Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008497.1 Hibiscus syriacus cultivar Beakdansim tig00111342_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: 1504768
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 1 of 6
Found at i:721 original size:92 final size:93
Alignment explanation
Indices: 515--892 Score: 717
Period size: 93 Copynumber: 4.1 Consensus size: 93
505 TAGATTGCTT
*
515 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
580 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
608 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
672 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
700 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAG--
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
763 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
791 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
856 TTTGTCTTTGTTTTGTCTTTTCGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
884 AGTAAATTT
1 AGTAAATTT
893 ATCCATTCAA
Statistics
Matches: 280, Mismatches: 2, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
91 91 0.32
92 92 0.33
93 97 0.35
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:825 original size:183 final size:185
Alignment explanation
Indices: 515--894 Score: 719
Period size: 183 Copynumber: 2.1 Consensus size: 185
505 TAGATTGCTT
515 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAG-A
580 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
645 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTCGTTGAA
*
700 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAG-T
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGAT
764 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
829 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTCGTTGAA
131 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTCGTTGAA
884 AGTAAATTTAT
1 AGTAAATTTAT
895 CCATTCAAGT
Statistics
Matches: 191, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
183 90 0.47
184 39 0.20
185 62 0.32
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (185 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGAT
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTCGTTGAA
Found at i:976 original size:19 final size:19
Alignment explanation
Indices: 936--1062 Score: 107
Period size: 19 Copynumber: 7.3 Consensus size: 19
926 TAGTTTACTT
* *
936 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
956 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
975 TCGCAACGCGAAA-TGAAA
1 TCGCAACGCGAAACCAAAA
*
993 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1007 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1026 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1040 TCGCAACGCGAAACC-AAA
1 TCGCAACGCGAAACCAAAA
1058 TCGCA
1 TCGCA
1063 TTGCGATTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 22
0.73 0.08 0.18
Matches are distributed among these distances:
14 19 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 18 0.21
19 28 0.32
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1032 original size:33 final size:31
Alignment explanation
Indices: 972--1062 Score: 137
Period size: 33 Copynumber: 2.8 Consensus size: 31
962 CGCGAAACCA
**
972 AAATCGCAACGCGAAATGAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAATCGCAACGAC
1003 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACC-AAATCGCAACGAC
1036 AAGATCGCAACGCGAAACCAAATCGCA
1 AA-ATCGCAACGCGAAACCAAATCGCA
1063 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
31 1 0.02
32 24 0.44
33 30 0.55
ACGTcount: A:0.45, C:0.29, G:0.19, T:0.08
Consensus pattern (31 bp):
AAATCGCAACGCGAAACCAAATCGCAACGAC
Found at i:1085 original size:19 final size:19
Alignment explanation
Indices: 1058--1192 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
1048 CGAAACCAAA
*
1058 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1077 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1093 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1110 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1126 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1143 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1162 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1182 TCGTGTTGCGA
1 TCGCGTTGCGA
1193 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1099 original size:14 final size:14
Alignment explanation
Indices: 1080--1136 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1070 TTTCATTTCG
1080 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1094 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1111 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
1127 CGTTGCGATT
1 CGTTGCGATT
1137 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1105 original size:33 final size:33
Alignment explanation
Indices: 1063--1155 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
1053 CCAAATCGCA
*
1063 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1096 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1129 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1156 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:3061 original size:19 final size:19
Alignment explanation
Indices: 2997--3061 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
2987 AGTTTAATTG
*
2997 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
3016 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
3034 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
3054 ATTGATTT
1 ATTGATTT
3062 GTAAAGATGA
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:3072 original size:13 final size:14
Alignment explanation
Indices: 3056--3090 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3046 ATTGTTTAAT
3056 TGATTTGT-AAAGA
1 TGATTTGTAAAAGA
*
3069 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3083 TGATTTGT
1 TGATTTGT
3091 GTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3212 original size:19 final size:19
Alignment explanation
Indices: 3196--3297 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
3186 AAAAATGACT
3196 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3215 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3234 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3248 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3267 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3287 ATCGCAATGCG
1 ATCGCAATGCG
3298 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3350 original size:19 final size:19
Alignment explanation
Indices: 3326--3760 Score: 570
Period size: 19 Copynumber: 24.4 Consensus size: 19
3316 GATTATCTCG
3326 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3345 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3364 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
3378 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3397 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3416 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
3435 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
3454 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3473 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
3487 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3506 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3525 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
3544 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
3563 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3582 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3596 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3615 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3634 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3648 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3667 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3686 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3700 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3720 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
3734 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
3753 TTGCGATT
1 TTGCGATT
3761 GTATTTTCCG
Statistics
Matches: 369, Mismatches: 16, Indels: 62
