Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 314 of 322
Found at i:104148702 original size:38 final size:39
Alignment explanation
Indices: 104148660--104148763 Score: 90
Period size: 38 Copynumber: 2.7 Consensus size: 39
104148650 AGTTCGAAGC
*
104148660 AAAGTTGACACCTAGTGTCTCATCG-GCCTAGCCAAAGT
1 AAAGTTGACACCTAGTGTCTCATCGAACCTAGCCAAAGT
* * * *
104148698 AAAGTGGTAC-CC-AGT-ACTTCATCGAATCTATCCAAAGT
1 AAAGTTG-ACACCTAGTGTC-TCATCGAACCTAGCCAAAGT
*
104148736 AAAATAGTGACACCTAGTGTCTCATCGA
1 AAAGT--TGACACCTAGTGTCTCATCGA
104148764 CTCGAGGTCG
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
36 1 0.02
37 9 0.18
38 22 0.44
39 4 0.08
40 3 0.06
41 10 0.20
42 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (39 bp):
AAAGTTGACACCTAGTGTCTCATCGAACCTAGCCAAAGT
Found at i:104154199 original size:18 final size:19
Alignment explanation
Indices: 104154164--104154206 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
104154154 TATTATTACC
* *
104154164 TTATTATCTATTATTTTA-
1 TTATCATCTATTAGTTTAT
*
104154182 TTATCATCTATTCGTTTAT
1 TTATCATCTATTAGTTTAT
104154201 TTATCA
1 TTATCA
104154207 CTCTTTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.26, C:0.12, G:0.02, T:0.60
Consensus pattern (19 bp):
TTATCATCTATTAGTTTAT
Found at i:104154283 original size:3 final size:3
Alignment explanation
Indices: 104154261--104154302 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
104154251 TTTTTAAACC
* *
104154261 TAT TAT CAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
104154303 ATTTTCTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:104154784 original size:10 final size:11
Alignment explanation
Indices: 104154766--104154798 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
104154756 TTTCTTCACA
104154766 TACATTTATTT
1 TACATTTATTT
104154777 TA-ATTTATTT
1 TACATTTATTT
104154787 TACCATTTATTT
1 TA-CATTTATTT
104154799 ATATCCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 2 0.10
12 8 0.40
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (11 bp):
TACATTTATTT
Found at i:104156267 original size:25 final size:25
Alignment explanation
Indices: 104156226--104156312 Score: 104
Period size: 25 Copynumber: 3.5 Consensus size: 25
104156216 TAATAATCAC
*
104156226 AAAAAATGAAACA-AAATAATATATA
1 AAAAAATTAAA-ATAAATAATATATA
* *
104156251 AAAAAATTAAAGTAAATAATATACA
1 AAAAAATTAAAATAAATAATATATA
**
104156276 AAAAGTTTAAAATAAATAATATATA
1 AAAAAATTAAAATAAATAATATATA
*
104156301 AAAAAATAAAAA
1 AAAAAATTAAAA
104156313 ATATATAAGA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.23
Consensus pattern (25 bp):
AAAAAATTAAAATAAATAATATATA
Found at i:104156308 original size:19 final size:19
Alignment explanation
Indices: 104156284--104156344 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
104156274 CAAAAAGTTT
104156284 AAAATAAATAATATATAAA
1 AAAATAAATAATATATAAA
*
104156303 AAAATAAAAAATATATAAGA
1 AAAATAAATAATATATAA-A
**
104156323 CAATTTCAAATAATATATAAA
1 -AAAAT-AAATAATATATAAA
104156344 A
1 A
104156345 GTTTAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 17 0.49
20 2 0.06
21 4 0.11
22 12 0.34
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAATAAATAATATATAAA
Found at i:104156347 original size:65 final size:72
Alignment explanation
Indices: 104156303--104156448 Score: 152
Period size: 72 Copynumber: 1.9 Consensus size: 72
104156293 AATATATAAA
* * * * *
104156303 AAAATAAAAAATATATAAGACAATTT-CAAATAATATATAAAAGTTTAAAATAAATTATGTA-AA
1 AAAATAAATAATATA-AAAACAATTTAAAAATAATATATAAAAGTTTAAAATAAATAATATATAA
104156366 AATAAATTT
65 AATAAA-TT
104156375 AAAATAAATAATATACAAAACAATTTAAAAATAAATAATACATATAACAGTTTAAAATAAATAAT
1 AAAATAAATAATATA-AAAACAATTTAAAAAT-AAT-AT--ATA-AA-AGTTTAAAATAAATAAT
104156440 ATATAAAAT
59 ATATAAAAT
104156449 TTAAAATGGA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
72 23 0.38
73 4 0.07
74 3 0.05
75 2 0.03
77 3 0.05
78 2 0.03
79 18 0.30
80 5 0.08
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (72 bp):
AAAATAAATAATATAAAAACAATTTAAAAATAATATATAAAAGTTTAAAATAAATAATATATAAA
ATAAATT
Found at i:104156376 original size:91 final size:92
Alignment explanation
Indices: 104156239--104156412 Score: 226
Period size: 91 Copynumber: 1.9 Consensus size: 92
104156229 AAATGAAACA
* * * *
104156239 AAATAATATATAAAAAAATTAAAGTAAATAATATACAAAAAGTTTAAAATAAATAATATATAAAA
1 AAATAATATATAAAAAAATTAAAATAAATAATATAAAAAAAATTTAAAATAAATAATATACAAAA
*
104156304 -AAATAAAAAATATATAAGACAATTTC
66 CAAATAAAAAATAAATAAGACAATTTC
** * *
104156330 AAATAATATAT-AAAAGTTTAAAATAAATTATGTAAAAATAAATTTAAAATAAATAATATACAAA
1 AAATAATATATAAAAAAATTAAAATAAATAATATAAAAA-AAATTTAAAATAAATAATATACAAA
* *
104156394 ACAATTTAAAAATAAATAA
65 ACAAATAAAAAATAAATAA
104156413 TACATATAAC
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
90 21 0.30
91 35 0.50
92 14 0.20
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (92 bp):
AAATAATATATAAAAAAATTAAAATAAATAATATAAAAAAAATTTAAAATAAATAATATACAAAA
CAAATAAAAAATAAATAAGACAATTTC
Found at i:104156405 original size:27 final size:26
Alignment explanation
Indices: 104156330--104156536 Score: 160
Period size: 26 Copynumber: 8.1 Consensus size: 26
104156320 AGACAATTTC
*
104156330 AAATAATATAT-AAA-AGTTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
* * *
104156354 AAATTATGTA-AAAATAAATTTAAAAT
1 AAATAATATATAAAA-CAATTTAAAAT
*
104156380 AAATAATATACAAAACAATTTAAAAAT
1 AAATAATATATAAAACAATTT-AAAAT
* * *
104156407 AAATAATACATATAACAGTTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
104156433 AAATAATATAT--AA-AATTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
** * * * *
104156456 GGATAATAGTTTGAAATAGTTTAAAAT
1 AAATAATA-TATAAAACAATTTAAAAT
* * * *
104156483 ACATAATATGTGAAAA-AACTTAAAGT
1 AAATAATATAT-AAAACAATTTAAAAT
104156509 AAATAATA-ATAAAACAATTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
104156534 AAA
1 AAA
104156537 AAATGTATGA
Statistics
Matches: 145, Mismatches: 27, Indels: 21
0.75 0.14 0.11
Matches are distributed among these distances:
23 15 0.10
24 19 0.13
25 12 0.08
26 55 0.38
27 44 0.30
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.31
Consensus pattern (26 bp):
AAATAATATATAAAACAATTTAAAAT
Found at i:104159204 original size:93 final size:93
Alignment explanation
Indices: 104159032--104159204 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
104159022 TTGCTATGCA
104159032 ATTGCTGGCCCTTCACGTCTCTGCAACTGCTCCCTGCTGCTATTATTTTTTGTTTTTTCGACAAC
1 ATTGCTGGCCCTTCACGTCTCTGCAACTGCTCCCTGCTGCTATTATTTTTTGTTTTTTCGACAAC
* *
104159097 TGGTGGTTGCTGCAACTGGTTCTACTCT
66 TGGTAGCTGCTGCAACTGGTTCTACTCT
* * * * *
104159125 ATTGCTGGCTCTTCACGTCTTTGCAACTGCTCCCTGCTGCTATTATTTTTTGTTTTTTGGGCAAT
1 ATTGCTGGCCCTTCACGTCTCTGCAACTGCTCCCTGCTGCTATTATTTTTTGTTTTTTCGACAAC
*
104159190 TGGTAGCTGTTGCAA
66 TGGTAGCTGCTGCAA
104159205 TTGTTGGTTG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.42
Consensus pattern (93 bp):
ATTGCTGGCCCTTCACGTCTCTGCAACTGCTCCCTGCTGCTATTATTTTTTGTTTTTTCGACAAC
TGGTAGCTGCTGCAACTGGTTCTACTCT
Found at i:104174245 original size:50 final size:51
Alignment explanation
Indices: 104174159--104174258 Score: 148
Period size: 50 Copynumber: 2.0 Consensus size: 51
104174149 TGTACTAGTG
* *
104174159 TTGCCAAAATCGAGCCATTTTGGGGTGGACCAGGGCATCCTACTAAAGACA
1 TTGCCAAAATCGAGCCATTTTGGGGTGGACCAGGGCAGCCCACTAAAGACA
* * *
104174210 TTGCCAAAATCGAGCGA-TTTGGGGTTGATCAGGGCAGCCCACTAAAGAC
1 TTGCCAAAATCGAGCCATTTTGGGGTGGACCAGGGCAGCCCACTAAAGAC
104174259 GCCGATGTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 28 0.64
51 16 0.36
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (51 bp):
TTGCCAAAATCGAGCCATTTTGGGGTGGACCAGGGCAGCCCACTAAAGACA
Found at i:104180372 original size:21 final size:20
Alignment explanation
Indices: 104180346--104180418 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 20
104180336 ACATATATGT
104180346 ATAATAATGATGAAAATAATA
1 ATAATAAT-ATGAAAATAATA
104180367 ATAATAATAGTGAAAATAAATA
1 ATAATAATA-TGAAAAT-AATA
104180389 AT-ATAATAAT-AAATATAATA
1 ATAATAAT-ATGAAA-ATAATA
* *
104180409 GTAACAATAT
1 ATAATAATAT
104180419 TAGTAATATG
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
20 11 0.24
21 27 0.60
22 7 0.16
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (20 bp):
ATAATAATATGAAAATAATA
Found at i:104180390 original size:16 final size:15
Alignment explanation
Indices: 104180361--104180403 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
104180351 AATGATGAAA
104180361 ATAATAAT-AATAAT
1 ATAATAATAAATAAT
104180375 AGTGAA-AATAAATAAT
1 A-T-AATAATAAATAAT
104180391 ATAATAATAAATA
1 ATAATAATAAATA
104180404 TAATAGTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.12
15 13 0.52
16 9 0.36
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (15 bp):
ATAATAATAAATAAT
Found at i:104182787 original size:9 final size:8
Alignment explanation
Indices: 104182775--104182888 Score: 51
Period size: 9 Copynumber: 13.9 Consensus size: 8
104182765 ATAAATATGC
104182775 TAATATGAA
1 TAATAT-AA
104182784 TAATGATAA
1 TAAT-ATAA
104182793 TAATACTAA
1 TAATA-TAA
104182802 TAATAATAA
1 TAAT-ATAA
* *
104182811 TAAAATAC
1 TAATATAA
* * *
104182819 GAAGA-AG
1 TAATATAA
104182826 TATATATAA
1 TA-ATATAA
104182835 T-ATAATAA
1 TAAT-ATAA
104182843 TAATATTAA
1 TAATA-TAA
104182852 -AATATAA
1 TAATATAA
104182859 TAAT-TAA
1 TAATATAA
104182866 -AA-ATAA
1 TAATATAA
*
104182872 TATTATATA
1 TAATATA-A
104182881 TAAATATA
1 T-AATATA
104182889 TACAATATTC
Statistics
Matches: 81, Mismatches: 10, Indels: 27
0.69 0.08 0.23
Matches are distributed among these distances:
6 5 0.06
7 11 0.14
8 25 0.31
9 32 0.40
10 8 0.10
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (8 bp):
TAATATAA
Found at i:104182797 original size:3 final size:3
Alignment explanation
Indices: 104182782--104182873 Score: 59
Period size: 3 Copynumber: 31.3 Consensus size: 3
104182772 TGCTAATATG
* * ** *
104182782 AAT AAT GAT AAT AAT ACT AAT AAT AAT AAT AA- AAT ACG AAG AAGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
* *
104182827 -AT ATAT AAT -AT AAT AAT AAT ATT AA- AAT -AT AAT AATT AAA AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
104182870 AAT A
1 AAT A
104182874 TTATATATAA
Statistics
Matches: 69, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
2 9 0.13
3 54 0.78
4 6 0.09
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:104182856 original size:26 final size:25
Alignment explanation
Indices: 104182827--104182888 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
104182817 ACGAAGAAGT
*
104182827 ATATATAATATAATAATAATATTAA
