Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001122.1 Hibiscus syriacus cultivar Beakdansim tig00002219_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: 113797
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:652 original size:49 final size:45
Alignment explanation
Indices: 542--662 Score: 172
Period size: 45 Copynumber: 2.6 Consensus size: 45
532 TGAGGTGATA
*
542 GTGGAGAAGAGGCTCGATGATGTGATGAAATAGGTGATGGTGGAG
1 GTGGAGAAGAGGCTCGATGATGTGATGGAATAGGTGATGGTGGAG
*
587 GTAGAGAAGAGGCTCGATGATGTGATGGAATAGGTGATGGTGGGTGGAG
1 GTGGAGAAGAGGCTCGATGATGTGATGGAATAGGTGA---T-GGTGGAG
*
636 GTGGAGAAGAGGCTCGATCA-GTGATGG
1 GTGGAGAAGAGGCTCGATGATGTGATGG
663 CTCCGGGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
45 35 0.51
48 8 0.12
49 25 0.37
ACGTcount: A:0.27, C:0.06, G:0.45, T:0.21
Consensus pattern (45 bp):
GTGGAGAAGAGGCTCGATGATGTGATGGAATAGGTGATGGTGGAG
Found at i:2204 original size:20 final size:20
Alignment explanation
Indices: 2177--2232 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
2167 AATTCACAAT
2177 GCGAAAATGAAAATCGCAAC
1 GCGAAAATGAAAATCGCAAC
* *
2197 GTGAAAATGAAAACCGCAAC
1 GCGAAAATGAAAATCGCAAC
*
2217 GCGAAACT-AAAATCGC
1 GCGAAAATGAAAATCGC
2233 GTTGCGATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 7 0.23
20 24 0.77
ACGTcount: A:0.48, C:0.21, G:0.20, T:0.11
Consensus pattern (20 bp):
GCGAAAATGAAAATCGCAAC
Found at i:2256 original size:20 final size:20
Alignment explanation
Indices: 2229--2279 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
2219 GAAACTAAAA
2229 TCGCGTTGCGATTTTCATGTT
1 TCGCGTTGCGATTTTCAT-TT
2250 T-GCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
*
2269 TCGTGTTGCGA
1 TCGCGTTGCGA
2280 ATTTAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 3 0.11
20 24 0.86
21 1 0.04
ACGTcount: A:0.10, C:0.18, G:0.25, T:0.47
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATTT
Found at i:2628 original size:21 final size:22
Alignment explanation
Indices: 2599--2656 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
2589 AGATAGAGAT
*
2599 AGACGGATTT-GCCGGAGATGG
1 AGACAGATTTCGCCGGAGATGG
*
2620 AGACAGATTTCGTCGGAGATAGG
1 AGACAGATTTCGCCGGAGAT-GG
* *
2643 -GACGGATGTCGCCG
1 AGACAGATTTCGCCG
2657 TAGAGAGTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 9 0.30
22 19 0.63
23 2 0.07
ACGTcount: A:0.24, C:0.17, G:0.40, T:0.19
Consensus pattern (22 bp):
AGACAGATTTCGCCGGAGATGG
Found at i:2829 original size:20 final size:20
Alignment explanation
Indices: 2804--2874 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
2794 TAAGCGCGCT
*
2804 TTGCGAATTTGACTAATGTG
1 TTGCGAATTTGACTTATGTG
*
2824 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTATGTG
*
2844 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTATGTG
2864 TTGCGAATTTG
1 TTGCGAATTTG
2875 GAAACTGGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.18, C:0.11, G:0.25, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:20132 original size:24 final size:24
Alignment explanation
Indices: 20104--20150 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
20094 TTTTAAAATA
* *
20104 TTAAATATGTCCCTTGTATTTTTT
1 TTAAAAATGTCCCTTATATTTTTT
20128 TTAAAAATGTCCCTTATATTTTT
1 TTAAAAATGTCCCTTATATTTTT
20151 AATTCTATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (24 bp):
TTAAAAATGTCCCTTATATTTTTT
Found at i:20406 original size:41 final size:41
Alignment explanation
Indices: 20361--20441 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
20351 AAGTCTGGCT
* *
20361 TATTTAACTAAACAGGTCAGGCCCAGGCCTTTTTAAAAGCA
1 TATTTAACTAAACAGGTCAGGCCCAGGCCTATTAAAAAGCA
* **
20402 TATTTAACTAAACAGTTCAGGCTTAGGCCTATTAAAAAGC
1 TATTTAACTAAACAGGTCAGGCCCAGGCCTATTAAAAAGC
20442 CTTATAAGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (41 bp):
TATTTAACTAAACAGGTCAGGCCCAGGCCTATTAAAAAGCA
Found at i:20611 original size:18 final size:17
Alignment explanation
Indices: 20572--20611 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
20562 TATTGTTAAA
*
20572 CAGGCTTTTAAACAGGC
1 CAGGCTTTTAAACAGCC
20589 CAGGCTTTTAAACAGACC
1 CAGGCTTTTAAACAG-CC