0.83 0.04 0.14
Matches are distributed among these distances:
14 41 0.11
16 39 0.11
17 36 0.10
18 3 0.01
19 238 0.64
20 12 0.03
ACGTcount: A:0.14, C:0.20, G:0.17, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3366 original size:52 final size:52
Alignment explanation
Indices: 3304--3732 Score: 696
Period size: 52 Copynumber: 8.0 Consensus size: 52
3294 TGCGTTTATA
*
3304 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
3356 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
3408 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
3465 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
3517 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
3574 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
3626 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
3678 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
3731 AT
1 AT
3733 GTTGGGATTT
Statistics
Matches: 359, Mismatches: 7, Indels: 21
0.93 0.02 0.05
Matches are distributed among these distances:
52 225 0.63
53 17 0.05
54 15 0.04
55 16 0.04
57 86 0.24
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:3456 original size:109 final size:107
Alignment explanation
Indices: 3326--3732 Score: 389
Period size: 109 Copynumber: 3.8 Consensus size: 107
3316 GATTATCTCG
3326 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * *
3388 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
61 CATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCA
*
3435 TTGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * *
3497 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
61 CATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCA
* *
3544 TTGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * *
3606 CATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG--
61 CATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCA
*
3648 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTCATTTCGATTGCGATTTT
3710 CATTTCCGCATTGCGATTTTCAT
61 CATTT-CGCATTGCGATTTTCAT
3733 GTTGGGATTT
Statistics
Matches: 292, Mismatches: 5, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
104 66 0.23
105 17 0.06
106 4 0.01
107 2 0.01
109 203 0.70
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.48
Consensus pattern (107 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCA
Found at i:6077 original size:12 final size:12
Alignment explanation
Indices: 6060--6084 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6050 TCTTCGGGGA
6060 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6072 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6084 C
1 C
6085 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:6292 original size:24 final size:24
Alignment explanation
Indices: 6258--6304 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6248 CTGAAACATC
6258 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
6282 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
6305 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:7006 original size:20 final size:20
Alignment explanation
Indices: 6978--7345 Score: 456
Period size: 20 Copynumber: 18.4 Consensus size: 20
6968 AAATTTCAGT
* * * *
6978 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
6998 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
7018 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
7038 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
7058 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
7078 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
7098 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
7118 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
7138 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
7158 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
7178 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
7198 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
7218 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
7238 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
7258 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
7278 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
** *
7298 GTTGCGATTTATTG-TTCGC
1 GTTGCGATTTACGGATACGC
* ** *
7317 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
7337 GTTGCGATT
1 GTTGCGATT
7346 ATGGAAAATC
Statistics
Matches: 308, Mismatches: 33, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
19 19 0.06
20 285 0.93
21 4 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:8157 original size:32 final size:32
Alignment explanation
Indices: 8083--8168 Score: 93
Period size: 37 Copynumber: 2.5 Consensus size: 32
8073 CCTAAACTCG
* *
8083 AACCCGACCCTACTCGAATATCACACTTAAAAAA
1 AACCCGA-CCGACCCGAATATCACACTT-AAAAA
8117 ACCCACCCGACTCGACCCGAATATCACACTT-AAAA
1 A---ACCCGAC-CGACCCGAATATCACACTTAAAAA
8152 AACCCGACCGACCCGAA
1 AACCCGACCGACCCGAA
8169 AAAAATAAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
31 9 0.20
32 7 0.15
34 1 0.02
35 5 0.11
36 1 0.02
37 23 0.50
ACGTcount: A:0.40, C:0.38, G:0.09, T:0.13
Consensus pattern (32 bp):
AACCCGACCGACCCGAATATCACACTTAAAAA
Found at i:13511 original size:20 final size:20
Alignment explanation
Indices: 13465--13511 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
13455 TTTTTTAACT
* *
13465 TTGTTTTTATTTTATTTTAA
1 TTGTTTTTATTTTAATATAA
*
13485 TTATTTTTATTTTAAATATAA
1 TTGTTTTTATTTT-AATATAA
13506 -TGTTTT
1 TTGTTTT
13512 CTAAATATAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (20 bp):
TTGTTTTTATTTTAATATAA
Found at i:13636 original size:45 final size:46
Alignment explanation
Indices: 13565--13657 Score: 116
Period size: 45 Copynumber: 2.0 Consensus size: 46
13555 ATTATATTAT
* * *
13565 AAATAGTTTTGAAAATATTATGTAGTACATATTATATAATTTTGAA
1 AAATAGTTGTGAAAATAATATATAGTACATATTATATAATTTTGAA
** * *
13611 AAATAG-TGTGAAAATAATATATAGTATTTATTGTATAGTTTTGAA
1 AAATAGTTGTGAAAATAATATATAGTACATATTATATAATTTTGAA
13656 AA
1 AA
13658 TAATTTTGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
45 34 0.85
46 6 0.15
ACGTcount: A:0.44, C:0.01, G:0.13, T:0.42
Consensus pattern (46 bp):
AAATAGTTGTGAAAATAATATATAGTACATATTATATAATTTTGAA
Found at i:13673 original size:25 final size:24
Alignment explanation
Indices: 13645--13698 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 24
13635 TATTTATTGT
*
13645 ATAGTTTTGAAAATAATTTTGGAAA
1 ATAGTTTTAAAAATAATTTT-GAAA
13670 ATAGTTTTAAAAATAATTTTGAAA
1 ATAGTTTTAAAAATAATTTTGAAA
13694 ATAGT
1 ATAGT
13699 ATACAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (24 bp):
ATAGTTTTAAAAATAATTTTGAAA
Found at i:13682 original size:12 final size:12
Alignment explanation
Indices: 13645--13698 Score: 72
Period size: 12 Copynumber: 4.4 Consensus size: 12
13635 TATTTATTGT
13645 ATAGTTTTGAAA
1 ATAGTTTTGAAA
*
13657 ATAATTTTGGAAA
1 ATAGTTTT-GAAA
*
13670 ATAGTTTTAAAA
1 ATAGTTTTGAAA
*
13682 ATAATTTTGAAA
1 ATAGTTTTGAAA
13694 ATAGT
1 ATAGT
13699 ATACAAATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 24 0.69
13 11 0.31
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (12 bp):
ATAGTTTTGAAA
Found at i:15287 original size:2 final size:2
Alignment explanation
Indices: 15282--15316 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15272 TTAATCATTA
15282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15317 CATAATTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25850 original size:24 final size:24
Alignment explanation
Indices: 25817--25998 Score: 222
Period size: 24 Copynumber: 7.6 Consensus size: 24
25807 TGGGTGTGGA
*
25817 GGATGAGGAGGGAACGGTCTTGGT
1 GGATGGGGAGGGAACGGTCTTGGT
* * *
25841 GGATCGGGAGGGAACGGTCGTGGC
1 GGATGGGGAGGGAACGGTCTTGGT
25865 GGATGGGGAGGGAACGGTCTTGGT
1 GGATGGGGAGGGAACGGTCTTGGT
* * * * *
25889 GGATCGGTAGGGAATGGTCTCGGCG
1 GGATGGGGAGGGAACGGTCTTGG-T
* * * *
25914 GGA-GAGGAGGTAACGGTCGTGGA
1 GGATGGGGAGGGAACGGTCTTGGT
25937 GGATGGGGAGGGAACGGTCTTGGT
1 GGATGGGGAGGGAACGGTCTTGGT
*
25961 GGATGGGGAGGGAACGGTCTTGGC
1 GGATGGGGAGGGAACGGTCTTGGT
25985 GGATGGGGAGGGAA
1 GGATGGGGAGGGAA
25999 TGGTTGTGGT
Statistics
Matches: 131, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
23 3 0.02
24 125 0.95
25 3 0.02