1 ATATATAATATAAAAATAATATTAA
*
104182852 A-ATATAATAATTAAAAATAATATTAT
1 ATATATAAT-A-TAAAAATAATATTAA
104182878 ATATA-AATATA
1 ATATATAATATA
104182889 TACAATATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
24 9 0.28
25 3 0.09
26 17 0.53
27 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATATATAATATAAAAATAATATTAA
Found at i:104182858 original size:16 final size:16
Alignment explanation
Indices: 104182839--104182888 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 16
104182829 ATATAATATA
104182839 ATAATAATATTAAAAT
1 ATAATAATATTAAAAT
104182855 ATAAT-A-ATTAAAA-
1 ATAATAATATTAAAAT
*
104182868 ATAATATTATATATAAAT
1 ATAATAATAT-TA-AAAT
104182886 ATA
1 ATA
104182889 TACAATATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
13 5 0.18
14 7 0.25
15 3 0.11
16 7 0.25
17 3 0.11
18 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAATAATATTAAAAT
Found at i:104182860 original size:13 final size:12
Alignment explanation
Indices: 104182831--104182876 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
104182821 AGAAGTATAT
*
104182831 ATAATA-TAATA
1 ATAATATTAAAA
104182842 ATAATATTAAAA
1 ATAATATTAAAA
104182854 TATAATAATTAAAA
1 -ATAAT-ATTAAAA
104182868 ATAATATTA
1 ATAATATTA
104182877 TATATAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
11 6 0.19
12 8 0.26
13 10 0.32
14 7 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAATATTAAAA
Found at i:104183446 original size:20 final size:19
Alignment explanation
Indices: 104183423--104183468 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
104183413 AGGAAGAGGA
*
104183423 GGGAGAGAAAAGAGGGAGCG
1 GGGAGAGAAAAGAGGG-GAG
* *
104183443 GGGAAAGAAGAGAGGGGAG
1 GGGAGAGAAAAGAGGGGAG
104183462 GGGAGAG
1 GGGAGAG
104183469 CTCCGGCCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.39, C:0.02, G:0.59, T:0.00
Consensus pattern (19 bp):
GGGAGAGAAAAGAGGGGAG
Found at i:104184091 original size:22 final size:22
Alignment explanation
Indices: 104184034--104184091 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
104184024 TACGAGGACT
* *
104184034 GTGGAGGTATGGGACTGTTGTA
1 GTGGGGGTATGGGGCTGTTGTA
104184056 GTGGGGGTATGGGGCTGTTGTA
1 GTGGGGGTATGGGGCTGTTGTA
104184078 GTGGGGGTATGGGG
1 GTGGGGGTATGGGG
104184092 TTGCTTCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.12, C:0.03, G:0.55, T:0.29
Consensus pattern (22 bp):
GTGGGGGTATGGGGCTGTTGTA
Found at i:104190614 original size:46 final size:46
Alignment explanation
Indices: 104190547--104190636 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
104190537 ACCATCTTGG
* *
104190547 ATCATATATGATGTGGAAATTAATTGAGAATTCATATAAACATTGA
1 ATCATATATAATGCGGAAATTAATTGAGAATTCATATAAACATTGA
104190593 ATCATATATAATGCGGAAATTAATTGAGAATTCATATAAACATT
1 ATCATATATAATGCGGAAATTAATTGAGAATTCATATAAACATT
104190637 CATTAAAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.34
Consensus pattern (46 bp):
ATCATATATAATGCGGAAATTAATTGAGAATTCATATAAACATTGA
Found at i:104192818 original size:13 final size:13
Alignment explanation
Indices: 104192800--104192826 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
104192790 TTTAAATTTT
104192800 AATAGTAATTAGA
1 AATAGTAATTAGA
104192813 AATAGTAATTAGA
1 AATAGTAATTAGA
104192826 A
1 A
104192827 GTAGATCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (13 bp):
AATAGTAATTAGA
Found at i:104195378 original size:21 final size:20
Alignment explanation
Indices: 104195354--104195392 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
104195344 TGGAGGAGAG
*
104195354 GAAGATAGGTTTAGTGAGAAT
1 GAAGATAGGGTTAG-GAGAAT
104195375 GAAGATAGGGTTAGGAGA
1 GAAGATAGGGTTAGGAGA
104195393 CCTCCTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (20 bp):
GAAGATAGGGTTAGGAGAAT
Found at i:104196522 original size:22 final size:22
Alignment explanation
Indices: 104196490--104196531 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
104196480 TCAGGACAAT
104196490 AAACACGAGTTTTAATATGAAA
1 AAACACGAGTTTTAATATGAAA
*
104196512 AAACACTAGTTTTAATATGA
1 AAACACGAGTTTTAATATGA
104196532 CAACTCCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.31
Consensus pattern (22 bp):
AAACACGAGTTTTAATATGAAA
Found at i:104196734 original size:23 final size:21
Alignment explanation
Indices: 104196698--104196755 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 21
104196688 TGGAGTTTTT
104196698 TTGTGGCATTCTGTATAGCCA
1 TTGTGGCATTCTGTATAGCCA
**
104196719 TTGTGGCGTATTCTGTATAGCTT
1 TTGTGGC--ATTCTGTATAGCCA
*
104196742 TTGTGACATTCTGT
1 TTGTGGCATTCTGT
104196756 TAACCTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 14 0.44
23 18 0.56
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.45
Consensus pattern (21 bp):
TTGTGGCATTCTGTATAGCCA
Found at i:104198684 original size:34 final size:35
Alignment explanation
Indices: 104198629--104198695 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
104198619 AGTTGTTTTC
104198629 TGATTATTTGATTTTTACAGAAATTTTACAAAAAT
1 TGATTATTTGATTTTTACAGAAATTTTACAAAAAT
*
104198664 TGATTGTTTGA-TTTTACAGAAATTTTACAAAA
1 TGATTATTTGATTTTTACAGAAATTTTACAAAA
104198696 TTTTTAATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 21 0.68
35 10 0.32
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (35 bp):
TGATTATTTGATTTTTACAGAAATTTTACAAAAAT
Found at i:104201614 original size:18 final size:18
Alignment explanation
Indices: 104201591--104201643 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
104201581 GAAAATGTGA
104201591 TAAATGATGTTCACATTT
1 TAAATGATGTTCACATTT
*
104201609 TAAATGGTGTTCACATTT
1 TAAATGATGTTCACATTT
*
104201627 CAAATGATGTTCACATT
1 TAAATGATGTTCACATT
104201644 GATGGAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (18 bp):
TAAATGATGTTCACATTT
Found at i:104202144 original size:72 final size:72
Alignment explanation
Indices: 104202068--104202404 Score: 412
Period size: 72 Copynumber: 4.7 Consensus size: 72
104202058 CAATGCTAAA
*
104202068 CTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTAAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTAAATTTATGTTCTACTTATTTAT
104202133 GTGTAAT
66 GTGTAAT
* * *
104202140 CTAGTTTTATCAATGGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATATTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTAAATTTATGTTCTACTTATTTAT
104202205 GTGTAAT
66 GTGTAAT
* * * * * * *
104202212 CTAGTTTTATTAATAGTTGTTTATATTTGGTCTTTGGATACTGAATTTATGGTCTAATTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTAAATTTATGTTCTACTTATTTAT
**
104202277 GCT-TAGGG
66 G-TGTA-AT
* *
104202285 CTAGTTTTATCAATAATTGTTTATGTTTGATTTTTGGATATTAAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTAAATTTATGTTCTACTTATTTAT
* *
104202350 ACT-AAAT
66 -GTGTAAT
* * * * * *
104202357 -TATTTTTATCAATAATTGTTTATATAT-GATTTTGGATATAAAATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTAAATTTAT
104202405 TCACAGGTGA
Statistics
Matches: 229, Mismatches: 33, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
70 18 0.08
71 24 0.10
72 128 0.56
73 59 0.26
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTAAATTTATGTTCTACTTATTTAT
GTGTAAT
Found at i:104203491 original size:3 final size:3
Alignment explanation
Indices: 104203438--104203478 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
104203428 GTGGAGAAAG
* * *
104203438 TGA TGA TGA TGA TGA TGA CGA CGA TGA TGA TGG TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
104203479 GCGGTGATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.29, C:0.05, G:0.37, T:0.29
Consensus pattern (3 bp):
TGA
Found at i:104203798 original size:22 final size:23
Alignment explanation
Indices: 104203762--104203804 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
104203752 AAAATGTGTT
104203762 AAAATCATTAATAAAA-AATAAA
1 AAAATCATTAATAAAATAATAAA
**
104203784 AAAATCATTTTTAAAATAATA
1 AAAATCATTAATAAAATAATA
104203805 CAATTGTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (23 bp):
AAAATCATTAATAAAATAATAAA
Found at i:104204133 original size:13 final size:13
Alignment explanation
Indices: 104204117--104204156 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
104204107 TTTAAACTAA
104204117 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
104204130 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
*
104204143 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
104204156 A
1 A
104204157 TGCCAAACTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:104211845 original size:28 final size:28
Alignment explanation
Indices: 104211763--104211908 Score: 231
Period size: 28 Copynumber: 5.1 Consensus size: 28
104211753 TGAGCATGAC
104211763 TATAAATGTGAATTGGGCCT-GATGGGCCA
1 TATAAATGTG-ATTGGGCCTAG-TGGGCCA
* *
104211792 TATAAATGTGATTTGGGCCTAATGGGCTA
1 TATAAATGTGA-TTGGGCCTAGTGGGCCA
104211821 TATAAATGTGATTGGGCCTAGTGGGCCA
1 TATAAATGTGATTGGGCCTAGTGGGCCA
*
104211849 TATAAATGTGACTGGGCCTAGTGGGCCA
1 TATAAATGTGATTGGGCCTAGTGGGCCA
104211877 TATAAATGTGATTGGGCCTAGTGGGCCA
1 TATAAATGTGATTGGGCCTAGTGGGCCA
104211905 TATA
1 TATA
104211909 CAGGTATGTG
Statistics
Matches: 109, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
28 74 0.68
29 35 0.32
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (28 bp):
TATAAATGTGATTGGGCCTAGTGGGCCA
Found at i:104215533 original size:16 final size:16
Alignment explanation
Indices: 104215512--104215547 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
104215502 AAAAGCAAAG
*
104215512 GAGAAAAATGTTTTTA
1 GAGAAAAATGTTTTCA
104215528 GAGAAAAATGTTTTCA
1 GAGAAAAATGTTTTCA
104215544 GAGA
1 GAGA
104215548 GGGTTGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (16 bp):
GAGAAAAATGTTTTCA
Found at i:104224737 original size:44 final size:45
Alignment explanation
Indices: 104224702--104224812 Score: 125
Period size: 45 Copynumber: 2.5 Consensus size: 45
104224692 TTATAGCTTT
* * *
104224702 AATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTGTCATG
1 AATCTACTCCACTGCAACTTCAGAGAGATAAGATTTGATGTCATG
* * * * *
104224747 AGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTG-TGACTTC
1 AATCTACTCCACTGCAACTTCAGAGAGATAAGATTTGATGTCATG
* *
104224791 AATCAACTCCACTGAAACTTCA
1 AATCTACTCCACTGCAACTTCA
104224813 AGGAGATCTA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
44 23 0.41
45 33 0.59
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (45 bp):
AATCTACTCCACTGCAACTTCAGAGAGATAAGATTTGATGTCATG
Found at i:104225460 original size:66 final size:66
Alignment explanation
Indices: 104225372--104225511 Score: 199
Period size: 66 Copynumber: 2.1 Consensus size: 66
