAAGCATTCTGCCCGAAGGTCTTATAAATGGCCCAAAGAACTCATCATCTTGCTCG
AAAGACTTACAGATGACCCGAAGGATTTAAGCATCAAGCTCGAAAGACTTACTGATGGCCCAAAG
GACTTACAAATTGTGGAAACAGTTTACTAGGAAAGAAACTTTTCTTACTTTTAAAAAATTTCAAT
TTTCAGATTTAAATGAGAAACATTTCTCATTTTTCGAAAAACATATGAAAACATCCTGCTCGAAG
GTCTTATGGATGGCCCGAAGGACTTATCATCTTG
Found at i:61732 original size:656 final size:651
Alignment explanation
Indices: 60678--61990 Score: 1878
Period size: 656 Copynumber: 2.0 Consensus size: 651
60668 AGGATTTAAG
* *
60678 CATCATGCGCGAAAGACTTATGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGC
1 CATCTTGCGCGAAAGACTTATGATGGCCCGAAGAACTTACCAATTTTGGAAATAGTTTACTAGGC
* * * *
60743 AAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAAAGTTTCACACTT
66 AAGAAACTTTTATTACTTTTCAAAAATTTAAATTTCCAGATTTAAATGAGAAAAGTTTCACACTT
* * *
60808 TTCGAAAAACATGTGAAAACATCTTGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATAT
131 TTCAAAAAACATGTGAAAACATCTTGCCCGAAGGTCTTATAAATGGCCCGAAGAACTTATCATAT
*
60873 TACTCGAAAGACTTACAGATGACCCGAAAGATTTAAGAATCATACTCGAAAGACTTACAGATGTA
196 TACTCGAAAGACTTACAGATGACCCGAAAGATTTAAGAATCATACTCGAAAGACTTACAGATGGA
* * * * * *
60938 CCTAAGGACTTATCAATTTTGGAAATAATTTAATAGGCAAGAAACTTTTTTTACTTTTCAAAAAT
261 CCAAAGGACTTACCAATTTTGGAAACAATTTAATAGGAAAGAAACTTTTCTTACTTTTAAAAAAT
* * *
61003 TTCAATTTTTAGATTTAAATGAGAAATTTTTCTCATTTTTTGAAAAACATTTAAAAGCATTCTGC
326 TTCAATTTTTAGATTTAAATGAGAAATTTTTCTCATTTTTCGAAAAACATTGAAAAGCATCCTGC
* **
61068 CCGAAGGTCTTGTGGATGGCCCAAAGGACTCATCATCTTGCTCGAAAGACTTACAGATGGCCCGA
391 CCGAAGGTCTTATGGATGGCCCAAAGGACTCATCATCTTGCTCGAAAGACTTACAGATAACCCGA
* * * * *
61133 AGGATTTAAGCATCAAGCTCGAAAGACTTACTGATGGCTCGAATGACTTACAAATTGTGGAAATT
456 AGGATTTAACCATCAAGCTCAAAAGAATTACTGATGGCCCGAATGACTTACAAATTGTGGAAATA
* *
61198 GTTTACTAGGTAAGAAACTTTTCTTATTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAAC
521 GTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAA-TTTCAGATTTAAATGAGAAAC
* * * * *
61263 ATTTCTCATTTTCGAAAAACATAT-ATAAACATCCTTCTC-GAAGGTCTTATGGATGGCCCGAAT
585 ATTTCTCA-TTT--AAAAAAATATGA-AAACATCATGC-CAGAAGGTCTTAGGGATGGCCCGAAG
61326 GACTTAT
645 GACTTAT
* *
61333 CATCTTGCTCGAAAGACTTACTGATGGCCCGAAGAACTTACCAATTTTGGAAATAGTTTATTAGG
1 CATCTTGCGCGAAAGACTTA-TGATGGCCCGAAGAACTTACCAATTTTGGAAATAGTTTACTAGG
* * ** * *
61398 TAATAAACTTTTATTACTTTTCAAAAATTTAAATTTCCAGATTTAAATGAGAATCGTTTCTCATT
65 CAAGAAACTTTTATTACTTTTCAAAAATTTAAATTTCCAGATTTAAATGAGAAAAGTTTCACACT
* *
61463 TTTCAAAAAATATGTGAAAACAT-TTGGCCCGAAGGTCTTATAAATGGCCCGAATAACTTATCAT
130 TTTCAAAAAACATGTGAAAACATCTT-GCCCGAAGGTCTTATAAATGGCCCGAAGAACTTATCAT
* * * * * * * * *
61527 CTTGCTCGAGAGTCTTACAGATGACCCGAAGGATTTAAGTATCATGCTCGAAATACTTACTGATG