ACGTcount: A:0.19, C:0.10, G:0.53, T:0.17
Consensus pattern (24 bp):
GGATGGGGAGGGAACGGTCTTGGT
Found at i:25908 original size:72 final size:71
Alignment explanation
Indices: 25823--26007 Score: 246
Period size: 72 Copynumber: 2.6 Consensus size: 71
25813 TGGAGGATGA
* *
25823 GGAGGGAACGGTCTTGGTGGATCGGGAGGGAACGGTCGTGGCGGATGGGGAGGGAACGGTCTTGG
1 GGAGGGAACGGTCTTGGCGGAT-GGGAGGGAACGGTCGTGGAGGATGGGGAGGGAACGGTCTTGG
25888 TGGATCG
65 TGGATCG
* * * *
25895 GTAGGGAATGGTCTCGGCGGGA-GAGGAGGTAACGGTCGTGGAGGATGGGGAGGGAACGGTCTTG
1 GGAGGGAACGGTCTTGGC-GGATG-GGAGGGAACGGTCGTGGAGGATGGGGAGGGAACGGTCTTG
*
25959 GTGGATGG
64 GTGGATCG
* *
25967 GGAGGGAACGGTCTTGGCGGATGGGGAGGGAATGGTTGTGG
1 GGAGGGAACGGTCTTGGCGGAT-GGGAGGGAACGGTCGTGG
26008 TGGCCATGCA
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
71 4 0.04
72 88 0.92
73 4 0.04
ACGTcount: A:0.18, C:0.10, G:0.54, T:0.18
Consensus pattern (71 bp):
GGAGGGAACGGTCTTGGCGGATGGGAGGGAACGGTCGTGGAGGATGGGGAGGGAACGGTCTTGGT
GGATCG
Found at i:27006 original size:59 final size:59
Alignment explanation
Indices: 26895--27008 Score: 142
Period size: 59 Copynumber: 1.9 Consensus size: 59
26885 ACTATTGGGT
** * *
26895 GTTGTTTTGTTGAGTCGCTTGACTATTAAAAGTTATTAAATGTTTCCTTGAATATAAAAC
1 GTTGTTTTGTTGAGTCGCCCGACTATTAAAAGTTATAAAATG-TTCATTGAATATAAAAC
*
26955 GTTGTTTTGTTGAGTC-CCCGACTATTCAAAGTTATAAAATAG-TCATATGAATAT
1 GTTGTTTTGTTGAGTCGCCCGACTATTAAAAGTTATAAAAT-GTTCAT-TGAATAT
27009 TCATATGTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
58 3 0.06
59 27 0.57
60 17 0.36
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (59 bp):
GTTGTTTTGTTGAGTCGCCCGACTATTAAAAGTTATAAAATGTTCATTGAATATAAAAC
Found at i:28285 original size:15 final size:15
Alignment explanation
Indices: 28258--28294 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
28248 TGAGACATTA
*
28258 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
*
28273 CCTGCCCCACATCCG
1 CCCGCCCCACATCCG
28288 CCCGCCC
1 CCCGCCC
28295 AACTAAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.08, C:0.68, G:0.16, T:0.08
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:29890 original size:22 final size:23
Alignment explanation
Indices: 29855--29899 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
29845 TAAATTTAAA
29855 TAAAATATTATTTAATAAATATT
1 TAAAATATTATTTAATAAATATT
* *
29878 TAAACTATT-TTTAGTAAATATT
1 TAAAATATTATTTAATAAATATT
29900 ATTTAGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAATATTATTTAATAAATATT
Found at i:29923 original size:159 final size:158
Alignment explanation
Indices: 29752--30048 Score: 495
Period size: 159 Copynumber: 1.9 Consensus size: 158
29742 TTCATGGATA
*
29752 ATTTAAAAATATTACTTTTAAAATAATAAGTATAATCCATACATTATTTGAATAGAATATTAATA
1 ATTTAAAAATATTACTTTTAAAATAATAAGTATAATCCATACAATATTTGAATAGAATATTAATA
*
29817 AACTAATTTTTTAATATATTTTAATATTTAAATTTAAATAAAATATTATTTAATAAATATTTAAA
66 AACTAA-TTTTTAATATATTTTAATAGTTAAATTTAAATAAAATATTATTTAATAAATATTTAAA
*
29882 CTATTTTTAGTAAATATTATTTAGTAAAT
130 CTAATTTTAGTAAATATTATTTAGTAAAT
* *
29911 ATTTTAAAATATTACTTTTAAAATAATAAGTATAATCCATACAATATTTGAATATAATATTAATA
1 ATTTAAAAATATTACTTTTAAAATAATAAGTATAATCCATACAATATTTGAATAGAATATTAATA
* * * * *
29976 AACTAATTTTTCATATTTTTTTATAGTTAAATTTAAATAAAATATTATTTAGTAAATATTTAACC
66 AACTAATTTTTAATATATTTTAATAGTTAAATTTAAATAAAATATTATTTAATAAATATTTAAAC
30041 TAATTTTA
131 TAATTTTA
30049 ATATTTTTAA
Statistics
Matches: 128, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
158 60 0.47
159 68 0.53
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (158 bp):
ATTTAAAAATATTACTTTTAAAATAATAAGTATAATCCATACAATATTTGAATAGAATATTAATA
AACTAATTTTTAATATATTTTAATAGTTAAATTTAAATAAAATATTATTTAATAAATATTTAAAC
TAATTTTAGTAAATATTATTTAGTAAAT
Found at i:30065 original size:14 final size:14
Alignment explanation
Indices: 30046--30108 Score: 55
Period size: 15 Copynumber: 4.6 Consensus size: 14
30036 TAACCTAATT
30046 TTAATATTTTTAAA
1 TTAATATTTTTAAA
30060 TTAATATATTTT-AA
1 TTAATAT-TTTTAAA
30074 -T--T-TTTTTAAA
1 TTAATATTTTTAAA
30084 TTAATATATTTTAATA
1 TTAATAT-TTTTAA-A
*
30100 TTTATATTT
1 TTAATATTT
30109 AAATAAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 15
0.71 0.02 0.27
Matches are distributed among these distances:
9 4 0.10
10 3 0.08
11 2 0.05
13 2 0.05
14 10 0.25
15 12 0.30
16 7 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTAATATTTTTAAA
Found at i:30106 original size:16 final size:15
Alignment explanation
Indices: 30046--30097 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 15
30036 TAACCTAATT
30046 TTAATAT-TTTTAAA
1 TTAATATATTTTAAA
30060 TTAATATATTTT-AA
1 TTAATATATTTTAAA
30074 -T--T-T-TTTTAAA
1 TTAATATATTTTAAA
30084 TTAATATATTTTAA
1 TTAATATATTTTAA
30098 TATTTATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 13
0.70 0.00 0.30
Matches are distributed among these distances:
9 4 0.13
10 3 0.10
11 2 0.06
13 2 0.06
14 10 0.32
15 10 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAATATATTTTAAA
Found at i:30113 original size:24 final size:24
Alignment explanation
Indices: 30043--30102 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
30033 ATTTAACCTA
30043 ATTTTAATATTTTTAAATTAATAT
1 ATTTTAATATTTTTAAATTAATAT
*
30067 ATTTTAATTTTTTTAAATTAATAT
1 ATTTTAATATTTTTAAATTAATAT
30091 ATTTTAATATTT
1 ATTTTAATATTT
30103 ATATTTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTAATATTTTTAAATTAATAT
Found at i:30845 original size:20 final size:20
Alignment explanation
Indices: 30820--30857 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30810 TATATATATC
* *
30820 TATTCAAACCTTTTTTAATT
1 TATTCAAAACTTCTTTAATT
30840 TATTCAAAACTTCTTTAA
1 TATTCAAAACTTCTTTAA
30858 ACCATTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTCAAAACTTCTTTAATT
Found at i:31597 original size:24 final size:24
Alignment explanation
Indices: 31545--31599 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
31535 AAGAATCGTG
* * * *
31545 CCACAAGAGCAGAGAAAACATGTG
1 CCACAAGAGCAAAGAAAAAACGTA
31569 CCACAAGAGCAAAGAAAAAACGTA
1 CCACAAGAGCAAAGAAAAAACGTA
*
31593 TCACAAG
1 CCACAAG
31600 GACAGAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.51, C:0.22, G:0.20, T:0.07
Consensus pattern (24 bp):
CCACAAGAGCAAAGAAAAAACGTA
Found at i:33722 original size:31 final size:30
Alignment explanation
Indices: 33670--33746 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
33660 ATTAATATAT
* * *
33670 AATTAAAAATAAAAA-AGTTGAAAGTTGAAAC
1 AATT-AAATTAAAAATAATTGAAAGCT-AAAC
* **
33701 GATTAAATTAAAAATAATTGAAAGCTAAGT
1 AATTAAATTAAAAATAATTGAAAGCTAAAC
33731 AATTAAATTAAAAATA
1 AATTAAATTAAAAATA
33747 TTAAATTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 26 0.68
31 12 0.32
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.27
Consensus pattern (30 bp):
AATTAAATTAAAAATAATTGAAAGCTAAAC
Found at i:39774 original size:18 final size:18
Alignment explanation
Indices: 39753--39794 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
39743 AGCTTCACAA
39753 CCTTTCTCACTCC-CTTTC
1 CCTTTCTC-CTCCACTTTC
39771 CCTTTCTCCTCCACTTTC
1 CCTTTCTCCTCCACTTTC
*
39789 CATTTC
1 CCTTTC
39795 AGCAGAGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.07, C:0.48, G:0.00, T:0.45
Consensus pattern (18 bp):
CCTTTCTCCTCCACTTTC
Found at i:41377 original size:49 final size:51
Alignment explanation
Indices: 41248--41379 Score: 162
Period size: 50 Copynumber: 2.6 Consensus size: 51
41238 AGATATACAT
* * * * * *
41248 ACTTACACCAGTGTAAGTATGTATTAAGTGTTACACTTTTTTATTTTATTT
1 ACTTACACCGGTGTAAGTATATGTTAAGTGCTACACTTGTTTATTTTATTC
* * *
41299 ACTTACGCAGGTGT-AGTATCTGTTAAGTGCTACACTTGTTTA-TTT-TTC
1 ACTTACACCGGTGTAAGTATATGTTAAGTGCTACACTTGTTTATTTTATTC
41347 ACTTACACCGGTGTAAGTATATGTTAAGTGCTA
1 ACTTACACCGGTGTAAGTATATGTTAAGTGCTA
41380 TATTTTTTGT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
48 14 0.20
49 20 0.29
50 24 0.35
51 11 0.16
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (51 bp):
ACTTACACCGGTGTAAGTATATGTTAAGTGCTACACTTGTTTATTTTATTC
Found at i:42847 original size:16 final size:15
Alignment explanation
Indices: 42826--42855 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
42816 CCTTAAGTCC
42826 TATTATTATAAATATA
1 TATTATT-TAAATATA
42842 TATTATTTAAATAT
1 TATTATTTAAATAT