104225362 ACTAGATGTG
** * * * *
104225372 ATGAATGTGTCAAATAATTAGGATGGTATGATCGAAATGAATTAAATGCTCTTAATTAAACGTGT
1 ATGAATGAATCAAATAACTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAATTAAACGTGT
104225437 T
66 T
* * *
104225438 ATGAATGAATCAAATAACTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAATTAGATGTGT
1 ATGAATGAATCAAATAACTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAATTAAACGTGT
104225503 T
66 T
104225504 ATGAATGA
1 ATGAATGA
104225512 TGTATGAATG
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (66 bp):
ATGAATGAATCAAATAACTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAATTAAACGTGT
T
Found at i:104233492 original size:19 final size:20
Alignment explanation
Indices: 104233464--104233505 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
104233454 GTCTTTTCGC
* *
104233464 GAAATTTAATGCACATG-AT
1 GAAATGTAATGCAAATGAAT
104233483 GAAATGTAATGCAAATGAAT
1 GAAATGTAATGCAAATGAAT
104233503 GAA
1 GAA
104233506 TACAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (20 bp):
GAAATGTAATGCAAATGAAT
Found at i:104241008 original size:18 final size:19
Alignment explanation
Indices: 104240967--104241008 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
104240957 AACTTACAAA
*
104240967 AAAAATTCAAAAAAATTTT
1 AAAAATTCAAAAAAATTCT
*
104240986 TAAAA-TCAAAAAAATTCT
1 AAAAATTCAAAAAAATTCT
104241004 AAAAA
1 AAAAA
104241009 ATATATAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAATTCAAAAAAATTCT
Found at i:104241039 original size:9 final size:9
Alignment explanation
Indices: 104240965--104241042 Score: 50
Period size: 9 Copynumber: 8.1 Consensus size: 9
104240955 AAAACTTACA
104240965 AAAAAAATT
1 AAAAAAATT
104240974 CAAAAAAATT
1 -AAAAAAATT
*** *
104240984 TTTAAAATC
1 AAAAAAATT
104240993 AAAAAAATTCT
1 AAAAAAA-T-T
104241004 AAAAAATATAT
1 AAAAAA-AT-T
*
104241015 AAAGAAAGTT
1 AAA-AAAATT
104241025 -AAAAAATT
1 AAAAAAATT
104241033 AAAAAAATT
1 AAAAAAATT
104241042 A
1 A
104241043 TTAAATAATA
Statistics
Matches: 52, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
8 5 0.10
9 20 0.38
10 11 0.21
11 12 0.23
12 4 0.08
ACGTcount: A:0.68, C:0.04, G:0.03, T:0.26
Consensus pattern (9 bp):
AAAAAAATT
Found at i:104242177 original size:25 final size:27
Alignment explanation
Indices: 104242124--104242178 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
104242114 AATTAATCAA
* * *
104242124 TTTTATTTAAGTTTAATTATAAAATAT
1 TTTTAATTAAGTTTAATAATAAAACAT
104242151 TTTTAATTAA-TTTAA-AATAAAACAT
1 TTTTAATTAAGTTTAATAATAAAACAT
104242176 TTT
1 TTT
104242179 GCAACGGTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.44
26 5 0.20
27 9 0.36
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
TTTTAATTAAGTTTAATAATAAAACAT
Found at i:104243270 original size:2 final size:2
Alignment explanation
Indices: 104243265--104243302 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
104243255 TATATATATT
*
104243265 AG AG AG AG AG AG AG AT AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
104243303 TTAGGTTAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:104248078 original size:3 final size:3
Alignment explanation
Indices: 104248070--104248115 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
104248060 GGTCAATCAA
104248070 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
104248116 GTAGTATTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:104250899 original size:21 final size:20
Alignment explanation
Indices: 104250866--104250905 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
104250856 AACTAAACTA
* *
104250866 AGAATAAGGAACAATTAAAG
1 AGAAGAAGGAACAACTAAAG
104250886 AGAAGAAGAGAACAACTAAA
1 AGAAGAAG-GAACAACTAAA
104250906 ATAGTCGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.62, C:0.07, G:0.20, T:0.10
Consensus pattern (20 bp):
AGAAGAAGGAACAACTAAAG
Found at i:104260435 original size:14 final size:14
Alignment explanation
Indices: 104260416--104260443 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
104260406 ATCTGATAAA
104260416 TCTGTATCTGATTT
1 TCTGTATCTGATTT
104260430 TCTGTATCTGATTT
1 TCTGTATCTGATTT
104260444 GGGGTGGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
TCTGTATCTGATTT
Found at i:104261870 original size:15 final size:16
Alignment explanation
Indices: 104261850--104261886 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
104261840 ATAAAAGTAT
104261850 AATAAAATAT-TAAAA
1 AATAAAATATGTAAAA
104261865 AAT-AAATATGTAAAA
1 AATAAAATATGTAAAA
*
104261880 AAGAAAA
1 AATAAAA
104261887 AGATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.32
15 10 0.53
16 3 0.16
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (16 bp):
AATAAAATATGTAAAA
Found at i:104263099 original size:32 final size:32
Alignment explanation
Indices: 104263058--104263122 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
104263048 TTATATTGTG
*
104263058 AAAATTAATGGAAGATGATGTCAATTTCCATT
1 AAAATTAATGGAAGATGATGTCAATCTCCATT
104263090 AAAATTAATGGAAGATGATGTCAATCTCCATT
1 AAAATTAATGGAAGATGATGTCAATCTCCATT
104263122 A
1 A
104263123 GTTTTAGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (32 bp):
AAAATTAATGGAAGATGATGTCAATCTCCATT
Found at i:104264349 original size:21 final size:20
Alignment explanation
Indices: 104264321--104264382 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
104264311 AAATATGTGA
104264321 AATT-ATGCTTAATTATATT
1 AATTCATGCTTAATTATATT
* * *
104264340 ATTTTCATGCATATTTTATATT
1 A-ATTCATGCTTA-ATTATATT
104264362 AATTCATG-TTAATT-TATT
1 AATTCATGCTTAATTATATT
104264380 AAT
1 AAT
104264383 GTATGTATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 7 0.21
19 3 0.09
20 4 0.12
21 12 0.35
22 8 0.24
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (20 bp):
AATTCATGCTTAATTATATT
Found at i:104267222 original size:27 final size:27
Alignment explanation
Indices: 104267162--104267223 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
104267152 ATTTAACATG
* *
104267162 AATAAAATATAAAACAATTTGAAATAA
1 AATAATATATAAAACAATTTCAAATAA
* *
104267189 AACAATATATAAACCAAATTTCAAAT-A
1 AATAATATATAAAAC-AATTTCAAATAA
104267216 AATAATAT
1 AATAATAT
104267224 GTTAAATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 20 0.69
28 9 0.31
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (27 bp):
AATAATATATAAAACAATTTCAAATAA
Found at i:104267799 original size:15 final size:15
Alignment explanation
Indices: 104267775--104267804 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
104267765 ATGTTGAAAA
104267775 AATAGAAATAATAAT
1 AATAGAAATAATAAT
*
104267790 AATAGTAATAATAAT
1 AATAGAAATAATAAT
104267805 GTAAATAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
AATAGAAATAATAAT
Found at i:104268185 original size:19 final size:20
Alignment explanation
Indices: 104268163--104268211 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
104268153 TAAGAAATGA
104268163 AAATCAATATAAAAT-AAA-T
1 AAATCAA-ATAAAATGAAATT
*
104268182 AAAT-AAATAAACTGAAATT
1 AAATCAAATAAAATGAAATT
104268201 AAATCAAATAA
1 AAATCAAATAA
104268212 GGACTAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 6 0.23
18 5 0.19
19 9 0.35
20 6 0.23
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.24
Consensus pattern (20 bp):
AAATCAAATAAAATGAAATT
Found at i:104269736 original size:45 final size:45
Alignment explanation
Indices: 104269674--104270102 Score: 279
Period size: 45 Copynumber: 9.6 Consensus size: 45
104269664 TTCAATACGT
* * * *
104269674 TCCACTGCAACTCCAGGGAAATAAGACTTGCTATATTCAATTTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTTATATTCAATCTGC
* * * *
104269719 TACACTGTAACTTCAGGGAGATAGGACTTG-T-T-TT-GATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTTATATTCAATCTGC
* * *
104269760 TCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTATAGGTTCAATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGA-CT-TG--TTATA--TTCAATCTGC
* * * * *
104269811 TCCACTGTAACTTCAGGGAAACAAGACTTGTTATCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTTATATTCAATCTGC
* * * *
104269856 TCCACTGCATCTTCAGGGAGATAAGACTTG-TA-ACTTCAACCCGT
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTTATA-TTCAATCTGC
* * * *** * *
104269900 TCCACTGTAACTT-TGGGAGATAAG-GTTAG-TGGCTTCGACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTT-GTTATATTCAATCTGC
* * * * *
104269943 CCCACTGCAACTTCAGGGAGAGAAGA-TTCGTCATCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTT-GTTATATTCAATCTGC
* * ** * *
104269988 TCCGCTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTTATATTCAATCTGC
* **
104270033 TCCACTGCAACTTCAGGGAGATAAGATTTGCGACT-TT-AATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTTA-TATTCAATCTGC
* * *
104270077 TTCACTGTAACTTCAGGAAGATAAGA
1 TCCACTGCAACTTCAGGGAGATAAGA
104270103 TTTGCCAAAA
Statistics
Matches: 305, Mismatches: 61, Indels: 37
0.76 0.15 0.09
Matches are distributed among these distances:
41 26 0.09
42 6 0.02
43 33 0.11
44 61 0.20
45 138 0.45
46 4 0.01
47 5 0.02
49 2 0.01
50 4 0.01
51 26 0.09
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (45 bp):
TCCACTGCAACTTCAGGGAGATAAGACTTGTTATATTCAATCTGC
Found at i:104273584 original size:16 final size:18
Alignment explanation
Indices: 104273557--104273592 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
104273547 TTTAATTTTC
104273557 AAAATTTCAAAAAA-AAA
1 AAAATTTCAAAAAATAAA
104273574 AAAATTT-AAAAAATAAA
1 AAAATTTCAAAAAATAAA
104273591 AA
1 AA
104273593 TTGCATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (18 bp):
AAAATTTCAAAAAATAAA
Found at i:104273630 original size:30 final size:30
Alignment explanation
Indices: 104273590--104273691 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
104273580 TAAAAAATAA
* *
104273590 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAAC-TTTCATT
* *
104273620 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
104273650 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
104273680 AAATTTCATTTT
1 AAATTTCATTTT
104273692 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 4 0.06
30 58 0.94
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCATT
Found at i:104274282 original size:14 final size:13
Alignment explanation
Indices: 104274260--104274312 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 13
104274250 AGACAAGAAG
104274260 AAGAGAAGAAGAAAA
1 AAGA-AAGAA-AAAA
104274275 AAGAAAGAAAAAA
1 AAGAAAGAAAAAA
104274288 AGAGAAAGAAAAAGA
1 A-AGAAAGAAAAA-A
104274303 AAGAAA-AAAA
1 AAGAAAGAAAA
104274313 GTAATTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.25
14 21 0.58