20607 CAGGC
1 CAGGC
20612 CAGACCTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.20
Consensus pattern (17 bp):
CAGGCTTTTAAACAGCC
Found at i:25939 original size:37 final size:35
Alignment explanation
Indices: 25888--26081 Score: 111
Period size: 37 Copynumber: 5.4 Consensus size: 35
25878 TTTAAAACGT
25888 TTTTGAAAACTTATAT-ACAATATATAAGTTTTAAAAT-A
1 TTTTGAAAA-TTATATAAC-ATATAT---TTTTAAAATCA
*
25926 TTTTGAAAATTATATAACATATATTTTTGAAATCA
1 TTTTGAAAATTATATAACATATATTTTTAAAATCA
** ** *
25961 TTTTG-AAA--ATATAATGTATAGTTTAAAAAAAACA
1 TTTTGAAAATTATATAACATATA-TTT-TTAAAATCA
* *
25995 TTTTTGAAAAATTTATATAATATATAGTTTTAAAAAT-A
1 -TTTTG-AAAA-TTATATAACATATA-TTTTTAAAATCA
26033 TTTTGGAAAACTTATAT---A-ATATTTTTAAAATCA
1 TTTT-GAAAA-TTATATAACATATATTTTTAAAATCA
*
26066 TTTTTGAAAACTATAT
1 -TTTTGAAAATTATAT
26082 GGTATATAGT
Statistics
Matches: 130, Mismatches: 13, Indels: 32
0.74 0.07 0.18
Matches are distributed among these distances:
32 24 0.18
33 12 0.09
34 21 0.16
35 11 0.08
37 29 0.22
38 13 0.10
39 5 0.04
40 15 0.12
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (35 bp):
TTTTGAAAATTATATAACATATATTTTTAAAATCA
Found at i:25964 original size:35 final size:35
Alignment explanation
Indices: 25853--25970 Score: 98
Period size: 39 Copynumber: 3.2 Consensus size: 35
25843 AACGGTTTCC
* *
25853 GAAAATATATATATAATATAGTTTGTTTAAAACGT-TTTT
1 GAAAAT-TATATACAATATA-TAT-TTTAAAA--TATTTT
25892 GAAAACTTATATACAATATATAAGTTTTAAAATATTTT
1 GAAAA-TTATATACAATATAT-A-TTTTAAAATATTTT
*
25930 GAAAATTATATA-ACATATAT-TTTTGAAATCATTTT
1 GAAAATTATATACA-ATATATATTTTAAAAT-ATTTT
25965 GAAAAT
1 GAAAAT
25971 ATAATGTATA
Statistics
Matches: 70, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
34 8 0.11
35 11 0.16
36 1 0.01
37 14 0.20
38 10 0.14
39 24 0.34
40 2 0.03
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (35 bp):
GAAAATTATATACAATATATATTTTAAAATATTTT
Found at i:26060 original size:33 final size:31
Alignment explanation
Indices: 26014--26081 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 31
26004 AATTTATATA
26014 ATATATAGTTTTAAAAAT-ATTTTGGAAAACTT
1 ATATATAGTTTT-AAAATCATTTTGGAAAAC-T
* *
26046 ATATAATATTTTTAAAATCATTTTTGAAAACT
1 ATAT-ATAGTTTTAAAATCATTTTGGAAAACT
26078 ATAT
1 ATAT
26082 GGTATATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (31 bp):
ATATATAGTTTTAAAATCATTTTGGAAAACT
Found at i:26063 original size:32 final size:32
Alignment explanation
Indices: 26014--26081 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
26004 AATTTATATA
26014 ATATATAGTTTTAAAAAT-ATTTTGGAAAACTT
1 ATATATAGTTTTAAAAATCATTTTGGAAAAC-T
* *
26046 ATATAATA-TTTTTAAAATCATTTTTGAAAACT
1 ATAT-ATAGTTTTAAAAATCATTTTGGAAAACT
26078 ATAT
1 ATAT
26082 GGTATATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 18 0.56
33 14 0.44
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (32 bp):
ATATATAGTTTTAAAAATCATTTTGGAAAACT
Found at i:26106 original size:107 final size:105
Alignment explanation
Indices: 25881--26080 Score: 264
Period size: 107 Copynumber: 1.9 Consensus size: 105
25871 TAGTTTGTTT
*
25881 AAAACGTTTTTGAAAACTTATATACAATATATAAGTTTTAAAATATTTTGAAAATTATATAACAT
1 AAAACGTTTTTGAAAAATTATATACAATATATAAGTTTTAAAATATTTTGAAAATTATAT-A-AT
*
25946 ATATTTTTGAAATCATTTTGAAAATATAATGTATAGTTTAAAA
64 ATATTTTTAAAATCATTTTGAAAATATAATGTATAGTTT-AAA
* *
25989 AAAACATTTTTGAAAAATT-TATATAATATAT-AGTTTTAAAAATATTTTGGAAAACTTATAT-A
1 AAAACGTTTTTGAAAAATTATATACAATATATAAGTTTT-AAAATATTTT-GAAAA-TTATATAA
26051 -ATATTTTTAAAATCATTTTTGAAAACTATA
63 TATATTTTTAAAATCA-TTTTGAAAA-TATA
26081 TGGTATATAG
Statistics
Matches: 83, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
105 14 0.17
106 16 0.19
107 25 0.30
108 22 0.27
109 6 0.07
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (105 bp):
AAAACGTTTTTGAAAAATTATATACAATATATAAGTTTTAAAATATTTTGAAAATTATATAATAT
ATTTTTAAAATCATTTTGAAAATATAATGTATAGTTTAAA
Found at i:26181 original size:13 final size:13
Alignment explanation
Indices: 26149--26194 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
26139 TTGAGATATA
*
26149 TATATATTA-TAG
1 TATATATTATTAT
*