42856 TCTACACTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTATTTAAATATA
Found at i:52023 original size:109 final size:109
Alignment explanation
Indices: 51831--52049 Score: 269
Period size: 109 Copynumber: 2.0 Consensus size: 109
51821 TGGAGGGTGT
* * * *
51831 ATGGGAGTTGAAGCAGAAAATGAACCCTGGCAGATTCTAGGGAAACATCTGCAGCTGGAGTAGAA
1 ATGGGAGTTGAAGCAGAAAATGAACCCTGGCAGATTCTAGGGAAACA-CCGCAACTGGACTAAAA
* *
51896 GTTGAAATACCAGAACAAACAGGATATTGGGGAATGTCTGTAGCA
65 GTTGAAACACCAGAACAAACAGGATATTCGGGAATGTCTGTAGCA
* * * ** *
51941 ATGGGAGTTGGAGCGGCAAATGAACTGTGGCATGATTCTAGGGAAAC-CCGTAACTGGACTAAAA
1 ATGGGAGTTGAAGCAGAAAATGAACCCTGGCA-GATTCTAGGGAAACACCGCAACTGGACTAAAA
* * * *
52005 GTTGAAACACCAGAACAAACTGGATCTTCGTGAATGTGTGTAGCA
65 GTTGAAACACCAGAACAAACAGGATATTCGGGAATGTCTGTAGCA
52050 GTGCGCCTTT
Statistics
Matches: 92, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
109 51 0.55
110 27 0.29
111 14 0.15
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.21
Consensus pattern (109 bp):
ATGGGAGTTGAAGCAGAAAATGAACCCTGGCAGATTCTAGGGAAACACCGCAACTGGACTAAAAG
TTGAAACACCAGAACAAACAGGATATTCGGGAATGTCTGTAGCA
Found at i:55519 original size:17 final size:16
Alignment explanation
Indices: 55497--55528 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
55487 ATCATTAATT
55497 TTAAATGTTTAATAAAA
1 TTAAATGTTT-ATAAAA
55514 TTAAATGTTTATAAA
1 TTAAATGTTTATAAA
55529 CATTTAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
TTAAATGTTTATAAAA
Found at i:55873 original size:37 final size:37
Alignment explanation
Indices: 55823--55893 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
55813 TTTTCACTAT
*
55823 AATCCTACCATCCTCGATTCTCACTTTCTATAATGAC
1 AATCCTACCATCCTCAATTCTCACTTTCTATAATGAC
55860 AATCCTACCATCCTCAATTCTCACTTTCTATAAT
1 AATCCTACCATCCTCAATTCTCACTTTCTATAAT
55894 AACATTTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.28, C:0.32, G:0.03, T:0.37
Consensus pattern (37 bp):
AATCCTACCATCCTCAATTCTCACTTTCTATAATGAC
Found at i:67433 original size:74 final size:74
Alignment explanation
Indices: 67351--67602 Score: 441
Period size: 74 Copynumber: 3.4 Consensus size: 74
67341 AAGTTCAAGA
67351 ACTTTCAGCTCAAACCAAGCAATACCCAGAAACGAGAACACTTCAAAAACTTCGAAGAAATTAAG
1 ACTTTCAGCTCAAACCAAGCAATACCCAGAAACGAGAACACTTCAAAAACTTCGAAGAAATTAAG
67416 AATTTGAGC
66 AATTTGAGC
* *
67425 ACTTTCAGCTCAAACCAAGCAATACCCAGAAACGAGAACACTCCAAAAACTTGGAAGAAATTAAG
1 ACTTTCAGCTCAAACCAAGCAATACCCAGAAACGAGAACACTTCAAAAACTTCGAAGAAATTAAG
67490 AATTTGAGC
66 AATTTGAGC
67499 ACTTTCAGCTCAAACCAAGCAATACCCAGAAACGAGAACACTTCAAAAACTTCGAAGAAATTAAG
1 ACTTTCAGCTCAAACCAAGCAATACCCAGAAACGAGAACACTTCAAAAACTTCGAAGAAATTAAG
*
67564 AATTTAAGC
66 AATTTGAGC
* * * *
67573 ACTTTCAACCCGAACAAAGCAATACCCAGA
1 ACTTTCAGCTCAAACCAAGCAATACCCAGA
67603 TTAGGAAAAA
Statistics
Matches: 169, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 169 1.00
ACGTcount: A:0.45, C:0.24, G:0.13, T:0.18
Consensus pattern (74 bp):
ACTTTCAGCTCAAACCAAGCAATACCCAGAAACGAGAACACTTCAAAAACTTCGAAGAAATTAAG
AATTTGAGC
Found at i:69341 original size:18 final size:16
Alignment explanation
Indices: 69318--69354 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
69308 AGATATTATA
69318 TATTTAATATAATATATT
1 TATTTAATAT-ATAT-TT
69336 TATTTAATATATATTT
1 TATTTAATATATATTT
69352 TAT
1 TAT
69355 GGTCAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 4 0.21
18 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTAATATATATTT
Found at i:69345 original size:13 final size:14
Alignment explanation
Indices: 69310--69347 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
69300 ATAAAGATAG
*
69310 ATATTATATATTTA
1 ATATAATATATTTA
69324 ATATAATATATTT-
1 ATATAATATATTTA
*
69337 ATTTAATATAT
1 ATATAATATAT
69348 ATTTTATGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATAATATATTTA
Found at i:72418 original size:34 final size:31
Alignment explanation
Indices: 72386--72446 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
72376 CACCTAACTT
* *
72386 CTTTTAGAAGGTTATCAATTTAATCACTTAA
1 CTTTTAGAACGTTATCAATTTAATCACCTAA
* *
72417 CTTTTAGAACGTTATCAATTGAGTCACCTA
1 CTTTTAGAACGTTATCAATTTAATCACCTA
72447 GTCGAAACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.39
Consensus pattern (31 bp):
CTTTTAGAACGTTATCAATTTAATCACCTAA
Found at i:97651 original size:2 final size:2
Alignment explanation
Indices: 97644--97750 Score: 84
Period size: 2 Copynumber: 57.0 Consensus size: 2
97634 AAATAATTAT
97644 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
97683 AA TT TA -A TT TA AA T- TA AA AA TA TA TA TA -A 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
* * *
97722 TA TA TA TA TA TT TA -A TT TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
97751 CCCGACCCGA
Statistics
Matches: 82, Mismatches: 16, Indels: 14
0.73 0.14 0.12
Matches are distributed among these distances:
1 7 0.09
2 75 0.91
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:98743 original size:2 final size:2
Alignment explanation
Indices: 98736--98823 Score: 169
Period size: 2 Copynumber: 44.5 Consensus size: 2
98726 CTACGATTTA
98736 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
98778 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
98819 AT AT A
1 AT AT A
98824 AATTTAGTAG
Statistics
Matches: 85, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 84 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:99317 original size:22 final size:22
Alignment explanation
Indices: 99265--99324 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 22
99255 TGAAAATACC
* *
99265 AAAAA-AACAAAGAGGAAGAAG
1 AAAAACAATAAAGAGGAAAAAG
* *
99286 AAAAAGAATAAAGAGGAAAAAT
1 AAAAACAATAAAGAGGAAAAAG
* *
99308 AGAAACAATAAAAAGGA
1 AAAAACAATAAAGAGGA
99325 TGAAAATACA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 5 0.16
22 27 0.84
ACGTcount: A:0.72, C:0.03, G:0.20, T:0.05
Consensus pattern (22 bp):
AAAAACAATAAAGAGGAAAAAG
Found at i:99407 original size:15 final size:15
Alignment explanation
Indices: 99387--99416 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
99377 AACAGTAGAG
99387 AAAATGAAAATGAGA
1 AAAATGAAAATGAGA
*
99402 AAAATGGAAATGAGA
1 AAAATGAAAATGAGA
99417 GGATGAAGAA
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:0.23, T:0.13
Consensus pattern (15 bp):
AAAATGAAAATGAGA
Found at i:113587 original size:23 final size:23
Alignment explanation
Indices: 113555--113609 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
113545 ATAATTTTTC
* * * *
113555 TTCGTTTCTTAGAATTTTATAAG
1 TTCGTCTCTTAAAATTTTAAAAA
113578 TTCGTCTCTTAAAATTTTAAAAA
1 TTCGTCTCTTAAAATTTTAAAAA
113601 TTCGTCTCT
1 TTCGTCTCT
113610 CGTAATACCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (23 bp):
TTCGTCTCTTAAAATTTTAAAAA
Found at i:114083 original size:2 final size:2
Alignment explanation
Indices: 114076--114103 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
114066 TGCATTATCT
114076 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
114104 TATATACATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:114108 original size:2 final size:2
Alignment explanation
Indices: 114103--114134 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
114093 ACACACACAC
*
114103 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
114135 GCATAGTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:116457 original size:88 final size:86
Alignment explanation
Indices: 116295--116462 Score: 246
Period size: 88 Copynumber: 1.9 Consensus size: 86
116285 TCTTTAAGAA
* * * *
116295 AGAATTTCTCAACATTATAATTCTGATCATAAAAGAAACATCCATCAGAAACTACAATAACACAA
1 AGAATTTCTCAACATAATAATTCTAATCACAAAAGAAACATCCATCAGAAACTACAAGAACACAA
*
116360 AAGCGTTCTTTGGTTTTAGAT
66 AAGCCTTCTTTGGTTTTAGAT
* *
116381 AGAATTTCTCAACATAATAATTCTAATCACAGAAGAAAACCATCCATCAGAAACTACAAGAACAT
1 AGAATTTCTCAACATAATAATTCTAATCACAAAAG-AAA-CATCCATCAGAAACTACAAGAACAC
*
116446 GAAAGCCTTCTTTGGTT
64 AAAAGCCTTCTTTGGTT
116463 CGTTTCTTCT
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 31 0.43
87 3 0.04
88 38 0.53
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (86 bp):
AGAATTTCTCAACATAATAATTCTAATCACAAAAGAAACATCCATCAGAAACTACAAGAACACAA
AAGCCTTCTTTGGTTTTAGAT
Found at i:117289 original size:2 final size:2