194 ATTACTCGAAAGACTTACAGATGACCCGAAAGATTTAAGAATCATACTCGAAAGACTTACAGATG
* * *
61592 GCCCAAAGGACTTACCAATTTTGGAAACAGTTTACTAGGAAAGAAACTTTTCTTACTTTTAAAAA
259 GACCAAAGGACTTACCAATTTTGGAAACAATTTAATAGGAAAGAAACTTTTCTTACTTTTAAAAA
61657 ATTTCAATTTTTAGATTTAAATGAGAAATTTTTCTCATTTTTCGAAAAACATGTGAAAA-CATCC
324 ATTTCAATTTTTAGATTTAAATGAGAAATTTTTCTCATTTTTCGAAAAACAT-TGAAAAGCATCC
** * * * * *
61721 TGCTTGAAGGTCTTATGGATTGCCCGAAGGACTTATCATCTTGTTCGAAAGACTTACAGATAACT
388 TGCCCGAAGGTCTTATGGATGGCCCAAAGGACTCATCATCTTGCTCGAAAGACTTACAGATAACC
* * *
61786 CGAAGGATTTAACCATCATGCTCAAAAGAATTACTGATGGCCCGAATGACTTACCAATTTTGGAA
453 CGAAGGATTTAACCATCAAGCTCAAAAGAATTACTGATGGCCCGAATGACTTACAAATTGTGGAA
* *
61851 GTAGTTTACTAGGTAAGAAACTTTTTTTACTTTTCAAAAATTTCAATTTCAGATTTAAATGAGAA
518 ATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTCAGATTTAAATGAGAA
* *
61916 ACTTTTCTCATTTAAAAAAATATGAAAACATCATGCCATAAGGTCTTAGGGATGGCCCGAAGGAC
583 ACATTTCTCATTTAAAAAAATATGAAAACATCATGCCAGAAGGTCTTAGGGATGGCCCGAAGGAC
61981 TTAT
648 TTAT
*
61985 TATCTT
1 CATCTT
61991 TGGAAATAGT
Statistics
Matches: 582, Mismatches: 71, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
651 1 0.00
652 51 0.09
653 1 0.00
654 3 0.01
655 47 0.08
656 474 0.81
657 5 0.01
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (651 bp):
CATCTTGCGCGAAAGACTTATGATGGCCCGAAGAACTTACCAATTTTGGAAATAGTTTACTAGGC
AAGAAACTTTTATTACTTTTCAAAAATTTAAATTTCCAGATTTAAATGAGAAAAGTTTCACACTT
TTCAAAAAACATGTGAAAACATCTTGCCCGAAGGTCTTATAAATGGCCCGAAGAACTTATCATAT
TACTCGAAAGACTTACAGATGACCCGAAAGATTTAAGAATCATACTCGAAAGACTTACAGATGGA
CCAAAGGACTTACCAATTTTGGAAACAATTTAATAGGAAAGAAACTTTTCTTACTTTTAAAAAAT
TTCAATTTTTAGATTTAAATGAGAAATTTTTCTCATTTTTCGAAAAACATTGAAAAGCATCCTGC
CCGAAGGTCTTATGGATGGCCCAAAGGACTCATCATCTTGCTCGAAAGACTTACAGATAACCCGA
AGGATTTAACCATCAAGCTCAAAAGAATTACTGATGGCCCGAATGACTTACAAATTGTGGAAATA
GTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTCAGATTTAAATGAGAAACA
TTTCTCATTTAAAAAAATATGAAAACATCATGCCAGAAGGTCTTAGGGATGGCCCGAAGGACTTA
T
Found at i:61748 original size:233 final size:233
Alignment explanation
Indices: 61333--61990 Score: 828
Period size: 233 Copynumber: 2.8 Consensus size: 233
61323 AATGACTTAT
* * *
61333 CATCTTGCTCGAAAGACTTACTGATGGCCCGAAGAACTTACCAATTTTGGAAATAGTTTATTAGG
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGG
* * * *
61398 TAATAAACTTTTATTACTTTTCAAAAATTTAAATTTCCAGATTTAAATGAG-AATCGTTTCTCAT
66 TAAGAAACTTTTATTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAT-TTTTCTCAT
* * *
61462 TTTTCAAAAAATATGTGAAAACATTTGGCCCGAAGGTCTTATAAATGGCCCGAATAACTTATCAT
130 TTTTCAAAAAACATGTGAAAACATCTGGCCCGAAGGTCTTATAAATGGCCCGAAGAACTTATCAT