26161 TCTATATTATTAT
1 TATATATTATTAT
26174 TATATATTATTAT
1 TATATATTATTAT
*
26187 TATTTATT
1 TATATATT
26195 TTCTTTTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 8 0.28
13 21 0.72
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (13 bp):
TATATATTATTAT
Found at i:27657 original size:3 final size:3
Alignment explanation
Indices: 27642--27680 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
27632 CCTTCTCTTT
27642 TTA TTA TGT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27681 CATATTGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 32 0.94
4 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27807 original size:14 final size:14
Alignment explanation
Indices: 27783--27817 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
27773 TAATTATCAT
27783 TATTTTTTTTTG-A
1 TATTTTTTTTTGAA
27796 TATTTCTTTTTTGAA
1 TATTT-TTTTTTGAA
27811 TATTTTT
1 TATTTTT
27818 AGTAATAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 9 0.45
15 6 0.30
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (14 bp):
TATTTTTTTTTGAA
Found at i:31803 original size:26 final size:27
Alignment explanation
Indices: 31717--31804 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
31707 AATATAGAAT
* *
31717 ATAAAAATAATATATATGATGGTAAT-A
1 ATAAAAA-GATATATATAATGGTAATAA
* * * *
31744 ATAATAAAGATATAAACATTGGGAA-AA
1 ATAA-AAAGATATATATAATGGTAATAA
31771 ATAAAAAGATATATATAATGGTAATAA
1 ATAAAAAGATATATATAATGGTAATAA
31798 ATAAAAA
1 ATAAAAA
31805 TAAATAAATA
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
26 16 0.33
27 29 0.60
28 3 0.06
ACGTcount: A:0.60, C:0.01, G:0.11, T:0.27
Consensus pattern (27 bp):
ATAAAAAGATATATATAATGGTAATAA
Found at i:31815 original size:27 final size:27
Alignment explanation
Indices: 31717--31815 Score: 76
Period size: 27 Copynumber: 3.7 Consensus size: 27
31707 AATATAGAAT
* * *
31717 ATAAAAATAATATATATGATGGTAAT-A
1 ATAAAAAGAA-ATAAATAATGGTAATAA
* * * *
31744 ATAATAAAGATATAAACATTGGGAA-AA
1 ATAA-AAAGAAATAAATAATGGTAATAA
* *
31771 ATAAAAAGATATATATAATGGTAATAA
1 ATAAAAAGAAATAAATAATGGTAATAA
*
31798 ATAAAAATAAATAAATAA
1 ATAAAAAGAAATAAATAA
31816 ATAGCTATAA
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
26 16 0.29
27 35 0.64
28 4 0.07
ACGTcount: A:0.62, C:0.01, G:0.10, T:0.27
Consensus pattern (27 bp):
ATAAAAAGAAATAAATAATGGTAATAA
Found at i:31954 original size:37 final size:37
Alignment explanation
Indices: 31913--32001 Score: 85
Period size: 37 Copynumber: 2.4 Consensus size: 37
31903 ATAATGATGT
* *
31913 TAAAAAACAAAAATATATATAAATATCAAATATAA-AA
1 TAAAAAACAAAAATAGAAATAAATAT-AAATATAATAA
*
31950 T--AAAACAAATGAATAGAAATAAATATACATATAATAA
1 TAAAAAACAAA--AATAGAAATAAATATAAATATAATAA
*
31987 TAAAAGAAAAAAAAT
1 TAAAA-AACAAAAAT
32002 GTATGTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
35 8 0.19
36 7 0.17
37 17 0.40
38 3 0.07
39 2 0.05
40 5 0.12
ACGTcount: A:0.70, C:0.04, G:0.03, T:0.22
Consensus pattern (37 bp):
TAAAAAACAAAAATAGAAATAAATATAAATATAATAA
Found at i:32066 original size:2 final size:2
Alignment explanation
Indices: 32059--32090 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
32049 GATGATTATG
32059 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
32091 AATAAAATAA
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:32116 original size:27 final size:29
Alignment explanation
Indices: 32086--32180 Score: 88
Period size: 27 Copynumber: 3.2 Consensus size: 29
32076 ATATATATAT
32086 ATATAAATAAAATAA-AATAAAATAAA-A
1 ATATAAATAAAATAATAATAAAATAAAGA
*
32113 ATATACATAAAATATATATATATAAATAAAGGA
1 ATATAAATAAAATA-ATA-ATA-AAATAAA-GA
* * *
32146 ATA-AAATATAATAATAATGAAAATATAGT
1 ATATAAATAAAATAATAAT-AAAATAAAGA
32175 ATATAA
1 ATATAA
32181 TAATAGTAGG
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
27 13 0.24
28 1 0.02
29 5 0.09
30 13 0.24
31 11 0.20
32 8 0.15
33 4 0.07
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (29 bp):
ATATAAATAAAATAATAATAAAATAAAGA
Found at i:32124 original size:11 final size:11
Alignment explanation
Indices: 32080--32156 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 11