Alignment explanation
Indices: 117284--117313 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
117274 TAATTTATCC
117284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
117314 TGAGTTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118372 original size:2 final size:2
Alignment explanation
Indices: 118365--118404 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
118355 TGTTTCAACA
118365 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
118405 GCATACCCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118996 original size:8 final size:8
Alignment explanation
Indices: 118985--119011 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
118975 ATAATAAATC
118985 ACTTCACA
1 ACTTCACA
118993 ACTTCACA
1 ACTTCACA
119001 ACTTCACA
1 ACTTCACA
119009 ACT
1 ACT
119012 CAAATCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (8 bp):
ACTTCACA
Found at i:119287 original size:25 final size:25
Alignment explanation
Indices: 119259--119309 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
119249 AATATTTTAT
119259 ATATAAT-TAATATAAAAAATATAAA
1 ATATAATAT-ATATAAAAAATATAAA
* **
119284 ATATTATATATATAATTAATATAAA
1 ATATAATATATATAAAAAATATAAA
119309 A
1 A
119310 AATATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
ATATAATATATATAAAAAATATAAA
Found at i:119294 original size:34 final size:34
Alignment explanation
Indices: 119247--119331 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
119237 TCCGAACCCA
*
119247 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
119281 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
119315 AAAATATTATATATATA
1 AAAATATTATATATATA
119332 TATATATATA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:119910 original size:20 final size:20
Alignment explanation
Indices: 119887--119937 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
119877 CACGGAATGT
119887 AAGATTACCAGTGAGAATAA
1 AAGATTACCAGTGAGAATAA
*
119907 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGAGAATAA
119927 AAGATTACCAG
1 AAGATTACCAG
119938 GGAATAGGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.20
Consensus pattern (20 bp):
AAGATTACCAGTGAGAATAA
Found at i:119942 original size:18 final size:18
Alignment explanation
Indices: 119887--119943 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 18
119877 CACGGAATGT
119887 AAGATTACCAGTGAGAATAA
1 AAGATTACCAG-G-GAATAA
119907 AAGATTACCAGTGGGAATAA
1 AAGATTACCA--GGGAATAA
119927 AAGATTACCAGGGAATA
1 AAGATTACCAGGGAATA
119944 GGATTACTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.20
20 26 0.74
21 1 0.03
22 1 0.03
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.19
Consensus pattern (18 bp):
AAGATTACCAGGGAATAA
Found at i:126726 original size:2 final size:2
Alignment explanation
Indices: 126719--126748 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
126709 ATTAACCCCG
126719 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
126749 ATGATCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128907 original size:3 final size:3
Alignment explanation
Indices: 128899--128942 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
128889 AAATATTACT
128899 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
128943 ACAAAATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:136457 original size:20 final size:21
Alignment explanation
Indices: 136418--136460 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
136408 ATTCTCTTGT
136418 ATGTTAGTTGGGAAAAATAGA
1 ATGTTAGTTGGGAAAAATAGA
*
136439 ATGTTAGTTGGG-CAAATAGA
1 ATGTTAGTTGGGAAAAATAGA
136459 AT
1 AT
136461 ATGGAGCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.40, C:0.02, G:0.28, T:0.30
Consensus pattern (21 bp):
ATGTTAGTTGGGAAAAATAGA
Found at i:139339 original size:228 final size:227
Alignment explanation
Indices: 138919--140502 Score: 1535
Period size: 228 Copynumber: 6.9 Consensus size: 227
138909 ACCACGGAGG
* * * *
138919 CGAAGGACAAGGTGCAGAGTGGACTCCTTCTGGATGTTGTAATCAGCAAGAGTACGACCATCCTC
1 CGAAGGACAAGGTGTAGGGTAGACTCCTTCTGGATGTTGTAATCAGCAAGTGTACGACCATCCT-
* * * *
138984 CAA-TTGCTTCCCAGCAAAGATCAACCTCTGCTGATCTGG-GGGAATCCCCTCCTTGTCCTGGAT
65 CAAGCTGCTTTCCAGCAAAGAT-AACCTCTGCTGGTCTGGTGGG-ATTCCCTCCTTGTCCTGGAT
* * * * * * * * *
139047 CTTTGCTTTCACATTGTCAATTGTGTCCGAGCTCTCAACCTCCAGGGTGATAGTTTTTCCAGTCA
128 CTTGGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCTCCAAGGTGATTGTCTTTCCAGTAA
* * * * * * * *
139112 GGGTCTTGACAAATATCTGCATCCCTCCTCTAAGG
193 GAGTTTTCACAAAAATCTGCATCCCACCCCTCAGA
* * * * * * * * ** *
139147 CGCAA-GACCAA-ATGCAGGGTTGACTCCTTCTGAATGTTATAGTCAGCAAGAGTCCTCCCGTCC
1 CG-AAGGA-CAAGGTGTAGGGTAGACTCCTTCTGGATGTTGTAATCAGCAAGTGTACGACCATCC
* * * * *
139210 TCGAGCTGCTTTCCAGCAAATATCAACCTCTGCTGGTCAGGTGGGATTCCCTCCTTATCTTGGAT
64 TCAAGCTGCTTTCCAGCAAAGAT-AACCTCTGCTGGTCTGGTGGGATTCCCTCCTTGTCCTGGAT
* * * * * * *
139275 CTTGGCCTTAACGTTATCAATTGTATCGGAGCTCTCCACCTCCAATGTAATGGTCTTACCAGTCA
128 CTTGGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCTCCAAGGTGATTGTCTTTCCAGT-A
* *
139340 AG-GTTTTCACAAAAATCTGCATCCCACCACGCAGA
192 AGAGTTTTCACAAAAATCTGCATCCCACCCCTCAGA
* * * * * * * * * **
139375 CGAAGAACCAA-GTGGAGGGTCGACTCTTTCTGAATATTATAATCGGCAAGTGTCCTCCCATCCT
1 CGAAGGA-CAAGGTGTAGGGTAGACTCCTTCTGGATGTTGTAATCAGCAAGTGTACGACCATCCT
* * * * * * * *
139439 CCAGCTGCTTACCAGCGAAGATCAGCCTCTGTTGATCTGGTGGAATCCCCTCCTTGTCCTGGATC
65 CAAGCTGCTTTCCAGCAAAGAT-AACCTCTGCTGGTCTGGTGGGATTCCCTCCTTGTCCTGGATC
* * * * * * * * * * *
139504 TTAGCTTTCACATTGTCAATTGTATCAGAACTCTCAACTTCCAATGTAATAGTCTTTCCAGTAAG
129 TTGGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCTCCAAGGTGATTGTCTTTCCAGTAAG
* * * * **
139569 AGTCTTCACAAAAATTTGCATGCCACCTCGGAGA
194 AGTTTTCACAAAAATCTGCATCCCACCCCTCAGA
* * * * * * * * * * *
139603 CGCAA-CACCAA-ATGGAGGGTAGACTCCTTTTGAATGTTATAGTCTGCTAGGGTCCTG-CCATC
1 CG-AAGGA-CAAGGTGTAGGGTAGACTCCTTCTGGATGTTGTAATCAGCAAGTGTAC-GACCATC
* * * * *
139665 TTCAAGCTG-TTTCCCAGCAAAAATTAACCTCTGCTGGTCCGGTGGGATGCCCTCCTTGTCCTGA
63 CTCAAGCTGCTTT-CCAGCAAAGA-TAACCTCTGCTGGTCTGGTGGGATTCCCTCCTTGTCCTGG
* *
139729 ATCTTAGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCT-CAAGGGTGATTGTCTTGCCAG
126 ATCTTGGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCTCCAA-GGTGATTGTCTTTCCAG
* * *
139793 TAAGAGTTTTCACAAAGATCTGCATGCCACCCCTGAGA
190 TAAGAGTTTTCACAAAAATCTGCATCCCACCCCTCAGA
* *
139831 CGAAGGACAAGGTGTAGGGTAGACTCCTTTTGGATGTTGTAGTCAGCAAGTGTACGACCATCCTC
1 CGAAGGACAAGGTGTAGGGTAGACTCCTTCTGGATGTTGTAATCAGCAAGTGTACGACCATCCTC
* * *
139896 AAGCTGTTTTCCAGCAAAGATAAGCCTCTGCTGGTCCGGTGGGATGCCCTCCTTGTCCTGGATCT
66 AAGCTGCTTTCCAGCAAAGATAA-CCTCTGCTGGTCTGGTGGGATTCCCTCCTTGTCCTGGATCT
* * * *
139961 TGGCCTTGACATTATCGATTGTGTCGGAGCTTTCCACCT-CAAGGGTGATTGTCTTGCCAGTAAG
130 TGGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCTCCAA-GGTGATTGTCTTTCCAGTAAG
* * * * *
140025 TGTTTTTACAAAGATCTGCATACCACCCCTCAGC
194 AGTTTTCACAAAAATCTGCATCCCACCCCTCAGA
140059 CGAAGGACAAGGTGTAGGGTAGACTCCTTCTGGATGTTGTAATCAGCAAGTGTACGACCATCCTC
1 CGAAGGACAAGGTGTAGGGTAGACTCCTTCTGGATGTTGTAATCAGCAAGTGTACGACCATCCTC
* * * * *
140124 AAGCTGTTTTCCAGCAAAGATAAGCCTCTGTTGGTCTGG-AGGAATCCCTTCCTTGTCTTGGATC
66 AAGCTGCTTTCCAGCAAAGATAA-CCTCTGCTGGTCTGGTGGGATTCCC-TCCTTGTCCTGGATC
* * *
140188 TTGGCCTTGACATTATCGATTGTGTCGGAGCTTTCCACCT-CAAGGGTGATTGTCTTTCCAGTAA
129 TTGGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCTCCAA-GGTGATTGTCTTTCCAGTAA
* * * *
140252 GTGTTTTTACAAAAATCTGCATACCACCCCTCAGC
193 GAGTTTTCACAAAAATCTGCATCCCACCCCTCAGA
*
140287 CGAAGGACAAGGTGTAGGGTAGACTCCTTCTGGATGTTGTAATCAGCAAGTGTACGGCCATCCTC
1 CGAAGGACAAGGTGTAGGGTAGACTCCTTCTGGATGTTGTAATCAGCAAGTGTACGACCATCCTC
* * * * *
140352 AAGCTGTTTTCCAGCAAAGATAAGCCTCTGTTGGTCGGGAGGGA-TCCCTTCCTTATCCTGGATC
66 AAGCTGCTTTCCAGCAAAGATAA-CCTCTGCTGGTCTGGTGGGATTCCC-TCCTTGTCCTGGATC
* * * * * *
140416 TTGGCCTTGACATTATCAATTGTGTCTGAGCTTTCCACCTCC-AGAGTGATGGTCTTACCGGTAA
129 TTGGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCTCCAAG-GTGATTGTCTTTCCAGTAA
*
140480 GAGTTTTCACAAATATCTGCATC
193 GAGTTTTCACAAAAATCTGCATC
140503 TGTTATGCAA
Statistics
Matches: 1171, Mismatches: 164, Indels: 42
0.85 0.12 0.03
Matches are distributed among these distances:
227 28 0.02