15 6 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAGAAAGAAAAAA
Found at i:104274285 original size:10 final size:10
Alignment explanation
Indices: 104274263--104274310 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
104274253 CAAGAAGAAG
*
104274263 AGAAGAAGAA
1 AGAAAAAGAA
*
104274273 AAAAGAAAGAA
1 AGAA-AAAGAA
104274284 A-AAAAGAGAA
1 AGAAAA-AGAA
104274294 AGAAAAAGAA
1 AGAAAAAGAA
104274304 AGAAAAA
1 AGAAAAA
104274311 AAGTAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 21 0.64
11 10 0.30
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AGAAAAAGAA
Found at i:104274322 original size:11 final size:11
Alignment explanation
Indices: 104274308--104274334 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
104274298 AAAGAAAGAA
104274308 AAAAAGTAATT
1 AAAAAGTAATT
104274319 AAAAAGTAATT
1 AAAAAGTAATT
104274330 AAAAA
1 AAAAA
104274335 AATAAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (11 bp):
AAAAAGTAATT
Found at i:104274323 original size:24 final size:23
Alignment explanation
Indices: 104274266--104274313 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
104274256 GAAGAAGAGA
104274266 AGAAGAAAAAAGAAAGAAAAAAAG
1 AGAA-AAAAAAGAAAGAAAAAAAG
104274290 AGAAAGAAAAAGAAAGAAAAAAAG
1 AGAAA-AAAAAGAAAGAAAAAAAG
104274314 TAATTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (23 bp):
AGAAAAAAAAGAAAGAAAAAAAG
Found at i:104282978 original size:78 final size:76
Alignment explanation
Indices: 104282727--104282989 Score: 329
Period size: 72 Copynumber: 3.5 Consensus size: 76
104282717 GTTTTTCAAA
* *
104282727 ATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG-T
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTT
*
104282791 TTT--CAAAAT
66 TTTAAAAAAAT
* * ** * *
104282800 -TCAACTTATATTGCGAAAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTT
* *
104282864 TTCAAAAAAAAA
66 TT-TAAAAAAAT
* *
104282876 ATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATTTCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAATTTCT
104282940 GTTTTTAAAAAAAT
63 GTTTTTAAAAAAAT
*
104282954 ATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
104282990 ATTACACACT
Statistics
Matches: 160, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
72 54 0.34
73 3 0.02
76 5 0.03
77 30 0.19
78 39 0.24
79 29 0.18
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (76 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTT
TTTAAAAAAAT
Found at i:104283048 original size:57 final size:57
Alignment explanation
Indices: 104282955--104283103 Score: 280
Period size: 57 Copynumber: 2.6 Consensus size: 57
104282945 TAAAAAAATA
*
104282955 TCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATTACACACTGTGGTGTTTTTT
1 TCAATTCATATTGCGAGAGGTGAGTTGAGCTTCAGATTACACACTGTGGTGTTTTTT
104283012 TCAATTCATATTGCGAGAGGTGAGTTGAGCTTCAGATTACACACTGTGGTGTTTTTT
1 TCAATTCATATTGCGAGAGGTGAGTTGAGCTTCAGATTACACACTGTGGTGTTTTTT
*
104283069 TCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAG
1 TCAATTCATATTGCGAGAGGTGAGTTGAGCTTCAG
104283104 GACACGATGA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 90 1.00
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (57 bp):
TCAATTCATATTGCGAGAGGTGAGTTGAGCTTCAGATTACACACTGTGGTGTTTTTT
Found at i:104283281 original size:72 final size:73
Alignment explanation
Indices: 104283200--104283341 Score: 232
Period size: 72 Copynumber: 2.0 Consensus size: 73
104283190 TCAAAATCAG
* * *
104283200 CTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTG-TGTTTT
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTGTTTT
104283264 AATTTCAA
66 AATTTCAA
* *
104283272 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTTTTTT
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTGTTTT
104283337 AATTT
66 AATTT
104283342 ATGTTTCAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
72 54 0.84
73 10 0.16
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (73 bp):
CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTGTTTT
AATTTCAA
Found at i:104283449 original size:160 final size:161
Alignment explanation
Indices: 104283192--104283483 Score: 455
Period size: 160 Copynumber: 1.8 Consensus size: 161
104283182 CTACTTTTTC
* * ** *
104283192 AAAATCAGCTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTT
1 AAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCGAAGCACGCTGAGGTAATTTCAATTTTT
* ** *
104283257 GTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
66 GTGTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGATATTTTC
104283322 AATTTTCGTTTTTTTAATTTATGTTTCAAAA
131 AATTTTCGTTTTTTTAATTTATGTTTCAAAA
*
104283353 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-AAG-ACGCTGAGGTAATTTCAATTTTT
1 AAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCGAAGCACGCTGAGGTAATTTCAATTTTT
104283416 GT-TTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGATATTT
66 GTGTT-T-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGATATTT
104283480 TCAA
129 TCAA
104283484 ATTCTATTTT
Statistics
Matches: 119, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
158 2 0.02
159 25 0.21
160 58 0.49
161 34 0.29
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (161 bp):
AAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCGAAGCACGCTGAGGTAATTTCAATTTTT
GTGTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGATATTTTC
AATTTTCGTTTTTTTAATTTATGTTTCAAAA
Found at i:104283551 original size:57 final size:58
Alignment explanation
Indices: 104283439--104283551 Score: 165
Period size: 57 Copynumber: 1.9 Consensus size: 58
104283429 CAACTCATAT
104283439 TGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGATATTTTCAAATTCTATTTTTATCG
1 TGCGAGAGGTGAGTTGAGCCTC--GACACGCTGAGATATTTTCAAATTCTATTTTTATCG
* * * *
104283499 TGCGAGAGGTGAGTTGAGCCTC-ACATGCTGAGGTGTTTTCAATTTCTATTTTT
1 TGCGAGAGGTGAGTTGAGCCTCGACACGCTGAGATATTTTCAAATTCTATTTTT
104283552 CAAAAAATCA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 27 0.55
60 22 0.45
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (58 bp):
TGCGAGAGGTGAGTTGAGCCTCGACACGCTGAGATATTTTCAAATTCTATTTTTATCG
Found at i:104283558 original size:131 final size:132
Alignment explanation
Indices: 104283368--104283628 Score: 357
Period size: 131 Copynumber: 2.0 Consensus size: 132
104283358 CAACTCATAT
* * *
104283368 TGCGAGAAGTGAGTTGAGCCTCAAGACGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAAC
1 TGCGAGAAGTGAGTTGAGCCTCAACACGCTGAGGTAATTTCAATTTCTATTTGTCAAAAATCAAC
*
104283433 TCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACG-CTGAGATATTTTCAAATTCTATTTTTA
66 TCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACACGTC-GAGATACTTTCAAATTCTATTTTTA
104283496 TCG
130 TCG
* * ** *
104283499 TGCGAGAGGTGAGTTGAGCCTC-ACATGCTGAGGTGTTTTCAATTTCTATTTTTCAAAAAATCAA
1 TGCGAGAAGTGAGTTGAGCCTCAACACGCTGAGGTAATTTCAATTTCTATTTGTC-AAAAATCAA
* * * *
104283563 CTCATATTGCGAGAGGTGAGTTGAGTCTCGGGCCACACGTCGAGGTCCTTTCAAATTCTATTTTT
65 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-CACACGTCGAGATACTTTCAAATTCTATTTTT
104283628 A
129 A
104283629 ATTTCTTTTT
Statistics
Matches: 113, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
130 25 0.22
131 60 0.53
133 27 0.24
134 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.33
Consensus pattern (132 bp):
TGCGAGAAGTGAGTTGAGCCTCAACACGCTGAGGTAATTTCAATTTCTATTTGTCAAAAATCAAC
TCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACACGTCGAGATACTTTCAAATTCTATTTTTAT
CG
Found at i:104283845 original size:71 final size:71
Alignment explanation
Indices: 104283745--104283882 Score: 231
Period size: 71 Copynumber: 1.9 Consensus size: 71
104283735 CTGTTTTAAT
* * *
104283745 TCAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAACCTCAAGTCACATTGAGGTATTTTCAAT
1 TCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACATTGAGATATTTTCAAT
104283810 TTATCA
66 TTATCA
* *
104283816 TCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACCCGTTGAGATATTTTCAAT
1 TCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACATTGAGATATTTTCAAT
104283881 TT
66 TT
104283883 CTGCTCAATT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 62 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (71 bp):
TCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACATTGAGATATTTTCAAT
TTATCA
Found at i:104283985 original size:155 final size:152
Alignment explanation
Indices: 104283654--104284155 Score: 480
Period size: 155 Copynumber: 3.3 Consensus size: 152
104283644 AATTTATGTG
*
104283654 TTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGA-CGCTGAGGTGTTTTCC
1 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACCGCTGAGGTGTTTT-C
* * * *
104283718 ATTTTTATTTTCAATTTCTGTTTTAATTCAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAAC
65 A---AT-TTTTCAATTTATG-TTT--TTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
104283783 CTCA-AGTCACATTGAGGTATTTTCAA-TT-TA-T
122 CTCACA-T-GC--TGAGGTATTTTCAATTTCTATT
** * * *
104283814 CATC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACCCGTTGAGATATTTTC
1 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGA-CCGCTGAGGTGTTTTC
104283878 AATTTCTGCTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAC
65 AATTT-T--TCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAC
*
104283943 ATGCTGAGGTGTTTTCAATTTCTATT
127 ATGCTGAGGTATTTTCAATTTCTATT
* * * *
104283969 TTTC-AAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-ACA-TGCTGAGGTGTTTTCA
1 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACCGCTGAGGTGTTTTCA
104284031 A--TTTC----TA--TTTTTCAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTT
66 ATTTTTCAATTTATGTTTTTCAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCC-T--C--
* *
104284088 ACACGCTGAGGTATTTTTCAATTTCTGTT
125 ACATGCTGAGGTA-TTTTCAATTTCTATT
* * *
104284117 TGTCAAAAAAACCAACTCATATTGTGAGAGGTGAGTTGA
1 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
104284156 GTCTCGGCTC
Statistics
Matches: 297, Mismatches: 28, Indels: 45
0.80 0.08 0.12
Matches are distributed among these distances:
141 11 0.04
142 31 0.10
143 3 0.01
145 1 0.00
147 13 0.04
148 17 0.06
149 32 0.11
150 1 0.00
152 26 0.09
153 2 0.01
154 5 0.02
155 78 0.26
156 6 0.02
157 2 0.01
158 3 0.01
159 51 0.17
160 4 0.01
161 11 0.04
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (152 bp):
TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACCGCTGAGGTGTTTTCA
ATTTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCACATGC
TGAGGTATTTTCAATTTCTATT
Found at i:104283996 original size:71 final size:71
Alignment explanation