32070 ATATATATAT
*
32080 ATATATATATAA
1 ATATAAATA-AA
32092 ATA-AAATAAA
1 ATATAAATAAA
32102 ATA-AAATAAAA
1 ATATAAAT-AAA
*
32113 ATATACATAAA
1 ATATAAATAAA
32124 ATATATATATATAA
1 ATATA-A-ATA-AA
*
32138 ATAAAGGAATAAA
1 ATATA--AATAAA
32151 ATATAA
1 ATATAA
32157 TAATAATGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
10 9 0.17
11 19 0.36
12 6 0.11
13 9 0.17
14 9 0.17
15 1 0.02
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATAAATAAA
Found at i:32149 original size:44 final size:46
Alignment explanation
Indices: 32078--32179 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 46
32068 ATATATATAT
32078 ATATATATATATAAATAAAATAAAATAAAATAAAA-ATATACAT-AAA
1 ATATATATATATAAATAAAATAAAATAAAATAAAATA-ATA-ATGAAA
** *
32124 ATATATATATATAAAT-AAA-GGAATAAAATATAATAATAATGAAA
1 ATATATATATATAAATAAAATAAAATAAAATAAAATAATAATGAAA
32168 ATATAGTATATA
1 ATATA-TATATA
32180 ATAATAGTAG
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 2 0.04
44 22 0.44
45 10 0.20
46 16 0.32
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (46 bp):
ATATATATATATAAATAAAATAAAATAAAATAAAATAATAATGAAA
Found at i:33319 original size:16 final size:14
Alignment explanation
Indices: 33287--33325 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
33277 AAAAGTATAA
33287 ATATATATATTATT
1 ATATATATATTATT
33301 ATATAATATATTCATT
1 ATAT-ATATATT-ATT
33317 ATATGATAT
1 ATAT-ATAT
33326 GGTCGAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.18
15 7 0.32
16 11 0.50
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (14 bp):
ATATATATATTATT
Found at i:34003 original size:105 final size:105
Alignment explanation
Indices: 33787--34562 Score: 1284
Period size: 105 Copynumber: 7.4 Consensus size: 105
33777 ATATTGTTCC
* * ** * * ** *
33787 GAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATCGTCGGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAAT-GTTTGTTGACAA
* * **** *
33852 TCAGCGGCCCCTTCGTCGTGAAGTTGAACTTATACTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
** *
33893 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGACAAC
* *
33958 CAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
33998 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGACAAC
*
34063 CAGCGGT-CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
34102 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGACAAC
* *
34167 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
34207 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGACAAC
34272 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
*
34312 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGACAAC
*
34377 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
34417 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGACAAC
34482 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
* *
34522 GAGTACAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGG
34563 GTAAAACCTG
Statistics
Matches: 640, Mismatches: 29, Indels: 3
0.95 0.04 0.00
Matches are distributed among these distances:
104 104 0.16
105 489 0.76
106 47 0.07
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
Found at i:35394 original size:8 final size:8
Alignment explanation
Indices: 35379--35439 Score: 113
Period size: 8 Copynumber: 7.6 Consensus size: 8
35369 CATTCTTCTC
35379 TTTTTGTT
1 TTTTTGTT
*
35387 TATTTGTT
1 TTTTTGTT
35395 TTTTTGTT
1 TTTTTGTT
35403 TTTTTGTT
1 TTTTTGTT
35411 TTTTTGTT
1 TTTTTGTT
35419 TTTTTGTT
1 TTTTTGTT
35427 TTTTTGTT
1 TTTTTGTT
35435 TTTTT
1 TTTTT
35440 TTTCAACTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 51 1.00
ACGTcount: A:0.02, C:0.00, G:0.11, T:0.87
Consensus pattern (8 bp):
TTTTTGTT
Found at i:35397 original size:1 final size:1
Alignment explanation
Indices: 35379--35442 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
35369 CATTCTTCTC
* * * * * * * *
35379 TTTTTGTTTATTTGTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
35443 CAACTTAGGA
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.02, C:0.00, G:0.11, T:0.88
Consensus pattern (1 bp):
T