228 1123 0.96
229 20 0.02
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (227 bp):
CGAAGGACAAGGTGTAGGGTAGACTCCTTCTGGATGTTGTAATCAGCAAGTGTACGACCATCCTC
AAGCTGCTTTCCAGCAAAGATAACCTCTGCTGGTCTGGTGGGATTCCCTCCTTGTCCTGGATCTT
GGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCTCCAAGGTGATTGTCTTTCCAGTAAGAG
TTTTCACAAAAATCTGCATCCCACCCCTCAGA
Found at i:140250 original size:684 final size:682
Alignment explanation
Indices: 138940--140502 Score: 1717
Period size: 684 Copynumber: 2.3 Consensus size: 682
138930 GTGCAGAGTG
* * * * * *
138940 GACTCCTTCTGGATGTTGTAATCAGCAAGAGTACGACCATCCTCCAA-TTGCTTCCCAGCAAAGA
1 GACTCCTTCTGAATGTTATAATCAGCAAGGGTACGGCCATCCT-CAAGCTGTTTCCCAGCAAAGA
* * * * * *
139004 TCAACCTCTGCTGATCTGGGGGAATCCCCTCCTTGTCCTGGATCTTTGCTTTCACATTGTCAATT
65 TTAACCTCTGCTGGTCCGGGGG-AT-CCCTCCTTGTCCTGGATCTTAGCCTTCACATTATCAATT
* * * * * * *
139069 GTGTCCGAGCTCTCAACCTCCAGGGTGATAGTTTTTCCAGTCAGGGTCTTGACAAATATCTGCAT
128 GTGTCCGAGCTCTCCACCTCCAGGGTGATAGTCTTACCAGTAAGAGTTTTCACAAATATCTGCAT
* * * *
139134 CCCTCCTCTAAGGCGCAAGACCAAATGCAGGGTTGACTCCTTCTGAATGTTATAGTCAGCAAGAG
193 CCCACCCCTAAGACGCAAGACCAAATGCAGGGTAGACTCCTTCTGAATGTTATAGTCAGCAAGAG
* ** * * * *
139199 TCCTCCCGTCCTCGAGCTGCTTTCCAGCAAATATCAACCTCTGCTGGTCAGGTGGGATTCCCTCC
258 TACGACCATCCTCAAGCTGCTTTCCAGCAAAGATCAACCTCTGCTGGTCAGGTGGGATGCCCTCC
* * *
139264 TTATCTTGGATCTTGGCCTTAACGTTATCAATTGTATCGGAGCTCTCCACCTCCAATGTAATGGT
323 TTATCCTGGATCTTGGCCTTAACATTATCAATTGTATCGGAGCTCTCCACCTCCAAGGTAATGGT
*
139329 CTTACCAGTCAAGGTTTTCACAAAAATCTGCATCCCACCACGCAGACGAAGAACCAAGTGGAGGG
388 CTTACCAGTCAAGGTTTTCACAAAAATCTGCATACCACCACGCAGACGAAGAACCAAGTGGAGGG
* * * * ** * *
139394 TCGACTCTTTCTGAATATTATAATCGGCAAGTGTCCTCCCATCCTCCAGCTGCTTACCAGCGAAG
453 TAGACTCCTTCTGAATATTATAATCAGCAAGTGTACGACCATCCTCAAGCTGCTTACCAGCAAAG
* * * *
139459 ATCAGCCTCTGTTGATCTGGTGGAATCCCCTCCTTGTCCTGGATCTTAGCTTTCACATTGTCAAT
518 ATAAGCCTCTGTTGATCTGGAGGAATCCCCTCCTTGTCCTGGATCTTAGCCTTCACATTATCAAT
* * *
139524 TGTATCAGAACTCTCAACTTCCAATGTAATAGTCTTTCCAGTAAGAGTCTTCACAAAAATTTGCA
583 TGTATCAGAACTCTCAACCTCCAAGGTAATAGTCTTTCCAGTAAGAGTCTTCACAAAAATCTGCA
* * *
139589 TGCCACCTCGGAGACGCAA-CACCAA-ATGGAGGGTA
648 TACCACCCCGCAGACG-AAGCA-CAAGATGGAGGGTA
* * * * * * * *
139624 GACTCCTTTTGAATGTTATAGTCTGCTAGGGTCCTGCCATCTTCAAGCTGTTTCCCAGCAAAAAT
1 GACTCCTTCTGAATGTTATAATCAGCAAGGGTACGGCCATCCTCAAGCTGTTTCCCAGCAAAGAT
*
139689 TAACCTCTGCTGGTCCGGTGGGATGCCCTCCTTGTCCTGAATCTTAGCCTTCACATTATCAATTG
66 TAACCTCTGCTGGTCCGG-GGGAT-CCCTCCTTGTCCTGGATCTTAGCCTTCACATTATCAATTG
* * * * * *
139754 TGTCGGAGCTCTCCACCTCAAGGGTGATTGTCTTGCCAGTAAGAGTTTTCACAAAGATCTGCATG
129 TGTCCGAGCTCTCCACCTCCAGGGTGATAGTCTTACCAGTAAGAGTTTTCACAAATATCTGCATC
* * * * * * *
139819 CCACCCCTGAGACG-AAGGA-CAAGGTGTAGGGTAGACTCCTTTTGGATGTTGTAGTCAGCAAGT
194 CCACCCCTAAGACGCAA-GACCAA-ATGCAGGGTAGACTCCTTCTGAATGTTATAGTCAGCAAGA
* *
139882 GTACGACCATCCTCAAGCTGTTTTCCAGCAAAGAT-AAGCCTCTGCTGGTCCGGTGGGATGCCCT
257 GTACGACCATCCTCAAGCTGCTTTCCAGCAAAGATCAA-CCTCTGCTGGTCAGGTGGGATGCCCT
* * * * * *
139946 CCTTGTCCTGGATCTTGGCCTTGACATTATCGATTGTGTCGGAGCTTTCCACCT-CAAGGGTGAT
321 CCTTATCCTGGATCTTGGCCTTAACATTATCAATTGTATCGGAGCTCTCCACCTCCAA-GGTAAT
* * * * * * * *
140010 TGTCTTGCCAGT-AAGTGTTTTTACAAAGATCTGCATACCACCCCTCAGCCGAAGGA-CAAGGTG
385 GGTCTTACCAGTCAAG-GTTTTCACAAAAATCTGCATACCACCACGCAGACGAAGAACCAA-GTG
* * * * * *
140073 TAGGGTAGACTCCTTCTGGATGTTGTAATCAGCAAGTGTACGACCATCCTCAAGCTGTTTTCCAG
448 GAGGGTAGACTCCTTCTGAATATTATAATCAGCAAGTGTACGACCATCCTCAAGCTGCTTACCAG
* * * * *
140138 CAAAGATAAGCCTCTGTTGGTCTGGAGGAATCCCTTCCTTGTCTTGGATCTTGGCCTTGACATTA
513 CAAAGATAAGCCTCTGTTGATCTGGAGGAATCCCCTCCTTGTCCTGGATCTTAGCCTTCACATTA
* * * * * * * * * * *
140203 TCGATTGTGTCGGAGCTTTCCACCT-CAAGGGTGATTGTCTTTCCAGTAAGTGTTTTTACAAAAA
578 TCAATTGTATCAGAACTCTCAACCTCCAA-GGTAATAGTCTTTCCAGTAAGAGTCTTCACAAAAA
* * * * *
140267 TCTGCATACCACCCCTCAGCCGAAGGACAAGGTGTAGGGTA
642 TCTGCATACCACCCCGCAGACGAAGCACAAGATGGAGGGTA
* * * *
140308 GACTCCTTCTGGATGTTGTAATCAGCAAGTGTACGGCCATCCTCAAGCTGTTTTCCAGCAAAGA-
1 GACTCCTTCTGAATGTTATAATCAGCAAGGGTACGGCCATCCTCAAGCTGTTTCCCAGCAAAGAT
* * * * *
140372 TAAGCCTCTGTTGGTCGGGAGGGATCCCTTCCTTATCCTGGATCTTGGCCTTGACATTATCAATT
66 TAA-CCTCTGCTGGTCCGG-GGGATCCC-TCCTTGTCCTGGATCTTAGCCTTCACATTATCAATT
* * * * *
140437 GTGTCTGAGCTTTCCACCTCCAGAGTGATGGTCTTACCGGTAAGAGTTTTCACAAATATCTGCAT
128 GTGTCCGAGCTCTCCACCTCCAGGGTGATAGTCTTACCAGTAAGAGTTTTCACAAATATCTGCAT
140502 C
193 C
140503 TGTTATGCAA
Statistics
Matches: 721, Mismatches: 145, Indels: 26
0.81 0.16 0.03
Matches are distributed among these distances:
683 33 0.05
684 685 0.95
685 3 0.00
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.30
Consensus pattern (682 bp):
GACTCCTTCTGAATGTTATAATCAGCAAGGGTACGGCCATCCTCAAGCTGTTTCCCAGCAAAGAT
TAACCTCTGCTGGTCCGGGGGATCCCTCCTTGTCCTGGATCTTAGCCTTCACATTATCAATTGTG
TCCGAGCTCTCCACCTCCAGGGTGATAGTCTTACCAGTAAGAGTTTTCACAAATATCTGCATCCC
ACCCCTAAGACGCAAGACCAAATGCAGGGTAGACTCCTTCTGAATGTTATAGTCAGCAAGAGTAC
GACCATCCTCAAGCTGCTTTCCAGCAAAGATCAACCTCTGCTGGTCAGGTGGGATGCCCTCCTTA
TCCTGGATCTTGGCCTTAACATTATCAATTGTATCGGAGCTCTCCACCTCCAAGGTAATGGTCTT
ACCAGTCAAGGTTTTCACAAAAATCTGCATACCACCACGCAGACGAAGAACCAAGTGGAGGGTAG
ACTCCTTCTGAATATTATAATCAGCAAGTGTACGACCATCCTCAAGCTGCTTACCAGCAAAGATA
AGCCTCTGTTGATCTGGAGGAATCCCCTCCTTGTCCTGGATCTTAGCCTTCACATTATCAATTGT
ATCAGAACTCTCAACCTCCAAGGTAATAGTCTTTCCAGTAAGAGTCTTCACAAAAATCTGCATAC
CACCCCGCAGACGAAGCACAAGATGGAGGGTA
Found at i:141845 original size:2 final size:2
Alignment explanation
Indices: 141833--141873 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
141823 ATCATATAAG
141833 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
141874 CAATTTCTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:142010 original size:18 final size:18
Alignment explanation
Indices: 141989--142026 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
141979 AGCATAATCG
* *
141989 TAAACGTAAGCTAAATTA
1 TAAACATAAACTAAATTA
142007 TAAACATAAACTAAATTA
1 TAAACATAAACTAAATTA
142025 TA
1 TA
142027 TTTAGGGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (18 bp):
TAAACATAAACTAAATTA
Found at i:142373 original size:6 final size:6
Alignment explanation
Indices: 142362--142387 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
142352 GATGACAACT
142362 GAACCC GAACCC GAACCC GAACCC GA
1 GAACCC GAACCC GAACCC GAACCC GA
142388 CGGGTTCCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.46, G:0.19, T:0.00
Consensus pattern (6 bp):
GAACCC
Found at i:146244 original size:19 final size:19
Alignment explanation
Indices: 146222--146260 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
146212 TGAAAAATAT
146222 AAAAA-TAAAAATAAATTAA
1 AAAAATTAAAAA-AAATTAA
146241 AAAAATTAAAAAAAATTAA
1 AAAAATTAAAAAAAATTAA
146260 A
1 A
146261 TACTTCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAATTAAAAAAAATTAA
Found at i:146253 original size:8 final size:9
Alignment explanation
Indices: 146222--146260 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
146212 TGAAAAATAT
*
146222 AAAAATAAA
1 AAAAATTAA
146231 AATAAATTAA
1 AA-AAATTAA
146241 AAAAATTAAA
1 AAAAATT-AA
146251 AAAAATTAA
1 AAAAATTAA
146260 A
1 A
146261 TACTTCTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 10 0.37
10 17 0.63
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAATTAA
Found at i:146443 original size:2 final size:2
Alignment explanation
Indices: 146436--146460 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
146426 AAAAGTAAAA
146436 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
146461 AAATAAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:147946 original size:20 final size:20
Alignment explanation
Indices: 147880--147947 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
147870 CTATATATCC
147880 ATACATAGTATTTGTGCATGT
1 ATACATA-TATTTGTGCATGT
* ** ** *
147901 ATTCATGCATACGTGTAT-T
1 ATACATATATTTGTGCATGT
147920 CATACATATATTTGTGCATGT
1 -ATACATATATTTGTGCATGT
147941 ATACATA
1 ATACATA
147948 CATGTATTCG
Statistics
Matches: 33, Mismatches: 12, Indels: 5
0.66 0.24 0.10
Matches are distributed among these distances:
19 1 0.03
20 26 0.79
21 6 0.18
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (20 bp):
ATACATATATTTGTGCATGT