Indices: 104283887--104284199 Score: 396
Period size: 71 Copynumber: 4.3 Consensus size: 71
104283877 CAATTTCTGC
* *
104283887 TCAATTTATGTTTTTCAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCACATGCTGAG
1 TCAATTTCTATTTTTCAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCACATGCTGAG
104283951 GTGTTT
66 GTGTTT
104283957 TCAATTTCTATTTTTCAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCACATGCTGAG
1 TCAATTTCTATTTTTCAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCACATGCTGAG
104284022 GTGTTT
66 GTGTTT
*
104284028 TCAATTTCTATTTTTCAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTTACACG
1 TCAATTTCTATTTTTCAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCC-T--C--ACATG
*
104284093 CTGAGGTATTTT
61 CTGAGGT-GTTT
* * ** *
104284105 TCAATTTCTGTTTGTCAAAAAAACCAACTCATATTGTGAGAGGTGAGTTGAGTCTCGGCTCACAT
1 TCAATTTCTATTTTTC-AAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAG---C--CTCACAT
*
104284170 GCTGAGGTCTTT
60 GCTGAGGTGTTT
*
104284182 TTAATTTCT-TCTTTTCAA
1 TCAATTTCTAT-TTTTCAA
104284200 TTTCTGTTTT
Statistics
Matches: 216, Mismatches: 13, Indels: 22
0.86 0.05 0.09
Matches are distributed among these distances:
70 19 0.09
71 102 0.47
72 1 0.00
74 1 0.00
76 14 0.06
77 32 0.15
78 43 0.20
80 1 0.00
81 1 0.00
82 1 0.00
83 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (71 bp):
TCAATTTCTATTTTTCAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCACATGCTGAG
GTGTTT
Found at i:104284213 original size:15 final size:14
Alignment explanation
Indices: 104284179--104284228 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
104284169 TGCTGAGGTC
104284179 TTTTT-AATTTCTT
1 TTTTTCAATTTCTT
*
104284192 CTTTTCAATTTCTGT
1 TTTTTCAATTTCT-T
* *
104284207 TTTTTCAATTTATA
1 TTTTTCAATTTCTT
104284221 TTTTTCAA
1 TTTTTCAA
104284229 AAATCAACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTTTCAATTTCTT
Found at i:104284338 original size:177 final size:181
Alignment explanation
Indices: 104284025--104284459 Score: 680
Period size: 177 Copynumber: 2.4 Consensus size: 181
104284015 TGCTGAGGTG
* * *
104284025 TTTTCAATTTCTATTTTTCAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTTAC
1 TTTTCAATTTATATTTTTCAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGC-GAC
* *
104284090 ACGCTGAGGTATTTTTCAATTTCTGTTTGTCAAAAAAACCAACTCATATTGTGAGAGGTGAGTTG
64 ACGCTGAGGTATATTTCAATTTCTGTTTGTC-AAAAAACCAACTCATATTGCGAGAGGTGAGTTG
*
104284155 AGTCTCGGCTCACATGCTGAGGTCTTTTTAATTTCTTCTTTTCAATTTCT-GTT
128 AGTCTCGGCTCACATGCTGAGGTCTTTTTAATTTCTGCTTTTCAATTTCTAGTT
*
104284208 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGG-GACAC
1 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCGACAC
**
104284272 GCTGAGGTA-ATTTCAATTTCTGTTTGTC-AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGT
66 GCTGAGGTATATTTCAATTTCTGTTTGTCAAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGT
*
104284335 CTCGGCTCACATGCTGAGGTCTTTTTAATTTCTGCTTTTCAATTTCTATTT
131 CTCGGCTCACATGCTGAGGTCTTTTTAATTTCTGCTTTTCAATTTCTAGTT
* * *
104284386 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGCGTCTCGGCTCACA
1 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGC-GACA
*
104284451 TGCTGAGGT
65 CGCTGAGGT
104284460 CTTTCTAATT
Statistics
Matches: 234, Mismatches: 15, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
177 78 0.33
178 58 0.25
179 18 0.08
180 24 0.10
182 33 0.14
183 23 0.10
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (181 bp):
TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCGACAC
GCTGAGGTATATTTCAATTTCTGTTTGTCAAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGT
CTCGGCTCACATGCTGAGGTCTTTTTAATTTCTGCTTTTCAATTTCTAGTT
Found at i:104284387 original size:14 final size:14
Alignment explanation
Indices: 104284356--104284406 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
104284346 TGCTGAGGTC
*
104284356 TTTTT-AATTTCTG
1 TTTTTCAATTTCTA
*
104284369 CTTTTCAATTTCTA
1 TTTTTCAATTTCTA
*
104284383 TTTTTTTCAATTTATA
1 --TTTTTCAATTTCTA
104284399 TTTTTCAA
1 TTTTTCAA
104284407 AAATCAACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
16 12 0.39
ACGTcount: A:0.22, C:0.12, G:0.02, T:0.65
Consensus pattern (14 bp):
TTTTTCAATTTCTA
Found at i:104284391 original size:16 final size:16
Alignment explanation
Indices: 104284370--104284403 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
104284360 TAATTTCTGC
*
104284370 TTTTCAATTTCTATTT
1 TTTTCAATTTATATTT
104284386 TTTTCAATTTATATTT
1 TTTTCAATTTATATTT
104284402 TT
1 TT
104284404 CAAAAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTCAATTTATATTT
Found at i:104284469 original size:105 final size:105
Alignment explanation
Indices: 104284282--104284543 Score: 461
Period size: 105 Copynumber: 2.5 Consensus size: 105
104284272 GCTGAGGTAA
* * * *
104284282 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGCTCACAT
1 TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGCTCACAT
*
104284347 GCTGAGGTCTTTTTAATTTCTGCTTTTCAATTTCTATTTT
66 GCTGAGGTCTTTCTAATTTCTGCTTTTCAATTTCTATTTT
*
104284387 TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGCGTCTCGGCTCACAT
1 TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGCTCACAT
104284452 GCTGAGGTCTTTCTAATTTCTGCTTTTCAATTTCTATTTT
66 GCTGAGGTCTTTCTAATTTCTGCTTTTCAATTTCTATTTT
*
104284492 TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAG
1 TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
104284544 CCTTGGGTTC
Statistics
Matches: 149, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 149 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (105 bp):
TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGCTCACAT
GCTGAGGTCTTTCTAATTTCTGCTTTTCAATTTCTATTTT
Found at i:104284496 original size:16 final size:16
Alignment explanation
Indices: 104284475--104284508 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
104284465 TAATTTCTGC
*
104284475 TTTTCAATTTCTATTT
1 TTTTCAATTTATATTT
104284491 TTTTCAATTTATATTT
1 TTTTCAATTTATATTT
104284507 TT
1 TT
104284509 CAAAAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTCAATTTATATTT
Found at i:104284681 original size:77 final size:77
Alignment explanation
Indices: 104284592--104285142 Score: 964
Period size: 77 Copynumber: 7.2 Consensus size: 77
104284582 TTTGCGAGAA
104284592 GTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACTC
1 GTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACTC
104284657 ATATTGTAAGAG
66 ATATTGTAAGAG
104284669 GTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACTC
1 GTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACTC
104284734 ATATTGTAAGAG
66 ATATTGTAAGAG
104284746 GTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACTC
1 GTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACTC
104284811 ATATTGTAAGAG
66 ATATTGTAAGAG
104284823 GTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACTC
1 GTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACTC
104284888 ATATTGTAAGAG
66 ATATTGTAAGAG
104284900 GTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACTC
1 GTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACTC
104284965 ATATTGTAAGAG
66 ATATTGTAAGAG
*
104284977 GTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAAAATCAACTC
1 GTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACTC
**
104285042 ATATTGCGAGAG
66 ATATTGTAAGAG
** * ** *
104285054 GTGAGTTGAGCCTCGGGTCACACGCTGAGGC-GTTTTCAATTTCTGCTTTTC-AAA-AATCAACT
1 GTGAGTTGAGCCTTTGCTCACGTGCTGA-GCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACT
** *
104285116 CATATTGCGAGAT
65 CATATTGTAAGAG
104285129 GTGAGTTGAGCCTT
1 GTGAGTTGAGCCTT
104285143 GGGTTTACAT
Statistics
Matches: 462, Mismatches: 11, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
75 33 0.07
76 3 0.01
77 424 0.92
78 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (77 bp):
GTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACTC
ATATTGTAAGAG
Found at i:104285891 original size:30 final size:30
Alignment explanation
Indices: 104285855--104285923 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
104285845 ACTTTTCTCA
104285855 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
*
104285885 ACTAGCCACACCTTTTCCACCACTAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
104285915 ACTAGCCAC
1 ACTAGCCAC
104285924 TCAAATCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.28, C:0.48, G:0.04, T:0.20
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:104287355 original size:2 final size:2
Alignment explanation
Indices: 104287348--104287375 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
104287338 TTATGAAGAA
104287348 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
104287376 GAATCCAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:104295182 original size:27 final size:27
Alignment explanation
Indices: 104295151--104295211 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
104295141 TAAATCCAAC
*
104295151 AAAAAGAG-GGATTAAATTTCTAGAA-AT
1 AAAAAGAGAAGATTAAATTT-TA-AATAT
104295178 AAAAATG-GAAGATTAAATTTTAAATAT
1 AAAAA-GAGAAGATTAAATTTTAAATAT
104295205 AAAAAGA
1 AAAAAGA
104295212 ATATAGGGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
26 3 0.10
27 15 0.52
28 11 0.38
ACGTcount: A:0.57, C:0.02, G:0.15, T:0.26
Consensus pattern (27 bp):
AAAAAGAGAAGATTAAATTTTAAATAT
Found at i:104295734 original size:13 final size:12
Alignment explanation
Indices: 104295704--104295740 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
104295694 AGTAATTTTA
104295704 ATTAAGTTTAAT
1 ATTAAGTTTAAT
*
104295716 AGTAAGTTCTAAT
1 ATTAAGTT-TAAT
104295729 ATTAAGTTTAAT
1 ATTAAGTTTAAT
104295741 TAAAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.46
Consensus pattern (12 bp):
ATTAAGTTTAAT
Found at i:104297727 original size:86 final size:85
Alignment explanation
Indices: 104297577--104297832 Score: 307
Period size: 86 Copynumber: 3.0 Consensus size: 85
104297567 AGATAAAAAC
* ** *
104297577 ATTTGTAATTACTGCCACTTGTTGTGAGTGCACAACATGGTTGCAGATTAAACAAACTGCCACTG
1 ATTTGCAATTACTGCCACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAATTGCCACTG
104297642 ATTTTTGTGGACAAGCCACGT
66 A-TTTTGTGGACAAGCCACGT
** * * * * *
104297663 ATTTGCAATTACTATCACTTGTTGTAAGTTCACAACATATTTTCAAATTAAACAAATTGTCACTG
1 ATTTGCAATTACTGCCACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAATTGCCACT-
* *
104297728 GGTTTTGTGGGCAAGCCACGT
65 GATTTTGTGGACAAGCCACGT
* * * *
104297749 ATTTACAGTTAATGCCACTTGTGGTGAGTGCACAACATATTTGCAGATTAAAC-AATCTGCCACT
1 ATTTGCAATTACTGCCACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAAT-TGCCACT
*
104297813 AGATTTTATGGACAAGCCAC
65 -GATTTTGTGGACAAGCCAC
104297833 CACTTGTATG
Statistics
Matches: 140, Mismatches: 28, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
85 3 0.02
86 136 0.97
87 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (85 bp):
ATTTGCAATTACTGCCACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAATTGCCACTG
ATTTTGTGGACAAGCCACGT
Found at i:104302450 original size:28 final size:28
Alignment explanation
Indices: 104302419--104302474 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
104302409 CATACAATGA
104302419 AAGCTTGTCGAATTAGGATACACTCTTT
1 AAGCTTGTCGAATTAGGATACACTCTTT
*
104302447 AAGCTTGTCGAATTAGGATATACTCTTT
1 AAGCTTGTCGAATTAGGATACACTCTTT
104302475 CATTATTGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (28 bp):
AAGCTTGTCGAATTAGGATACACTCTTT
Found at i:104305314 original size:18 final size:17
Alignment explanation
Indices: 104305267--104305321 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 17
104305257 TTCCCATAAA
104305267 AAAACATTAAAAA-TATT
1 AAAA-ATTAAAAATTATT
* * *
104305284 ATAACTTATAAATTTATT
1 AAAAATTA-AAAATTATT
104305302 AAAAATTAAAAA-TATT
1 AAAAATTAAAAATTATT
104305318 AAAA
1 AAAA
104305322 TTGACATAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 11 0.37
17 9 0.30
18 10 0.33
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAAATTAAAAATTATT
Found at i:104305935 original size:15 final size:15
Alignment explanation
Indices: 104305915--104305945 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
104305905 GTTCACCATC
104305915 GCACTGTGACCTGAA
1 GCACTGTGACCTGAA
104305930 GCACTGTGACCTGAA
1 GCACTGTGACCTGAA
104305945 G
1 G
104305946 TTCAAAGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (15 bp):
GCACTGTGACCTGAA
Found at i:104307846 original size:12 final size:12
Alignment explanation
Indices: 104307829--104307869 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
104307819 ATGAGAGTCA
104307829 ATTTTGATAAAT
1 ATTTTGATAAAT
104307841 ATTTTGATAAAT
1 ATTTTGATAAAT
104307853 A-TTT-ATAAAT
1 ATTTTGATAAAT
104307863 ATTTTGA
1 ATTTTGA
104307870 ATTTTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.26
11 6 0.22
12 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (12 bp):
ATTTTGATAAAT
Found at i:104310580 original size:11 final size:11
Alignment explanation
Indices: 104310559--104310602 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
104310549 TAATAACAAC
*
104310559 AAAATAGTAGT
1 AAAATAATAGT
*
104310570 AATATAATAGT
1 AAAATAATAGT
*
104310581 AAAATAATAGC
1 AAAATAATAGT
*
104310592 AAAACAATAGT
1 AAAATAATAGT
104310603 GAAACATCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.25
Consensus pattern (11 bp):
AAAATAATAGT
Found at i:104322320 original size:17 final size:17
Alignment explanation
Indices: 104322286--104322331 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
104322276 TTGCATTCTT
* *
104322286 ATATT-TTTAAATTGAC
1 ATATTATTTGAATTAAC
*
104322302 ATTTTATTTGAATTAAC
1 ATATTATTTGAATTAAC
104322319 ATATTATTTGAAT
1 ATATTATTTGAAT
104322332 AGGTGAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (17 bp):
ATATTATTTGAATTAAC
Found at i:104326121 original size:50 final size:51
Alignment explanation
Indices: 104326045--104326153 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 51
104326035 CCTTGTAGTA
* *
104326045 AAAGCTACCTTCTTCACAAAGTGGCCTTCACATAGTA-CACACT-TGCGACC
1 AAAGCTATCTTCTTCACAAAGTGGCCTGCACATAGTATCACA-TATGCGACC
* * * *
104326095 AAAGCTATCTT-TTACACATAGTGGCCTGCACTTAGTATCACATATGTGATC
1 AAAGCTATCTTCTT-CACAAAGTGGCCTGCACATAGTATCACATATGCGACC
104326146 AAAGCTAT
1 AAAGCTAT
104326154 TGGGTATGCA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
49 2 0.04
50 31 0.62
51 17 0.34
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (51 bp):
AAAGCTATCTTCTTCACAAAGTGGCCTGCACATAGTATCACATATGCGACC
Found at i:104332846 original size:20 final size:20
Alignment explanation
Indices: 104332821--104332860 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
104332811 CCAAAAATGA
*
104332821 TTTCTGGAAAATAATTTACT
1 TTTCTGAAAAATAATTTACT
*
104332841 TTTCTGAAAAATGATTTACT
1 TTTCTGAAAAATAATTTACT
104332861 GAAAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (20 bp):
TTTCTGAAAAATAATTTACT
Found at i:104332938 original size:33 final size:32
Alignment explanation
Indices: 104332851--104332936 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 32
104332841 TTTCTGAAAA
*
104332851 ATGATTTACTGAAAATATTTTCTGATGTTTGG
1 ATGATTTCCTGAAAATATTTTCTGATGTTTGG
* * *
104332883 ATGA-ATCTGTGTAAAATATTTTCTGTTGTTTGG
1 ATGATTTC-CTG-AAAATATTTTCTGATGTTTGG
104332916 CA-GATTTCCTGAAAATATTTT
1 -ATGATTTCCTGAAAATATTTT
104332937 TCAGAAAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
31 1 0.02
32 16 0.36
33 24 0.55
34 3 0.07
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (32 bp):
ATGATTTCCTGAAAATATTTTCTGATGTTTGG
Found at i:104332983 original size:20 final size:20
Alignment explanation
Indices: 104332958--104332996 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
104332948 GTTTTTACAT
104332958 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
104332978 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
104332997 ATTTAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:104335341 original size:16 final size:16
Alignment explanation
Indices: 104335320--104335350 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
104335310 AAATTATCAG
104335320 TAACTACAGAAAATTT
1 TAACTACAGAAAATTT
104335336 TAACTACAGAAAATT
1 TAACTACAGAAAATT
104335351 ATAGCAGACA
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:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (16 bp):
TAACTACAGAAAATTT
Found at i:104338351 original size:12 final size:13
Alignment explanation
Indices: 104338328--104338356 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
104338318 TACAAAATCA
104338328 AAATTCACATATT
1 AAATTCACATATT
104338341 AAATT-ACATATT
1 AAATTCACATATT
104338353 AAAT
1 AAAT
104338357 CAAATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTCACATATT
Found at i:104341797 original size:36 final size:35
Alignment explanation
Indices: 104341732--104341799 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
104341722 AAAATAATAG
*
104341732 CAAAAATAACAATAAAACAAGAGTCATATAATATC
1 CAAAAATAACAATAAAACAAGAGTAATATAATATC
*
104341767 CAAACAATAACAATAAAA-TAGTAGTAATATAAT
1 CAAA-AATAACAATAAAACAAG-AGTAATATAAT
104341800 GATGAAATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
35 6 0.21
36 23 0.79
ACGTcount: A:0.60, C:0.12, G:0.06, T:0.22
Consensus pattern (35 bp):
CAAAAATAACAATAAAACAAGAGTAATATAATATC
Found at i:104347834 original size:28 final size:28
Alignment explanation
Indices: 104347765--104347834 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
104347755 ATGTTTGACA
*
104347765 AACCCCTATGGTAAACTCGTATTTAGCG
1 AACCCCTATGGTGAACTCGTATTTAGCG
* *
104347793 AACCCCTATAGTGAACTCGTATTTGGCG
1 AACCCCTATGGTGAACTCGTATTTAGCG
*
104347821 AACCCCTAGGGTGA
1 AACCCCTATGGTGA
104347835 TCACAAGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (28 bp):
AACCCCTATGGTGAACTCGTATTTAGCG
Found at i:104347902 original size:25 final size:26
Alignment explanation
Indices: 104347861--104347921 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 26
104347851 CTTATGTTGA
* *
104347861 ACTACTATGGCGTACCC-TATGGAGG
1 ACTACTATGGCGAACCCTTAAGGAGG
* *
104347886 ACTACTATGGTGAACCCTTAAGGAGT
1 ACTACTATGGCGAACCCTTAAGGAGG
*
104347912 ACTCCTATGG
1 ACTACTATGG
104347922 AAAACCCTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 15 0.50
26 15 0.50
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (26 bp):
ACTACTATGGCGAACCCTTAAGGAGG
Found at i:104354241 original size:21 final size:21
Alignment explanation
Indices: 104354217--104354271 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
104354207 CTTTATCTTA
*
104354217 AACCCCAAACTTAGAATCTCG
1 AACCCTAAACTTAGAATCTCG
*
104354238 AACCTTAAACATT-GAATCTCG
1 AACCCTAAAC-TTAGAATCTCG
104354259 AACCCTAAACTTA
1 AACCCTAAACTTA
104354272 AAGCCGAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.40, C:0.29, G:0.07, T:0.24
Consensus pattern (21 bp):
AACCCTAAACTTAGAATCTCG
Found at i:104356146 original size:18 final size:19
Alignment explanation
Indices: 104356108--104356157 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
104356098 TTACAAAGAA
*
104356108 AAAATT-AAAATATTTTTT
1 AAAATTCAAAATATTTTAT
104356126 AAAATTCAAAATA-TTTAT
1 AAAATTCAAAATATTTTAT
104356144 AAAAGTTCTAAAAT
1 AAAA-TTC-AAAAT
104356158 TCAAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 14 0.50
19 9 0.32
20 5 0.18
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATTCAAAATATTTTAT
Found at i:104358954 original size:46 final size:46
Alignment explanation
Indices: 104358901--104358995 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
104358891 GTCGTGTAGT
*
104358901 AAATCTGGCTCATCCCATGCCACCTGAAAAAATATGTTAATTCGAG
1 AAATCTGGCTCATCCCATGCCACCTGAAAAAAGATGTTAATTCGAG
*
104358947 AAATCTGGCTCATCCCATGCCACCTGAAAAAAGATGTTAATTTGAG
1 AAATCTGGCTCATCCCATGCCACCTGAAAAAAGATGTTAATTCGAG
104358993 AAA
1 AAA
104358996 AAATTATTAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (46 bp):
AAATCTGGCTCATCCCATGCCACCTGAAAAAAGATGTTAATTCGAG
Found at i:104361965 original size:21 final size:21
Alignment explanation
Indices: 104361939--104362075 Score: 85
Period size: 21 Copynumber: 6.5 Consensus size: 21
104361929 TTGAAGGTTG
*
104361939 AACAGAAGCTCATGAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* * * * *
104361960 AACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTA
* * *
104361981 AACGGAAGCTCTTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTA
* * * *
104362002 AACAGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTA
* * *
104362023 AATAGAAGCTCAAAAGAGCTG
1 AACAGAAGCTCATAAGAGCTA
** * * *
104362044 AATGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTA
104362065 AACAGAAGCTC
1 AACAGAAGCTC
104362076 GTGAGATCTA
Statistics
Matches: 81, Mismatches: 35, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 81 1.00
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.17
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:104361981 original size:42 final size:42
Alignment explanation
Indices: 104361934--104362093 Score: 158
Period size: 42 Copynumber: 3.8 Consensus size: 42
104361924 GAAGCTTGAA
* *
104361934 GGTTGAACAGAAGCTCATGAGAGCTAAACAGAAACCCATAAG