* * * *
61527 CTTGCTCGAGAGTCTTACAGATGACCCGAAGGATTTAAG
195 CTTGCTCGAAAGACTTACAGATAACCCGAAGGATTTAAC
* * * *
61566 TATCATGCTCGAAATACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAACAGTTTACTAGG
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGG
* * * *
61631 AAAGAAACTTTTCTTACTTTTAAAAAATTTCAATTTTTAGATTTAAATGAGAAATTTTTCTCATT
66 TAAGAAACTTTTATTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAATTTTTCTCATT
* ** ** * *
61696 TTTCGAAAAACATGTGAAAACATCCT-GCTTGAAGGTCTTATGGATTGCCCGAAGGACTTATCAT
131 TTTCAAAAAACATGTGAAAACAT-CTGGCCCGAAGGTCTTATAAATGGCCCGAAGAACTTATCAT
* *
61760 CTTGTTCGAAAGACTTACAGATAACTCGAAGGATTTAAC
195 CTTGCTCGAAAGACTTACAGATAACCCGAAGGATTTAAC
* * * *
61799 CATCATGCTCAAAAGAATTACTGATGGCCCGAATGACTTACCAATTTTGGAAGTAGTTTACTAGG
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGG
* *
61864 TAAGAAACTTTTTTTACTTTTCAAAAATTTCAA-TTTCAGATTTAAATGAGAAACTTTTCTCA--
66 TAAGAAACTTTTATTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAATTTTTCTCATT
* ** *** * *
61926 TTT-AAAAAA-ATATGAAAACATCAT-GCCATAAGGTCTTAGGGATGGCCCGAAGGACTTATTAT
131 TTTCAAAAAACATGTGAAAACATC-TGGCCCGAAGGTCTTATAAATGGCCCGAAGAACTTATCAT
61988 CTT
195 CTT
61991 TGGAAATAGT
Statistics
Matches: 370, Mismatches: 52, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
227 1 0.00
228 47 0.13
229 5 0.01
230 3 0.01
232 27 0.07
233 283 0.76
234 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (233 bp):
CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGG
TAAGAAACTTTTATTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAATTTTTCTCATT
TTTCAAAAAACATGTGAAAACATCTGGCCCGAAGGTCTTATAAATGGCCCGAAGAACTTATCATC
TTGCTCGAAAGACTTACAGATAACCCGAAGGATTTAAC
Found at i:72581 original size:111 final size:108
Alignment explanation
Indices: 72326--72608 Score: 342
Period size: 108 Copynumber: 2.6 Consensus size: 108
72316 TTGTTAATGT
* * * *
72326 TTAGCAGAG-TCCATACCATAATAATGTGGATCGTATCCTAGATC-AGGTCACCACAAAGTCGAA
1 TTAGCAGAGTTCGA-ACCATAATAATGTGGATCGTACCCCAGATCGA-GTCACCACAAGGTCGAA
*
72389 TAATAATTCAAACAAATTAATGAAAAAAATAAAAAAAGTTAGTGG
64 TAATAAATCAAACAAATTAATGAAAAAAATAAAAAAAGTTAGTGG
* *
72434 TTAGCAGAGTTCGAACCATAATAATGTGGATCGTACCCCATATTGAGTCACCACAAGGTCGAATA
1 TTAGCAGAGTTCGAACCATAATAATGTGGATCGTACCCCAGATCGAGTCACCACAAGGTCGAATA
*
72499 ATAAATCAATCAAATTAAT-AAAAATAATAAAAAAAATGGTTAG-GAG
66 ATAAATCAAACAAATTAATGAAAAA-AAT-AAAAAAA--GTTAGTG-G
* * * * *
72545 TTAGTAGAG-TCTGAACTATAATAATGTGGATTGTACCCCGGATCGGGTCACCACAAGGTCGAAT
1 TTAGCAGAGTTC-GAACCATAATAATGTGGATCGTACCCCAGATCGAGTCACCACAAGGTCGAAT
72609 CAAATATGAG
Statistics
Matches: 152, Mismatches: 15, Indels: 13
0.84 0.08 0.07
Matches are distributed among these distances:
107 5 0.03
108 73 0.48
109 11 0.07
110 3 0.02
111 60 0.39
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.25
Consensus pattern (108 bp):
TTAGCAGAGTTCGAACCATAATAATGTGGATCGTACCCCAGATCGAGTCACCACAAGGTCGAATA
ATAAATCAAACAAATTAATGAAAAAAATAAAAAAAGTTAGTGG
Found at i:78391 original size:12 final size:12
Alignment explanation
Indices: 78371--78403 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
78361 GACCAGACTT
*
78371 TTCTACACACCA
1 TTCTTCACACCA
78383 TTCTTCACACCA
1 TTCTTCACACCA
78395 TTCTTCACA
1 TTCTTCACA
78404 ATATTTCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.27, C:0.39, G:0.00, T:0.33
Consensus pattern (12 bp):
TTCTTCACACCA
Found at i:91853 original size:23 final size:24
Alignment explanation
Indices: 91827--91905 Score: 61
Period size: 24 Copynumber: 3.1 Consensus size: 24
91817 ATGAGAATAA
* *
91827 AATACTAAAC-ATAATTCCTAATT
1 AATACTAAACTAAAAATCCTAATT
*
91850 AATAGTAAACTAAAAATCCTAATT
1 AATACTAAACTAAAAATCCTAATT
* *
91874 GAAATTCTAAACAAACTAGAATCCTAATT
1 --AATACTAAACTAA--A-AATCCTAATT
91903 AAT
1 AAT
91906 TAAATAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
23 9 0.20
24 11 0.25
26 10 0.23
27 3 0.07
28 1 0.02
29 10 0.23
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.30
Consensus pattern (24 bp):
AATACTAAACTAAAAATCCTAATT
Found at i:93471 original size:21 final size:23
Alignment explanation
Indices: 93442--93489 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
93432 TTCATAACGT
*
93442 AAATGACAA-TCTTAA-CACTTCA
1 AAATGACAACTCTAAATC-CTTCA
93464 AAAT-ACAACTCTAAATCCTTCA
1 AAATGACAACTCTAAATCCTTCA
93486 AAAT
1 AAAT
93490 TCAAATCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.17
22 18 0.78
23 1 0.04
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (23 bp):
AAATGACAACTCTAAATCCTTCA
Found at i:94450 original size:2 final size:2
Alignment explanation
Indices: 94443--94500 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
94433 TCTAACCATA
94443 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
94485 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
94501 TCTTTCATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:95006 original size:159 final size:154
Alignment explanation
Indices: 94778--95083 Score: 420
Period size: 159 Copynumber: 2.0 Consensus size: 154
94768 TATGGTAGAT
* *** *
94778 GAGCATGTGGTTCAAATTTGTTAAAAAGGGACTTAAAATAAATCAAAAATTGAAGGAATAAAGAG
1 GAGCATGTGGCTCAAATTTGTTAAAAACAAACTTAAAATAAATCAAAAATTGAAGAAATAAAGAG
* *
94843 ATTATG-AAAATTGAAGGACTAAATTGAAAAATAAAAAAAATTGTTATCAAAA-AGAGGAATTGA
66 ATTATGAAAAACTAAAGGACTAAATTG-AAAAT-AAAAAAA-TGTTATCAAAATAGA--AATTGA