Found at i:147955 original size:36 final size:38
Alignment explanation
Indices: 147879--147978 Score: 141
Period size: 36 Copynumber: 2.6 Consensus size: 38
147869 ACTATATATC
*
147879 CATACATAGTATTTGTGCATGTATTCATGCATACGTGTATT
1 CATACATA-TATTTGTGCATGTA-TCA-GCATACATGTATT
147920 CATACATATATTTGTGCATGTAT-A-CATACATGTATT
1 CATACATATATTTGTGCATGTATCAGCATACATGTATT
*
147956 CGTACATATATTTGTGCATGTAT
1 CATACATATATTTGTGCATGTAT
147979 TCAATTACCA
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
36 33 0.58
38 1 0.02
39 1 0.02
40 14 0.25
41 8 0.14
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (38 bp):
CATACATATATTTGTGCATGTATCAGCATACATGTATT
Found at i:150771 original size:4 final size:4
Alignment explanation
Indices: 150764--150789 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
150754 ATATATATAG
150764 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
150790 AGCCTCTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:155376 original size:20 final size:22
Alignment explanation
Indices: 155351--155404 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
155341 TCATGCTTGG
155351 AAGAGATAG-AA-AGAAAACAA
1 AAGAGATAGCAAGAGAAAACAA
* * *
155371 AAGAGAAAGCAAGAGAAGAGAA
1 AAGAGATAGCAAGAGAAAACAA
155393 AAGAGAT-GCAAG
1 AAGAGATAGCAAG
155405 TACTTGTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 8 0.29
21 7 0.25
22 13 0.46
ACGTcount: A:0.63, C:0.06, G:0.28, T:0.04
Consensus pattern (22 bp):
AAGAGATAGCAAGAGAAAACAA
Found at i:159517 original size:34 final size:34
Alignment explanation
Indices: 159474--159539 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
159464 TCAAAGATTA
* *
159474 TTAAATAATTATGTTTGAATTTTTTGGAAAACAC
1 TTAAATAATTATGTCTGAATTTTCTGGAAAACAC
*
159508 TTAAATAATTATGTCTGAATTTTCTGGGAAAC
1 TTAAATAATTATGTCTGAATTTTCTGGAAAAC
159540 GTGAATTTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (34 bp):
TTAAATAATTATGTCTGAATTTTCTGGAAAACAC
Found at i:163244 original size:28 final size:28
Alignment explanation
Indices: 163212--163269 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
163202 GTCTAAATAT
163212 AATTTCTTTAAAAGAAGCGTAAATTACA
1 AATTTCTTTAAAAGAAGCGTAAATTACA
*
163240 AATTTCTTTAAAAGAAGGGTAAATTACA
1 AATTTCTTTAAAAGAAGCGTAAATTACA
163268 AA
1 AA
163270 CTTGGTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (28 bp):
AATTTCTTTAAAAGAAGCGTAAATTACA
Found at i:168159 original size:15 final size:15
Alignment explanation
Indices: 168139--168197 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 15
168129 CATGAAATAA
*
168139 AAAAATATTAAAATT
1 AAAAATATTAAATTT
**
168154 AAAAATAAGAGAATTT
1 AAAAATATTA-AATTT
*
168170 TAAAATATTTAAATTT
1 AAAAATA-TTAAATTT
168186 AAAAAT-TTAAAT
1 AAAAATATTAAAT
168198 ATTTATTAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
14 6 0.17
15 8 0.23
16 20 0.57
17 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (15 bp):
AAAAATATTAAATTT
Found at i:168184 original size:16 final size:15
Alignment explanation
Indices: 168165--168202 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
168155 AAAATAAGAG
168165 AATTTTAAAATATTTA
1 AATTTTAAAA-ATTTA
168181 AA-TTTAAAAATTTA
1 AATTTTAAAAATTTA
168195 AATATTTA
1 AAT-TTTA
168203 TTAAACCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.35
15 7 0.35
16 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTTAAAAATTTA
Found at i:168195 original size:14 final size:15
Alignment explanation
Indices: 168168--168197 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
168158 ATAAGAGAAT
168168 TTTAAAATATTTAAA
1 TTTAAAATATTTAAA
168183 TTTAAAA-ATTTAAA
1 TTTAAAATATTTAAA
168197 T
1 T
168198 ATTTATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAAAATATTTAAA
Found at i:168708 original size:2 final size:2
Alignment explanation
Indices: 168701--168750 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
168691 TGTTTGTACG
168701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
168743 AT AT AT AT
1 AT AT AT AT
168751 CTCAATTAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:175496 original size:41 final size:41
Alignment explanation
Indices: 175450--175532 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
175440 ATGTTCACGG
175450 GCAAATAATCAGTTTCTTGACTTGAAAATGTAAATGCATGT
1 GCAAATAATCAGTTTCTTGACTTGAAAATGTAAATGCATGT
175491 GCAAATAATCAGTTTCTTGACTTGAAAATGTAAATGCATGT
1 GCAAATAATCAGTTTCTTGACTTGAAAATGTAAATGCATGT
175532 G
1 G
175533 AGCTTTCACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (41 bp):
GCAAATAATCAGTTTCTTGACTTGAAAATGTAAATGCATGT
Found at i:183360 original size:21 final size:22
Alignment explanation
Indices: 183334--183375 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
183324 TATTTACGGT
183334 CATTTAAGGGTC-GGTCAAAGC
1 CATTTAAGGGTCTGGTCAAAGC
*
183355 CATTTAAGGTTCTGGTCAAAG
1 CATTTAAGGGTCTGGTCAAAG
183376 AAAATCAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (22 bp):
CATTTAAGGGTCTGGTCAAAGC
Found at i:183457 original size:9 final size:9
Alignment explanation
Indices: 183424--183475 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
183414 GGTCGGGTCG
183424 GGTCAAACC
1 GGTCAAACC
*
183433 GGTTCAGACC
1 GG-TCAAACC
*
183443 GATCAAACC
1 GGTCAAACC
183452 GGTCAAAACC
1 GGTC-AAACC
183462 GGTTCAAAACC
1 GG-TC-AAACC
183473 GGT
1 GGT
183476 TTTCCAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 11 0.31
10 15 0.42
11 10 0.28
ACGTcount: A:0.33, C:0.29, G:0.23, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:183470 original size:11 final size:11
Alignment explanation
Indices: 183447--183476 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
183437 CAGACCGATC
183447 AAACCGG-TCA
1 AAACCGGTTCA
183457 AAACCGGTTCA
1 AAACCGGTTCA
183468 AAACCGGTT
1 AAACCGGTT
183477 TTCCAGCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.17
Consensus pattern (11 bp):
AAACCGGTTCA
Found at i:184851 original size:25 final size:24
Alignment explanation
Indices: 184793--184854 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
184783 TTCACATCTT
* *
184793 CTAAAATCTTGTAATTTCGTACCC
1 CTAAAATTTTGTAATTTCGCACCC
184817 CTAAAATTTTGTAATTTCGGCACCC
1 CTAAAATTTTGTAATTTC-GCACCC
184842 CT-AAATTTT-TAAT
1 CTAAAATTTTGTAAT
184855 ATAATTTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
23 4 0.11
24 24 0.69
25 7 0.20
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (24 bp):
CTAAAATTTTGTAATTTCGCACCC
Found at i:186117 original size:26 final size:26
Alignment explanation
Indices: 186034--186119 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
186024 CTGCATCATA
*
186034 CGGGTTTTAATCCAACCCGATCTGAT
1 CGGGTTTTAATCTAACCCGATCTGAT
* * * * *
186060 TGGGTTAGGTAATTTCACCAGCATC--AT
1 CGGGTT--TTAATCTAACCCG-ATCTGAT
186087 ACGGGTTTTAATCTAACCCGATCTGAT
1 -CGGGTTTTAATCTAACCCGATCTGAT
186114 CGGGTT
1 CGGGTT
186120 AGATTTTTTT
Statistics
Matches: 43, Mismatches: 11, Indels: 12
0.65 0.17 0.18
Matches are distributed among these distances:
25 3 0.07
26 20 0.47
27 4 0.09
28 13 0.30
29 3 0.07
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (26 bp):
CGGGTTTTAATCTAACCCGATCTGAT
Found at i:189629 original size:35 final size:35
Alignment explanation
Indices: 189578--189653 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
189568 AATACAATCC
* *
189578 TCAATTTTATTCTAAACCCTAAATTCTAAAATAAT
1 TCAATTATATTCTAAACCCCAAATTCTAAAATAAT
*
189613 TCAATTATATTTTAAACCCCAAATTCTAAAATAAT
1 TCAATTATATTCTAAACCCCAAATTCTAAAATAAT
*
189648 TTAATT
1 TCAATT
189654 TAGGGTTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (35 bp):
TCAATTATATTCTAAACCCCAAATTCTAAAATAAT
Found at i:189696 original size:35 final size:35
Alignment explanation
Indices: 189657--189724 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
189647 TTTAATTTAG
*
189657 GGTTTAGAATATAATTAAAATATTTTGGAATTTGA
1 GGTTTAAAATATAATTAAAATATTTTGGAATTTGA
* * * *
189692 GGTTTAAAATGTAATTGAAGTGTTTTGGAATTT
1 GGTTTAAAATATAATTAAAATATTTTGGAATTT
189725 TGAACATGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
GGTTTAAAATATAATTAAAATATTTTGGAATTTGA
Found at i:192757 original size:35 final size:35
Alignment explanation
Indices: 192706--192781 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
192696 AACACAATTC
* *
192706 TCAATTTTATTCTAAACCCTAAATTCTAAAATAAT