1 GGTTAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
* * * *
104361976 GGTTGAACGGAAGCTCTTAAGAGCTGAACAGAAACCCATAAG
1 GGTTAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
* * * ** * *
104362018 GGTTAAATAGAAGCTCAAAAGAGCTGAATGGAAACTCATATG
1 GGTTAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
* * * * *
104362060 AGTTAAACAGAAGCTCGTGAGATCTAAACGGAAA
1 GGTTAAACAGAAGCTCATAAGAGCTAAACAGAAA
104362094 GTAAACACGA
Statistics
Matches: 97, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 97 1.00
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.17
Consensus pattern (42 bp):
GGTTAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
Found at i:104368301 original size:85 final size:85
Alignment explanation
Indices: 104368158--104368745 Score: 1176
Period size: 85 Copynumber: 6.9 Consensus size: 85
104368148 NNNNNNNNNN
104368158 TATTAATCTTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATAACATCTTG
1 TATTAATCTTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATAACATCTTG
104368223 TCCACCCATGCTCTTTATTT
66 TCCACCCATGCTCTTTATTT
104368243 TATTAATCTTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATAACATCTTG
1 TATTAATCTTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATAACATCTTG
104368308 TCCACCCATGCTCTTTATTT
66 TCCACCCATGCTCTTTATTT
104368328 TATTAATCTTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATAACATCTTG
1 TATTAATCTTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATAACATCTTG
104368393 TCCACCCATGCTCTTTATTT
66 TCCACCCATGCTCTTTATTT
104368413 TATTAATCTTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATAACATCTTG
1 TATTAATCTTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATAACATCTTG
104368478 TCCACCCATGCTCTTTATTT
66 TCCACCCATGCTCTTTATTT
104368498 TATTAATCTTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATAACATCTTG
1 TATTAATCTTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATAACATCTTG
104368563 TCCACCCATGCTCTTTATTT
66 TCCACCCATGCTCTTTATTT
104368583 TATTAATCTTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATAACATCTTG
1 TATTAATCTTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATAACATCTTG
104368648 TCCACCCATGCTCTTTATTT
66 TCCACCCATGCTCTTTATTT
104368668 TATTAATCTTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATAACATCTTG
1 TATTAATCTTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATAACATCTTG
104368733 TCCACCCATGCTC
66 TCCACCCATGCTC
104368746 ATGGCCGACC
Statistics
Matches: 503, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 503 1.00
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.39
Consensus pattern (85 bp):
TATTAATCTTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATAACATCTTG
TCCACCCATGCTCTTTATTT
Found at i:104378913 original size:40 final size:40
Alignment explanation
Indices: 104378834--104379179 Score: 642
Period size: 40 Copynumber: 8.7 Consensus size: 40
104378824 GCAAACACAT
* *
104378834 TTGCCTTCGGGTCTTAGCCC-GA-ACATCACCTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCACCTCGCATAA
104378872 TTGCCTTCGGGTCCTAGCCCGGATATATCACCTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCACCTCGCATAA
104378912 TTGCCTTCGGGTCCTAGCCCGGATATATCACCTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCACCTCGCATAA
104378952 TTGCCTTCGGGTCCTAGCCCGGATATATCACCTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCACCTCGCATAA
104378992 TTGCCTTCGGGTCCTAGCCCGGATATATCACCTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCACCTCGCATAA
104379032 TTGCCTTCGGGTCCTAGCCCGGATATATCACCTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCACCTCGCATAA
104379072 TTGCCTTCGGGTCCTAGCCCGGATATATCACCTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCACCTCGCATAA
*
104379112 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCACCTCGCATAA
*
104379152 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCCTAGCCCGGATATAT
104379180 TCCAATGCTC
Statistics
Matches: 302, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
38 19 0.06
39 2 0.01
40 281 0.93
ACGTcount: A:0.20, C:0.32, G:0.20, T:0.28
Consensus pattern (40 bp):
TTGCCTTCGGGTCCTAGCCCGGATATATCACCTCGCATAA
Found at i:104387561 original size:40 final size:40
Alignment explanation
Indices: 104387517--104387649 Score: 212
Period size: 40 Copynumber: 3.3 Consensus size: 40
104387507 GCAAACACAT
* * *
104387517 TTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATAA
1 TTGCCTTCAGGTCTTAGCCCGGATATATCAACTCGCATAA
104387557 TTGCCTTCAGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCAGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
104387597 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCAGGTCTTAGCCCGGATATATCAACTCGCATAA
*
104387637 CTGCCTTCAGGTC
1 TTGCCTTCAGGTC
104387650 AAATACCATT
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 86 1.00
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.29
Consensus pattern (40 bp):
TTGCCTTCAGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:104387881 original size:290 final size:290
Alignment explanation
Indices: 104387361--104387914 Score: 1081
Period size: 290 Copynumber: 1.9 Consensus size: 290
104387351 CGATCGCACG
104387361 AATACCATTTAAAACAAACCGACTTTCCAATGCACATGCAAACATACCTTATCATTCGGGTTGGT
1 AATACCATTTAAAACAAACCGACTTTCCAATGCACATGCAAACATACCTTATCATTCGGGTTGGT
104387426 CAAGCATAATTATTAAATTAGTTACAGCACAAAATGCTCACATTCAACCCAAGTTTCTTCGGTAT
66 CAAGCATAATTATTAAATTAGTTACAGCACAAAATGCTCACATTCAACCCAAGTTTCTTCGGTAT
104387491 TTAACCGAATGCAACCGCAAACACATTTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATA
131 TTAACCGAATGCAACCGCAAACACATTTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATA
* *
104387556 ATTGCCTTCAGGTCTTAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCCTAGCCCGGAT
196 ATTGCCTTCAGGTCCTAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCATAGCCCGGAT
104387621 ATATCAACTCGCATAACTGCCTTCAGGTCA
261 ATATCAACTCGCATAACTGCCTTCAGGTCA
104387651 AATACCATTTAAAACAAACCGACTTTCCAATGCACATGCAAACATACCTTATCATTCGGGTTGGT
1 AATACCATTTAAAACAAACCGACTTTCCAATGCACATGCAAACATACCTTATCATTCGGGTTGGT
104387716 CAAGCATAATTATTAAATTAGTTACAGCACAAAATGCTCACATTCAACCCAAGTTTCTTCGGTAT
66 CAAGCATAATTATTAAATTAGTTACAGCACAAAATGCTCACATTCAACCCAAGTTTCTTCGGTAT
104387781 TTAACCGAATGCAACCGCAAACACATTTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATA
131 TTAACCGAATGCAACCGCAAACACATTTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATA
*
104387846 ATTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCATAGCCCGGAT
196 ATTGCCTTCAGGTCCTAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCATAGCCCGGAT
104387911 ATAT
261 ATAT
104387915 TCCAATGCTC
Statistics
Matches: 261, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
290 261 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (290 bp):
AATACCATTTAAAACAAACCGACTTTCCAATGCACATGCAAACATACCTTATCATTCGGGTTGGT
CAAGCATAATTATTAAATTAGTTACAGCACAAAATGCTCACATTCAACCCAAGTTTCTTCGGTAT
TTAACCGAATGCAACCGCAAACACATTTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATA
ATTGCCTTCAGGTCCTAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCATAGCCCGGAT
ATATCAACTCGCATAACTGCCTTCAGGTCA
Found at i:104387908 original size:40 final size:40
Alignment explanation
Indices: 104387807--104387914 Score: 180
Period size: 40 Copynumber: 2.7 Consensus size: 40
104387797 GCAAACACAT
* * *
104387807 TTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
*
104387847 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
104387887 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCATAGCCCGGATATAT
104387915 TCCAATGCTC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (40 bp):
TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
Found at i:104394279 original size:19 final size:19
Alignment explanation
Indices: 104394255--104394293 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
104394245 TATACAGAAC
104394255 AGATCAGAGTCAGATGTAG
1 AGATCAGAGTCAGATGTAG
*
104394274 AGATCAGAGTTAGATGTAG
1 AGATCAGAGTCAGATGTAG
104394293 A
1 A
104394294 TATTCCTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (19 bp):
AGATCAGAGTCAGATGTAG
Found at i:104394782 original size:13 final size:13
Alignment explanation
Indices: 104394764--104394795 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
104394754 TTATATACGC
104394764 CACACGGCCAGGA
1 CACACGGCCAGGA
104394777 CACACGGCCAGGA
1 CACACGGCCAGGA
104394790 CACACG
1 CACACG
104394796 TCTATGTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.31, C:0.41, G:0.28, T:0.00
Consensus pattern (13 bp):
CACACGGCCAGGA
Found at i:104395599 original size:12 final size:12
Alignment explanation
Indices: 104395574--104395617 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
104395564 CAAAGAAGTA
*
104395574 AAAAGAAGAAAG
1 AAAAGAAAAAAG
*
104395586 AAAGGAAAAAAG
1 AAAAGAAAAAAG
104395598 AAAAAGAAAAAAG
1 -AAAAGAAAAAAG
*
104395611 AATAGAA
1 AAAAGAA
104395618 GAAGAAATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:104395608 original size:13 final size:13
Alignment explanation
Indices: 104395573--104395612 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
104395563 TCAAAGAAGT
*
104395573 AAAAAGAAGAAAG
1 AAAAAGAAAAAAG
*
104395586 -AAAGGAAAAAAG
1 AAAAAGAAAAAAG
104395598 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
104395611 AA
1 AA
104395613 TAGAAGAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:104398094 original size:15 final size:15
Alignment explanation
Indices: 104398076--104398107 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
104398066 CAAAAAAAAG
104398076 AAATATAATAATAAT
1 AAATATAATAATAAT
104398091 AAATATAATAATAAT
1 AAATATAATAATAAT
104398106 AA
1 AA
104398108 CTAATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATAATAATAAT
Found at i:104398103 original size:18 final size:18
Alignment explanation
Indices: 104398077--104398122 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 18
104398067 AAAAAAAAGA
104398077 AATATAATAATAAT-A--
1 AATATAATAATAATAACT
104398092 AATATAATAATAATAACT
1 AATATAATAATAATAACT
*
104398110 AATTTAATAATAA
1 AATATAATAATAA
104398123 AGTAGCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 14 0.52
16 1 0.04
18 12 0.44
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATAATAATAATAACT
Found at i:104399481 original size:44 final size:43
Alignment explanation
Indices: 104399432--104399812 Score: 196
Period size: 45 Copynumber: 8.4 Consensus size: 43
104399422 TGACCTGCTA
* * * *
104399432 CAACTTCAAAGGTATAGGATTTGTTGCTTCAATCTGCTCCACTG
1 CAACTTC-AAGGAATAAGATTAGTAGCTTCAATCTGCTCCACTG