94906 AAGTACACATGTATTCTACTATCTTTAAG
126 AAGTACACATGTATTCTACTATCTTTAAG
* **
94935 GAGCATGTGGCTCAAATTTGGTTAAAATACAAACTTAAAATAAATGATGAATTGAAGAAAT-AAG
1 GAGCATGTGGCTCAAATTT-GTTAAAA-ACAAACTTAAAATAAATCAAAAATTGAAGAAATAAAG
*
94999 TAGATTATGAAAAACTAAAGGACTAAATTGAAAATTAAAAAATGTTATCAAAATAGAAATTGAAA
64 -AGATTATGAAAAACTAAAGGACTAAATTGAAAATAAAAAAATGTTATCAAAATAGAAATTGAAA
95064 GTACACATGTATTCTACTAT
128 GTACACATGTATTCTACTAT
95084 AGTGTAGAAT
Statistics
Matches: 133, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
156 28 0.21
157 29 0.22
158 19 0.14
159 39 0.29
160 18 0.14
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.28
Consensus pattern (154 bp):
GAGCATGTGGCTCAAATTTGTTAAAAACAAACTTAAAATAAATCAAAAATTGAAGAAATAAAGAG
ATTATGAAAAACTAAAGGACTAAATTGAAAATAAAAAAATGTTATCAAAATAGAAATTGAAAGTA
CACATGTATTCTACTATCTTTAAG
Found at i:95118 original size:156 final size:156
Alignment explanation
Indices: 94779--95144 Score: 411
Period size: 156 Copynumber: 2.3 Consensus size: 156
94769 ATGGTAGATG
* ** *** * * *
94779 AGCATGTGGTTCAAATTTGTTAAAAAGGGACTTAAAATAAATCAAAAATTGAAGGAATAAAGAGA
1 AGCATGTGGCTCAAATTTGGGAAAAATAAACTTAAAATAAATGAAGAATTGAAGAAATAAAGAGA
* *
94844 TTATGAAAATTGAAGGACTAAATTGAAAAATAAAAAAAATTGTTATCAAAAAGAGGAATTGAAAG
66 TTATGAAAACTAAAGGACTAAATTGAAAAATAAAAAAAATTGTTATCAAAAAGA-GAATTGAAAG
* *
94909 TACACATGTATTCTACTATCTTTAAGG
130 TACACATGTATTCTACTATCTGTAAGA
* * *
94936 AGCATGTGGCTCAAATTTGGTTAAAATACAAACTTAAAATAAATGATGAATTGAAGAAAT-AAGT
1 AGCATGTGGCTCAAATTTGG-GAAAA-ATAAACTTAAAATAAATGAAGAATTGAAGAAATAAAG-
*
95000 AGATTATGAAAAACTAAAGGACTAAATTG-AAAAT-TAAAAAA-TGTTATCAAAATAGA-AATTG
63 AGATTATG-AAAACTAAAGGACTAAATTGAAAAATAAAAAAAATTGTTATCAAAA-AGAGAATTG
*
95061 AAAGTACACATGTATTCTACTATAGTGT-AGA
126 AAAGTACACATGTATTCTACTAT-CTGTAAGA
* * * * * *
95092 ATCATGTGGTTCAAATTTGGGAAAAATAGACCTAAAATGAATGAGGAATTGAA
1 AGCATGTGGCTCAAATTTGGGAAAAATAAACTTAAAATAAATGAAGAATTGAA
95145 AAAAAATAAT
Statistics
Matches: 180, Mismatches: 23, Indels: 15
0.83 0.11 0.07
Matches are distributed among these distances:
154 23 0.13
155 4 0.02
156 48 0.27
157 31 0.17
158 17 0.09
159 39 0.22
160 18 0.10
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (156 bp):
AGCATGTGGCTCAAATTTGGGAAAAATAAACTTAAAATAAATGAAGAATTGAAGAAATAAAGAGA
TTATGAAAACTAAAGGACTAAATTGAAAAATAAAAAAAATTGTTATCAAAAAGAGAATTGAAAGT
ACACATGTATTCTACTATCTGTAAGA
Found at i:96154 original size:2 final size:2
Alignment explanation
Indices: 96147--96183 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
96137 ATGGTCAATA
96147 AT AT AT AT 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 AT AT AT AT A