Found at i:44896 original size:10 final size:10
Alignment explanation
Indices: 44871--44905 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
44861 AGGTTAGTAA
*
44871 AAATAGAAAT
1 AAATAAAAAT
*
44881 AGATAAAAAT
1 AAATAAAAAT
44891 AAATAAAAAT
1 AAATAAAAAT
44901 AAATA
1 AAATA
44906 TTAAATGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:45966 original size:26 final size:27
Alignment explanation
Indices: 45880--45967 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
45870 AATATAGAAT
* *
45880 ATAAAAATAATATATATGATGGTAAT-A
1 ATAAAAA-GATATATATAATGGTAATAA
* * * *
45907 ATAATAAAGATATAAACATTGGGAA-AA
1 ATAA-AAAGATATATATAATGGTAATAA
45934 ATAAAAAGATATATATAATGGTAATAA
1 ATAAAAAGATATATATAATGGTAATAA
45961 ATAAAAA
1 ATAAAAA
45968 CAAAAAAATA
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
26 16 0.33
27 29 0.60
28 3 0.06
ACGTcount: A:0.60, C:0.01, G:0.11, T:0.27
Consensus pattern (27 bp):
ATAAAAAGATATATATAATGGTAATAA
Found at i:46240 original size:2 final size:2
Alignment explanation
Indices: 46233--46312 Score: 69
Period size: 2 Copynumber: 42.0 Consensus size: 2
46223 GATGATTATG
* *
46233 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA AA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
46274 TA -A AA TA -A AA TA AA AA TA TA CA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46313 AATAAAGGAA
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
1 4 0.06
2 60 0.94
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (2 bp):
TA
Found at i:47485 original size:16 final size:14
Alignment explanation
Indices: 47453--47491 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
47443 AAAAGTATAA
47453 ATATATATATTATT
1 ATATATATATTATT
47467 ATATAATATATTCATT
1 ATAT-ATATATT-ATT
47483 ATATGATAT
1 ATAT-ATAT
47492 GGTCGAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.18
15 7 0.32
16 11 0.50
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (14 bp):
ATATATATATTATT
Found at i:47759 original size:106 final size:106
Alignment explanation
Indices: 47627--48716 Score: 1837
Period size: 106 Copynumber: 10.3 Consensus size: 106
47617 CTCGAGAGTA
*
47627 AATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
47692 GACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
47733 AATTTCAACTTCACAACGAAGGATATTGGACCCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
47798 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
47839 AATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
47904 GACTGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
47945 AATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
48010 GA-CGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
48050 AATTTCAA-TTCACAACGAAGGATATTGGACCCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
48114 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
48155 AATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
48220 GACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
* *
48261 AATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
48326 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
48367 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
48432 GACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
48473 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * **
48538 GACCGCTGGTTGTCAATAAACAATTTCCCAAACTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
** * * * *
48579 AATTTCAACTTCACTGCGAAGGATATTGGACTCGAGGCAACACAAGTTCAACTTCACAACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
48644 GA-CGACTGGTTGTCAATAAACAA-TTTTCCAGTTCCAGAGCC
66 GACCG-CTGGTTGTCAATAAACAACTTCT-CAATTTCAGAGCC
** *
48685 AATTTCAACTTCACGGCGGAGGATATTGGACT
1 AATTTCAACTTCACAACGAAGGATATTGGACT
48717 TGGAACAATA
Statistics
Matches: 934, Mismatches: 46, Indels: 8
0.95 0.05 0.01
Matches are distributed among these distances:
104 56 0.06
105 90 0.10
106 788 0.84
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
Found at i:49534 original size:35 final size:35
Alignment explanation
Indices: 49424--49541 Score: 105
Period size: 39 Copynumber: 3.2 Consensus size: 35