* *
104399476 CAACTTCAAGGAATAAGATTAGTAGCTTCAATCTGCTTCATTG
1 CAACTTCAAGGAATAAGATTAGTAGCTTCAATCTGCTCCACTG
* * * ** *
104399519 CAAATT-TAGAGAGATAAGATTCGTTATATTCAGTCTGCTCCACTG
1 CAACTTCAAG-GA-ATAAGATTAG-TAGCTTCAATCTGCTCCACTG
* * * * * *
104399564 TAATTTTAGGGAGATAAGACTT-GTAACTTCAATATGCTCCACTG
1 CAACTTCAAGGA-ATAAGA-TTAGTAGCTTCAATCTGCTCCACTG
* * * *
104399608 CAACTTCAGGGAGATAAGGTCT-GCTATCTTCAATCTACTCCACTG
1 CAACTTCAAGGA-ATAAGAT-TAG-TAGCTTCAATCTGCTCCACTG
* *
104399653 CAACTTC-AGAGAGATAAGATTTGTAATTTGTAGCTTTAATCTGTTCCACTG
1 CAACTTCAAG-GA-ATAAGA--T-T-A---GTAGCTTCAATCTGCTCCACTG
* * * * * * *
104399704 CAACTTCAATGAAATGAGATTTACTATCTTCAGTTTGCTCCGCTG
1 CAACTTCAA-GGAATAAGA-TTAGTAGCTTCAATCTGCTCCACTG
** *
104399749 CAACTTCAAGGAGATAAGACTT-GTAATTTCAACCTGCTCCACTG
1 CAACTTCAAGGA-ATAAGA-TTAGTAGCTTCAATCTGCTCCACTG
* *
104399793 CACCTTCAGGGAGATAAGAT
1 CAACTTCAAGGA-ATAAGAT
104399813 CTGTCATGGT
Statistics
Matches: 262, Mismatches: 57, Indels: 37
0.74 0.16 0.10
Matches are distributed among these distances:
42 2 0.01
43 39 0.15
44 85 0.32
45 94 0.36
46 3 0.01
47 2 0.01
48 1 0.00
49 1 0.00
50 2 0.01
51 29 0.11
52 3 0.01
53 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (43 bp):
CAACTTCAAGGAATAAGATTAGTAGCTTCAATCTGCTCCACTG
Found at i:104399622 original size:89 final size:89
Alignment explanation
Indices: 104399458--104400002 Score: 318
Period size: 89 Copynumber: 5.9 Consensus size: 89
104399448 GGATTTGTTG
* * *
104399458 CTTCAATCTGCTCCACTGCAACTTCAAGGA-ATAAGA-TTAGTAGCTTCAATCTGCTTCATTGCA
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGACTT-GTAACTTCAATCTGCTCCACTGCA
* * * *
104399521 AATTTAGAGAGATAAGATTCGTTAT
65 ACTTCAGGGAGATAAGATTCGCTAT
* * * * * * *
104399546 ATTCAGTCTGCTCCACTGTAATTTTAGGGAGATAAGACTTGTAACTTCAATATGCTCCACTGCAA
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAA
*
104399611 CTTCAGGGAGATAAG-GTCTGCTAT
66 CTTCAGGGAGATAAGATTC-GCTAT
* * * *
104399635 CTTCAATCTACTCCACTGCAACTTC-AGAGAGATAAGATTTGTAATTTGTAGCTTTAATCTGTTC
1 CTTCAATCTGCTCCACTGCAACTTCAAG-GAGATAAGACTTGT-A-----A-CTTCAATCTGCTC
** * * **
104399699 CACTGCAACTTCAATGAAATGAGATTTACTAT
58 CACTGCAACTTCAGGGAGATAAGATTCGCTAT
* * * * * *
104399731 CTTCAGTTTGCTCCGCTGCAACTTCAAGGAGATAAGACTTGTAATTTCAACCTGCTCCACTGCAC
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAA
* *
104399796 CTTCAGGGAGATAAGATCTGTCATGGTAG
66 CTTCAGGGAGATAAGA--T-TC--GCTAT
* * * * * * *
104399825 ATTTAATC--CAACCTACTGCAACTTCAGAGGTATAGGATTTATGACTTGTAGCTT-GATCT-AT
1 CTTCAATCTGC-TCC-ACTGCAACTTCA-AGG---A-GA--TAAGACTTGTAACTTCAATCTGCT
* * *
104399886 CCCACTACAACTTCAAGGAAATAAGATTCGCTAT
57 -CCACTGCAACTTCAGGGAGATAAGATTCGCTAT
* ** * ** * *
104399920 CTTCAGTCTGCTCCACTGCAACTTC-AGAGAGATAAGGTTTATGGCTTTAATCCT-CTCCACTGT
1 CTTCAATCTGCTCCACTGCAACTTCAAG-GAGATAAGACTTGTAACTTCAAT-CTGCTCCACTGC
104399983 AACTTCAGGGAGATAAGATT
64 AACTTCAGGGAGATAAGATT
104400003 TGTCATAACA
Statistics
Matches: 340, Mismatches: 84, Indels: 65
0.70 0.17 0.13
Matches are distributed among these distances:
88 37 0.11
89 128 0.38
90 9 0.03
91 2 0.01
92 2 0.01
93 4 0.01
94 18 0.05
95 24 0.07
96 69 0.20
97 6 0.02
98 2 0.01
99 3 0.01
100 24 0.07
101 12 0.04
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (89 bp):
CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAA
CTTCAGGGAGATAAGATTCGCTAT
Found at i:104400039 original size:189 final size:185
Alignment explanation
Indices: 104399532--104400053 Score: 495
Period size: 189 Copynumber: 2.8 Consensus size: 185
104399522 ATTTAGAGAG
* * * * * * *
104399532 ATAAGATTCGTTATATTCAGTCTGCTCCACTGTAATTTTAGGGAGATAAGACTTGTAACTTCAAT
1 ATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGT-ACTTTAAT
* * * *
104399597 -ATGCTCCACTGCAACTTCAGGGAGATAAGGTCTG-C-TATCTTCAATCTACTCCACTGCAACTT
65 CCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTCATAACTTCAATCCAC-CCACTGCAACTT
* * * * * * *
104399659 CAGAGAGATAAGATTTGTAATTTGTAGCTTTAATCTGTTCCACTGCAACTTCAATGAA
129 CAGAG-GATAGGATTTATAACTTGTAGCTTTAATCTATCCCACTACAACTTCAAGGAA
* ** * * *
104399717 ATGAGATTTACTATCTTCAGTTTGCTCCGCTGCAACTTCA-AGGAGATAAGACTTGTAATTTCAA
1 ATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGA-GAGATAAGACTTGTACTTT-AA
* * *
104399781 -CCTGCTCCACTGCACCTTCAGGGAGATAAGATCTGTCATGGTAGA-TTTAATCCAACCTACTGC
64 TCCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTCA---TA-ACTTCAATCC-ACCCACTGC
* *
104399844 AACTTCAGAGGTATAGGATTTATGACTTGTAGC-TTGATCTATCCCACTACAACTTCAAGGAA
124 AACTTCAGAGG-ATAGGATTTATAACTTGTAGCTTTAATCTATCCCACTACAACTTCAAGGAA
** * *
104399906 ATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGGTTTATGGCTTTAAT
1 ATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGT-ACTTTAAT
* * *
104399971 CCT-CTCCACTGTAACTTCAGGGAGATAAGATTTGTCATAACAACTTCAATCCATCCCACTGTAA
65 CCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTCAT---AACTTCAATCCA-CCCACTGCAA
104400035 CTTCA-AGGGCATAGGATTT
126 CTTCAGA-GG-ATAGGATTT
104400054 GTGATTCGTT
Statistics
Matches: 271, Mismatches: 46, Indels: 36
0.77 0.13 0.10
Matches are distributed among these distances:
184 3 0.01
185 77 0.28
186 2 0.01
188 3 0.01
189 136 0.50
190 48 0.18
191 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (185 bp):
ATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTACTTTAATC
CTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTCATAACTTCAATCCACCCACTGCAACTTCA
GAGGATAGGATTTATAACTTGTAGCTTTAATCTATCCCACTACAACTTCAAGGAA
Found at i:104408559 original size:27 final size:26
Alignment explanation
Indices: 104408526--104408579 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
104408516 TCAGCCTTAC
104408526 TCTTTCCCTTTCTCAGCTTCTCAGCT
1 TCTTTCCCTTTCTCAGCTTCTCAGCT
* *
104408552 TCNTTTCCCTTTCTTAGCTTCTCGGCT
1 TC-TTTCCCTTTCTCAGCTTCTCAGCT
104408579 T
1 T
104408580 TTAGTTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.06, C:0.35, G:0.09, T:0.48
Consensus pattern (26 bp):
TCTTTCCCTTTCTCAGCTTCTCAGCT
Found at i:104411690 original size:3 final size:3
Alignment explanation
Indices: 104411682--104411744 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
104411672 TTAAAGAAAC
* * *
104411682 ATA ATA ATA ATA ATA ATA ATA ATGA A-A A-A ATGA TTA AT- TTG ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA AT-A ATA ATA ATA ATA
104411726 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
104411745 CGTATAAGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 5 0.10
3 42 0.82
4 4 0.08
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:104412815 original size:16 final size:16
Alignment explanation
Indices: 104412796--104412830 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
104412786 TTGAAAATGT
104412796 TTTAGTTTGGGCCTGA
1 TTTAGTTTGGGCCTGA
*
104412812 TTTAGTTTGGGTCTGA
1 TTTAGTTTGGGCCTGA
104412828 TTT
1 TTT
104412831 TTGAGCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.09, G:0.29, T:0.51
Consensus pattern (16 bp):
TTTAGTTTGGGCCTGA
Found at i:104414042 original size:20 final size:20
Alignment explanation
Indices: 104414017--104414055 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
104414007 TTAAAATTTA
104414017 AATTTTTGGACTTTCTTTTG
1 AATTTTTGGACTTTCTTTTG
104414037 AATTTTTGGACTTTCTTTT
1 AATTTTTGGACTTTCTTTT
104414056 AATAAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.10, G:0.13, T:0.62
Consensus pattern (20 bp):
AATTTTTGGACTTTCTTTTG
Found at i:104423344 original size:17 final size:17
Alignment explanation
Indices: 104423299--104423344 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
104423289 AAAGAGAAAG
*
104423299 AAAAGAAAAA-TAAGAT
1 AAAATAAAAATTAAGAT
*
104423315 AAAATAAACATTAAGA-
1 AAAATAAAAATTAAGAT
104423331 AAAATAAATAATTA
1 AAAATAAA-AATTA
104423345 TTTATCTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.20
Consensus pattern (17 bp):
AAAATAAAAATTAAGAT
Found at i:104425470 original size:8 final size:8
Alignment explanation
Indices: 104425457--104425488 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
104425447 TATATGTATG
104425457 ATTGTGAA
1 ATTGTGAA
104425465 ATTGTGAA
1 ATTGTGAA
104425473 ATTGTGAA
1 ATTGTGAA
*
104425481 ATTATGAA
1 ATTGTGAA
104425489 CATATATGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (8 bp):
ATTGTGAA
Found at i:104428334 original size:43 final size:43
Alignment explanation
Indices: 104428231--104428371 Score: 114
Period size: 44 Copynumber: 3.3 Consensus size: 43
104428221 GTCCCAGAAT
* * * * *
104428231 TGGTCTTACA-TTTAATCAAATATTGATGCCACTGTCCCAGATA
1 TGGTCTTACACGTAAATCAAATA-TGATGCAACTGTCCCAAACA
* *
104428274 GGGTCTTACAC--AGAATCAAATATGATGTCGA-TGTCCCAAACA
1 TGGTCTTACACGTA-AATCAAATATGATG-CAACTGTCCCAAACA
*
104428316 TGGTCTTACACGTAAATCATAAGT-CGATGCCAACT-TCCCAAACA
1 TGGTCTTACACGTAAATCA-AA-TATGATG-CAACTGTCCCAAACA
104428360 TGGTCTTACACG
1 TGGTCTTACACG
104428372 AAAACACATA
Statistics
Matches: 81, Mismatches: 9, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
42 24 0.30
43 25 0.31
44 30 0.37
45 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (43 bp):
TGGTCTTACACGTAAATCAAATATGATGCAACTGTCCCAAACA
Found at i:104429894 original size:23 final size:24
Alignment explanation
Indices: 104429846--104430000 Score: 73
Period size: 23 Copynumber: 6.6 Consensus size: 24
104429836 GATATATCAA
*
104429846 CTCATAGGAGCTTACTATTTTCAG
1 CTCATAGGAGCTTACTAGTTTCAG
* *
104429870 CTCATTGGAGCTTAC-CGTTTCAG
1 CTCATAGGAGCTTACTAGTTTCAG
* *
104429893 CTCGT-GTGAGCTTACT-G-TTCAA
1 CTCATAG-GAGCTTACTAGTTTCAG
*
104429915 CTCGATA-GAGCTTA-TCA-TTTCAA
1 CTC-ATAGGAGCTTACT-AGTTTCAG
104429938 CTCGATA-GAGCTTATCT--TTTCAG
1 CTC-ATAGGAGCTTA-CTAGTTTCAG
*
104429961 CTCAATA-GAGCTTA-TTGTTCATCAG
1 CTC-ATAGGAGCTTACTAGTT--TCAG
*
104429986 CTCAGGAGGAGCTTA
1 CTCA-TAGGAGCTTA
104430001 TCGATCATGG
Statistics
Matches: 107, Mismatches: 9, Indels: 28
0.74 0.06 0.19
Matches are distributed among these distances:
21 2 0.02
22 15 0.14
23 59 0.55
24 15 0.14
25 9 0.08
26 7 0.07
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (24 bp):
CTCATAGGAGCTTACTAGTTTCAG
Found at i:104431727 original size:34 final size:34
Alignment explanation
Indices: 104431684--104431752 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
104431674 GCTAAGCTCC
* *
104431684 ATTCATCAGGATATGTATGTATGGTGTGTTGGAG
1 ATTCATCAGGATATGTATATATGGTGTGTTAGAG
*
104431718 ATTCATCAGGATATGTATATGTGGTGTGTTAGAG
1 ATTCATCAGGATATGTATATATGGTGTGTTAGAG
104431752 A
1 A
104431753 GTTTTAGCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.26, C:0.06, G:0.30, T:0.38
Consensus pattern (34 bp):
ATTCATCAGGATATGTATATATGGTGTGTTAGAG
Done.