96184 AAGTTCCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:109159 original size:17 final size:18
Alignment explanation
Indices: 109131--109166 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
109121 ATTGAATTTT
*
109131 TTAAATAATAATAATATA
1 TTAAATAATAATAAAATA
109149 TTAAA-AATAATAAAATA
1 TTAAATAATAATAAAATA
109166 T
1 T
109167 ATAACGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TTAAATAATAATAAAATA
Found at i:109371 original size:19 final size:19
Alignment explanation
Indices: 109347--109394 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
109337 GTCTACAATG
109347 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
109366 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
109385 TCGTTGCGAT
1 TCGTTGCGAT
109395 AGTTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:109497 original size:5 final size:5
Alignment explanation
Indices: 109481--109523 Score: 70
Period size: 5 Copynumber: 8.6 Consensus size: 5
109471 ACCACAACCA
109481 CGACC ACGACC CGACC CGACC CGACC CGACC C-ACC CGACC CGA
1 CGACC -CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGA
109524 GACGAGACGA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.11
5 27 0.75
6 5 0.14
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:109507 original size:15 final size:15
Alignment explanation
Indices: 109481--109523 Score: 70
Period size: 14 Copynumber: 2.9 Consensus size: 15
109471 ACCACAACCA
109481 CGACCACGACCCGACC
1 CGACC-CGACCCGACC
109497 CGACCCGACCCGACC
1 CGACCCGACCCGACC
109512 C-ACCCGACCCGA
1 CGACCCGACCCGA
109524 GACGAGACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 11 0.41
15 11 0.41
16 5 0.19
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (15 bp):
CGACCCGACCCGACC
Found at i:109529 original size:5 final size:5
Alignment explanation
Indices: 109521--109550 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
109511 CCACCCGACC
109521 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA
109551 TGGACGGACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:109921 original size:38 final size:39
Alignment explanation
Indices: 109871--109963 Score: 156
Period size: 38 Copynumber: 2.5 Consensus size: 39
109861 CCTGAATAAT
109871 CACA-TGTA-TGGAAACAAGTGTTGGTAATGCTC-ATCC
1 CACATTGTATTGGAAACAAGTGTTGGTAATGCTCAATCC
109907 CACATTGTATTGGAAACAAGTGTTGGTAATGCTCAATCC
1 CACATTGTATTGGAAACAAGTGTTGGTAATGCTCAATCC
*
109946 CACATAGTATTGGAAACA
1 CACATTGTATTGGAAACA
109964 CTATTGAGAA
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
36 4 0.08
37 4 0.08
38 24 0.45
39 21 0.40
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (39 bp):
CACATTGTATTGGAAACAAGTGTTGGTAATGCTCAATCC
Done.