49414 AACGGTTTCC
* * *
49424 GAAAATATATATATAATATAGTTTGTTTAAAACGTTTTT
1 GAAAAT-TATATACAATATA-TAT-TTTAAAAC-ATTTT
49463 GAAAACTTATATACAATATATAAGTTTTAAAACATTTT
1 GAAAA-TTATATACAATATAT-A-TTTTAAAACATTTT
*
49501 GAAAATTATATA-ACATATAT-TTTTGAAATCATTTT
1 GAAAATTATATACA-ATATATATTTT-AAAACATTTT
49536 GAAAAT
1 GAAAAT
49542 ATAATGTATA
Statistics
Matches: 70, Mismatches: 4, Indels: 14
0.80 0.05 0.16
Matches are distributed among these distances:
34 4 0.06
35 15 0.21
36 1 0.01
37 13 0.19
38 10 0.14
39 25 0.36
40 2 0.03
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (35 bp):
GAAAATTATATACAATATATATTTTAAAACATTTT
Found at i:49591 original size:108 final size:109
Alignment explanation
Indices: 49452--49652 Score: 270
Period size: 108 Copynumber: 1.9 Consensus size: 109
49442 TAGTTTGTTT
* *
49452 AAAACGTTTTTGAAAACTTATATACAATATATAAGTTTT-AAAACATTTT-GAAAA-TTATATAA
1 AAAACATTTTTGAAAAATTATATACAATATAT-AGTTTTAAAAACATTTTGGAAAACTTATAT--
*
49514 CATATATTTTTGAAATCA-TTTTGAAAA-TATAATGTATAGTTTTAAAA
63 -A-ATATTTTTAAAATCATTTTTGAAAACTATAATGTATAGTTTTAAAA
* *
49561 AAAACATTTTTGAAAAATT-TATATAATATATAGTTTTAAAAATATTTTGGAAAACTTATATAAT
1 AAAACATTTTTGAAAAATTATATACAATATATAGTTTTAAAAACATTTTGGAAAACTTATATAAT
49625 ATTTTTAAAATCATTTTTGAAAACTATA
66 ATTTTTAAAATCATTTTTGAAAACTATA
49653 TGGTATATAG
Statistics
Matches: 82, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
106 14 0.17
107 16 0.20
108 24 0.29
109 22 0.27
110 6 0.07
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.42
Consensus pattern (109 bp):
AAAACATTTTTGAAAAATTATATACAATATATAGTTTTAAAAACATTTTGGAAAACTTATATAAT
ATTTTTAAAATCATTTTTGAAAACTATAATGTATAGTTTTAAAA
Found at i:49609 original size:37 final size:35
Alignment explanation
Indices: 49392--49702 Score: 162
Period size: 35 Copynumber: 8.6 Consensus size: 35
49382 TTTTTAAAAA
* * *
49392 ATATAACATATAGTTTTCAAAAAACGGTTTCCGAAAA-T
1 ATATAATATATAGTTTT--AAAAAC-ATTT-TGAAAATT
* *
49430 ATATATATAATATAGTTTGTTTAAAACGTTTTTGAAAACTT
1 ATATA-AT-ATATAG-TT-TTAAAAAC-ATTTTGAAAA-TT
49471 ATATACAATATATAAGTTTT-AAAACATTTTGAAAATT
1 ATAT--AATATAT-AGTTTTAAAAACATTTTGAAAATT
* * * *
49508 ATATAACATATATTTTTGAAATCATTTTG-AAA--
1 ATATAATATATAGTTTTAAAAACATTTTGAAAATT
*
49540 ATATAATGTATAGTTTTAAAAAAAACATTTTTGAAAAATTT
1 ATATAATATATAGTTTT---AAAAACA-TTTTG-AAAA-TT
*
49581 ATATAATATATAGTTTTAAAAATATTTTGGAAAACTT
1 ATATAATATATAGTTTTAAAAACATTTT-GAAAA-TT
* *
49618 ATAT-A-ATAT--TTTTAAAATCATTTTTGAAAACT
1 ATATAATATATAGTTTTAAAAACA-TTTTGAAAATT
** * * *
49650 ATATGGTATATAGTTTTGAAAACGTTTT--TAA--
1 ATATAATATATAGTTTTAAAAACATTTTGAAAATT
*
49681 ATATAATATATAGTTTAAAAAA
1 ATATAATATATAGTTTTAAAAA
49703 TATATTTTTT
Statistics
Matches: 220, Mismatches: 28, Indels: 57
0.72 0.09 0.19
Matches are distributed among these distances:
31 18 0.08
32 19 0.09
33 16 0.07
34 16 0.07
35 29 0.13
36 14 0.06
37 20 0.09
38 24 0.11
39 11 0.05
40 17 0.08
41 29 0.13
42 6 0.03
43 1 0.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (35 bp):
ATATAATATATAGTTTTAAAAACATTTTGAAAATT
Found at i:49635 original size:32 final size:32
Alignment explanation
Indices: 49586--49653 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
49576 AATTTATATA
49586 ATATATAGTTTTAAAAAT-ATTTTGGAAAACTT
1 ATATATAGTTTTAAAAATCATTTTGGAAAAC-T
* *
49618 ATATAATA-TTTTTAAAATCATTTTTGAAAACT
1 ATAT-ATAGTTTTAAAAATCATTTTGGAAAACT
49650 ATAT
1 ATAT
49654 GGTATATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 18 0.56
33 14 0.44
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (32 bp):
ATATATAGTTTTAAAAATCATTTTGGAAAACT
Found at i:49738 original size:16 final size:16
Alignment explanation
Indices: 49717--49758 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
49707 TTTTTTGAGA
49717 TATATATATTATATAGTC
1 TATAT-TATTAT-TAGTC
*
49735 TATATTATTATTAGTA
1 TATATTATTATTAGTC
49751 T-TATTATT
1 TATATTATT
49759 TTTATTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 5 0.22
17 6 0.26
18 5 0.22
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (16 bp):
TATATTATTATTAGTC
Found at i:49792 original size:18 final size:18
Alignment explanation
Indices: 49759--49807 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
49749 TATTATTATT
*
49759 TTTATTTCTTTTCATTTTA
1 TTTATTT-TATTCATTTTA
49778 TTTATTTTATTCATTTTA
1 TTTATTTTATTCATTTTA
49796 TTTCA-TTTATTC
1 TTT-ATTTTATTC
49808 TGTTTTGTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTTATTCATTTTA
Found at i:49806 original size:9 final size:10
Alignment explanation
Indices: 49768--49803 Score: 58
Period size: 9 Copynumber: 3.8 Consensus size: 10
49758 TTTTATTTCT
49768 TTTCATTTTA
1 TTTCATTTTA
49778 TTT-ATTTTA
1 TTTCATTTTA
49787 -TTCATTTTA
1 TTTCATTTTA
49796 TTTCATTT
1 TTTCATTT
49804 ATTCTGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 2 0.08
9 12 0.50
10 10 0.42
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTCATTTTA
Found at i:51356 original size:13 final size:13
Alignment explanation
Indices: 51333--51365 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
51323 TAATTATCAT
51333 TATTTTTTTTG-A
1 TATTTTTTTTGAA
51345 TATTTCTTTTTGAA
1 TATTT-TTTTTGAA
51359 TATTTTT
1 TATTTTT
51366 AGTAATAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.26
13 8 0.42
14 6 0.32
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.73
Consensus pattern (13 bp):
TATTTTTTTTGAA
Found at i:65358 original size:18 final size:19
Alignment explanation
Indices: 65335--65372 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
65325 ATCAGTAATC
65335 TTATTCT-CTGATAATCTT
1 TTATTCTACTGATAATCTT
65353 TTATTCTCACTGATAATCTT
1 TTATTCT-ACTGATAATCTT
65373 ACATTTCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.24, C:0.18, G:0.05, T:0.53
Consensus pattern (19 bp):
TTATTCTACTGATAATCTT
Found at i:66030 original size:14 final size:14
Alignment explanation
Indices: 66011--66041 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
66001 TTTAATCTTA
66011 AAATTTAAAATATT
1 AAATTTAAAATATT
*
66025 AAATTTAATATATT
1 AAATTTAAAATATT
66039 AAA
1 AAA
66042 ATAAACAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATTTAAAATATT
Found at i:74235 original size:3 final size:3
Alignment explanation
Indices: 74227--74258 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
74217 AATCAACAAA
*
74227 AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
74259 ACCAGATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:93867 original size:17 final size:17
Alignment explanation
Indices: 93845--93877 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
93835 TGAAAGTTTT
93845 AAAATATGTTCGAATGA
1 AAAATATGTTCGAATGA
93862 AAAATATGTTCGAATG
1 AAAATATGTTCGAATG
93878 GAAGGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (17 bp):
AAAATATGTTCGAATGA
Found at i:94157 original size:165 final size:165
Alignment explanation
Indices: 93951--94280 Score: 579
Period size: 165 Copynumber: 2.0 Consensus size: 165
93941 GAGATGATCT
* *
93951 GGTTTTCAAGAGGAAAACAACATTAATAGCATGGTTTGAAAGTTTTAATATTTTTATTTTAATTT
1 GGTTTTCAAGAGGAAAACAACATGAATAACATGGTTTGAAAGTTTTAATATTTTTATTTTAATTT
* * *
94016 CAGATTTATTTTTCTAATGTTTTACGAAATCTTATGTTTTTTTCTCATTTTAGTTATGTTATTGT
66 CAGATTTATTTTTCTAATGTTTTACGAAATCTTATGTTTTTATCTCATTTTAGCTATGCTATTGT
94081 CTCACTAAGTTTTATTTTGAGTGTGATGATTTTCA
131 CTCACTAAGTTTTATTTTGAGTGTGATGATTTTCA
* * *
94116 GGTTTTCAAGAGGAAAGCAACATGAATAATATGTTTTGAAAGTTTTAATATTTTTATTTTAATTT
1 GGTTTTCAAGAGGAAAACAACATGAATAACATGGTTTGAAAGTTTTAATATTTTTATTTTAATTT
*
94181 TAGATTTATTTTTCTAATGTTTTACGAAATCTTATGTTTTTATCTCATTTTAGCTATGCTATTGT
66 CAGATTTATTTTTCTAATGTTTTACGAAATCTTATGTTTTTATCTCATTTTAGCTATGCTATTGT
94246 CTCACTAAGTTTTATTTTGAGTGTGATGATTTTCA
131 CTCACTAAGTTTTATTTTGAGTGTGATGATTTTCA
94281 TGCGTAGATT
Statistics
Matches: 156, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
165 156 1.00
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.50
Consensus pattern (165 bp):
GGTTTTCAAGAGGAAAACAACATGAATAACATGGTTTGAAAGTTTTAATATTTTTATTTTAATTT
CAGATTTATTTTTCTAATGTTTTACGAAATCTTATGTTTTTATCTCATTTTAGCTATGCTATTGT
CTCACTAAGTTTTATTTTGAGTGTGATGATTTTCA
Found at i:96222 original size:6 final size:7
Alignment explanation
Indices: 96203--96228 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
96193 AATAGTGTAT
96203 AGAAAAA
1 AGAAAAA
96210 AGAAAAA
1 AGAAAAA
96217 AGAAAAA
1 AGAAAAA
96224 AGAAA
1 AGAAA
96229 TGATGGACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:98574 original size:3 final size:3
Alignment explanation
Indices: 98566--98611 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
98556 TCCGGGTTTT
**
98566 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
98612 ATTAATTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:112993 original size:141 final size:141
Alignment explanation
Indices: 112775--113045 Score: 386
Period size: 141 Copynumber: 1.9 Consensus size: 141
112765 AACATCAACT
*
112775 GACCAGATCTCCTCATCACGTAGGAGAGTGTCAACATTAGGGTAACCAGCCGTCCTCATCACGTA
1 GACCAGATCTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
* * ** *
112840 GGAACTGAGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCATC
66 GGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATC
112905 TACCCTTAGAC
131 TACCCTTAGAC
*
112916 GACCAGA-CTTCCTCATCACGTAGGAGCCA-TGTCAACCTTA-GATAACCAGCCGTCCTCATCAC
1 GACCAGATC-TCCTCATCACGTAGGAG--AGTGTCAACATTAGGATAACCAGCCGTCCTCATCAC
* * * * *
112978 GTAGGAACCGAGTTATCACCCTTCTTAAGGATGACCAGAACTCTTCATCGCGTATGACCCGTGTC
63 GTAGGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTC
113043 ATC
128 ATC
113046 CCTTGACCAG
Statistics
Matches: 115, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
140 1 0.01
141 103 0.90
142 10 0.09
143 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.25
Consensus pattern (141 bp):
GACCAGATCTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
GGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATC
TACCCTTAGAC
Found at i:113034 original size:23 final size:23
Alignment explanation
Indices: 113008--113074 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 23
112998 CTTCTTAAGG
113008 ATGACCAGAACTCTTCATCGCGT
1 ATGACCAGAACTCTTCATCGCGT
* * *
113031 ATGACCCG---T-GTCATC-CCT
1 ATGACCAGAACTCTTCATCGCGT
113049 -TGACCAGAACTCTTCATCGCGT
1 ATGACCAGAACTCTTCATCGCGT
113071 ATGA
1 ATGA
113075 GCCGTGTCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
17 6 0.19
18 2 0.06
19 5 0.16
20 2 0.06
21 5 0.16
22 2 0.06
23 10 0.31
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (23 bp):
ATGACCAGAACTCTTCATCGCGT
Found at i:113064 original size:40 final size:40
Alignment explanation
Indices: 113009--113111 Score: 170
Period size: 40 Copynumber: 2.6 Consensus size: 40
112999 TTCTTAAGGA
113009 TGACCAGAACTCTTCATCGCGTATGACCCGTGTCATCCCT
1 TGACCAGAACTCTTCATCGCGTATGACCCGTGTCATCCCT
*
113049 TGACCAGAACTCTTCATCGCGTATGAGCCGTGTCATCCCT
1 TGACCAGAACTCTTCATCGCGTATGACCCGTGTCATCCCT
** *
113089 TGACCAGATTTCTTCATCACGTA
1 TGACCAGAACTCTTCATCGCGTA
113112 GGAATCGTGT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.21, C:0.32, G:0.17, T:0.29
Consensus pattern (40 bp):
TGACCAGAACTCTTCATCGCGTATGACCCGTGTCATCCCT
Found at i:113121 original size:40 final size:40
Alignment explanation
Indices: 113009--113157 Score: 165
Period size: 40 Copynumber: 3.6 Consensus size: 40
112999 TTCTTAAGGA
*
113009 TGACCAGAACTCTTCATCGCGTATGACCCGTGTCATCCCT
1 TGACCAGAACTCTTCATCGCGTATGAACCGTGTCATCCCT
*
113049 TGACCAGAACTCTTCATCGCGTATGAGCCGTGTCATCCCT
1 TGACCAGAACTCTTCATCGCGTATGAACCGTGTCATCCCT
** * * * *
113089 TGACCAGATTTCTTCATCACGTAGGAATCGTGT-TTCCCT
1 TGACCAGAACTCTTCATCGCGTATGAACCGTGTCATCCCT
* *
113128 TAGACGACCCGAACTCTTCATCACGTATGA
1 T----GACCAGAACTCTTCATCGCGTATGA
113158 GCAGTGTCGT
Statistics
Matches: 93, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
39 6 0.06
40 66 0.71
43 21 0.23
ACGTcount: A:0.22, C:0.31, G:0.18, T:0.29
Consensus pattern (40 bp):
TGACCAGAACTCTTCATCGCGTATGAACCGTGTCATCCCT
Found at i:113321 original size:3 final size:3
Alignment explanation
Indices: 113313--113354 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
113303 TTTTCCGGGT
**
113313 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA TTTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TT
113355 TTAATTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Done.