1 TCAATTATATTCTAAACCCCAAATTCTAAAATAAT
*
192741 TCAATTATATTTTAAACCCCAAATTCTAAAATAAT
1 TCAATTATATTCTAAACCCCAAATTCTAAAATAAT
*
192776 TTAATT
1 TCAATT
192782 TAAGGTTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (35 bp):
TCAATTATATTCTAAACCCCAAATTCTAAAATAAT
Found at i:192824 original size:35 final size:36
Alignment explanation
Indices: 192778--192853 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 36
192768 AAAATAATTT
*
192778 AATTTAAGGTTTAGGATATAATTAAAAT-ATTTTGG
1 AATTTAAGGTTTAGAATATAATTAAAATGATTTTGG
* * * * *
192813 AATTTAGGGTTTAGAATGTAATTGAAGTGTTTTTGG
1 AATTTAAGGTTTAGAATATAATTAAAATGATTTTGG
192849 AATTT
1 AATTT
192854 TGAACATGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 23 0.68
36 11 0.32
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (36 bp):
AATTTAAGGTTTAGAATATAATTAAAATGATTTTGG
Found at i:207143 original size:25 final size:27
Alignment explanation
Indices: 207115--207164 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
207105 CATAGTTGTT
*
207115 TATATTTGTT-GAAAAAT-ATTGTTAG
1 TATAATTGTTAGAAAAATAATTGTTAG
*
207140 TATAATTGTTAGAAATATAATTGTT
1 TATAATTGTTAGAAAAATAATTGTT
207165 TATGGCAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 6 0.29
27 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (27 bp):
TATAATTGTTAGAAAAATAATTGTTAG
Found at i:208074 original size:57 final size:58
Alignment explanation
Indices: 207964--208089 Score: 164
Period size: 57 Copynumber: 2.2 Consensus size: 58
207954 CTTAACATTA
* ** * * *
207964 AAAAATATATTTTATTTTTTTCTTAACTTATTGAATATACTTTATTTTTATCTTAACT
1 AAAAATATATTTTAATCCTATCTTAACTTAATAAATATACTTTATTTTTATCTTAACT
*
208022 AAAAATATATTTTAATCCTATCTTAA-TTAATAAATATATTTTATTTTTATCTTAACT
1 AAAAATATATTTTAATCCTATCTTAACTTAATAAATATACTTTATTTTTATCTTAACT
* *
208079 TAAATTATATT
1 AAAAATATATT
208090 ACAAAATGGT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
57 37 0.63
58 22 0.37
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.54
Consensus pattern (58 bp):
AAAAATATATTTTAATCCTATCTTAACTTAATAAATATACTTTATTTTTATCTTAACT
Found at i:215168 original size:2 final size:2
Alignment explanation
Indices: 215161--215198 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
215151 CTATTTTTAC
215161 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
215199 ATTATCAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:216838 original size:22 final size:22
Alignment explanation
Indices: 216788--216829 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
216778 CGTATAATTA
*
216788 TAAATTAGTTAAAATTTAAAAG
1 TAAATTAGTTAAAATATAAAAG
216810 TAAATTAGTTAAAATATAAA
1 TAAATTAGTTAAAATATAAA
216830 TATTTATTAT
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:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (22 bp):
TAAATTAGTTAAAATATAAAAG
Found at i:223469 original size:25 final size:23
Alignment explanation
Indices: 223426--223489 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 23
223416 AATATTTTCA
*
223426 AAAAAAATTCAGATCAATTAACGGTT
1 AAAAAAATTC-GATTAATT--CGGTT
223452 AAAAAAATTCGATTAATTCGGTT
1 AAAAAAATTCGATTAATTCGGTT
*
223475 AATAAAAATTTGATT
1 AA-AAAAATTCGATT
223490 CGGTCGATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 7 0.20
24 11 0.31
25 7 0.20
26 10 0.29
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33
Consensus pattern (23 bp):
AAAAAAATTCGATTAATTCGGTT
Found at i:223780 original size:14 final size:14
Alignment explanation
Indices: 223761--223789 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
223751 TTATTAATCT
223761 AGAGTAAGTATAAG
1 AGAGTAAGTATAAG
223775 AGAGTAAGTATAAG
1 AGAGTAAGTATAAG
223789 A
1 A
223790 TAATATCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.28, T:0.21
Consensus pattern (14 bp):
AGAGTAAGTATAAG
Found at i:225769 original size:17 final size:18
Alignment explanation
Indices: 225733--225783 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
225723 AACTTTTCAG
225733 TATTTTTATTATAAACTTAT-
1 TATTTTTA--ATAAA-TTATC
225753 TATTTTTAATAAATTATC
1 TATTTTTAATAAATTATC
*
225771 AATTTTTAA-AAAT
1 TATTTTTAATAAAT
225784 AATTTATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.28
18 13 0.45
20 8 0.28
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTTTAATAAATTATC
Found at i:226436 original size:16 final size:16
Alignment explanation
Indices: 226417--226461 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
226407 TTCAGGTTAA
226417 TTTTAGTTCGGGTTGC
1 TTTTAGTTCGGGTTGC
* *
226433 TTTTGGTTTGGGTTGC
1 TTTTAGTTCGGGTTGC
* *
226449 TTTCAATTCGGGT
1 TTTTAGTTCGGGT
226462 AATTTTAGTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.07, C:0.11, G:0.31, T:0.51
Consensus pattern (16 bp):
TTTTAGTTCGGGTTGC
Found at i:228063 original size:63 final size:63
Alignment explanation
Indices: 227991--228113 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 63
227981 TAATATTATC
*
227991 TTTTAATTTGAAATATGTAAAATATATATACA-CAT-TTTACTATTCAAACTTAAATAGATATTA
1 TTTTAATTTGAAATATGTAAAA-ATATATA-ATCATCTTTAATATTCAAACTTAAATAGATATTA
* * *
228054 TTTTAATTTGAAATATTTAAAAATATATAATTATCTTTAATATTCAAATTTAAATAGATA
1 TTTTAATTTGAAATATGTAAAAATATATAATCATCTTTAATATTCAAACTTAAATAGATA
228114 ATAAATACCT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
61 1 0.02
62 9 0.17
63 44 0.81
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (63 bp):
TTTTAATTTGAAATATGTAAAAATATATAATCATCTTTAATATTCAAACTTAAATAGATATTA
Found at i:238878 original size:2 final size:2
Alignment explanation
Indices: 238871--238938 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
238861 ACTGGATTTA
238871 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
238913 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
238939 GACTTTAGCT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:241273 original size:29 final size:30
Alignment explanation
Indices: 241218--241338 Score: 113
Period size: 32 Copynumber: 3.9 Consensus size: 30
241208 GAATGACCTA
*
241218 TCCATATGTGC-CG-AAGAACATATGTAACTG
1 TCCATATGT-CTCGAAAG-ACATAGGTAACTG
* *
241248 TCCATATG-CTCGGAGGACATAGGTAATACTG
1 TCCATATGTCTCGAAAGACATAGGT-A-ACTG
*
241279 TCCATATGTCTCGAAAGACATAGGTAATACTA
1 TCCATATGTCTCGAAAGACATAGGT-A-ACTG
* *
241311 TCCATATGTCTTGAAAGAAATAGGTAAC
1 TCCATATGTCTCGAAAGACATAGGTAAC
241339 CCTCGACTCT
Statistics
Matches: 79, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
28 1 0.01
29 9 0.11
30 13 0.16
31 13 0.16
32 43 0.54
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (30 bp):
TCCATATGTCTCGAAAGACATAGGTAACTG
Found at i:241304 original size:32 final size:32
Alignment explanation
Indices: 241244--241337 Score: 136
Period size: 32 Copynumber: 3.0 Consensus size: 32
241234 AACATATGTA
* *
241244 ACTGTCCATATG-CTCGGAGGACATAGGTAAT
1 ACTGTCCATATGTCTCGAAAGACATAGGTAAT
241275 ACTGTCCATATGTCTCGAAAGACATAGGTAAT
1 ACTGTCCATATGTCTCGAAAGACATAGGTAAT
* * *
241307 ACTATCCATATGTCTTGAAAGAAATAGGTAA
1 ACTGTCCATATGTCTCGAAAGACATAGGTAA
241338 CCCTCGACTC
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 12 0.21
32 45 0.79
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (32 bp):
ACTGTCCATATGTCTCGAAAGACATAGGTAAT
Found at i:242537 original size:20 final size:20
Alignment explanation
Indices: 242512--242585 Score: 78
Period size: 20 Copynumber: 3.5 Consensus size: 20
242502 ATTTAAAGTA
242512 GGTATCGGTACCCTCTATAG
1 GGTATCGGTACCCTCTATAG
*
242532 GGTATCGGTACATCCT-TAACTGG
1 GGTATCGGTAC--CCTCT-A-TAG
*
242555 GGTATCGATACCCTCTATAG
1 GGTATCGGTACCCTCTATAG
*
242575 GGAATCGGTAC
1 GGTATCGGTAC
242586 ATCCTTAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
20 22 0.50
21 5 0.11
22 5 0.11
23 12 0.27
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (20 bp):
GGTATCGGTACCCTCTATAG
Found at i:242561 original size:23 final size:23
Alignment explanation
Indices: 242531--242607 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
242521 ACCCTCTATA
242531 GGGTATCGGTACATCCTTAACTG
1 GGGTATCGGTACATCCTTAACTG
* *
242554 GGGTATCGATAC--CCTCT-A-TA
1 GGGTATCGGTACATCCT-TAACTG
*
242574 GGGAATCGGTACATCCTTAACTG
1 GGGTATCGGTACATCCTTAACTG
242597 GGGTATCGGTA
1 GGGTATCGGTA
242608 TCCACCCCTA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
20 11 0.26
21 5 0.12
22 5 0.12
23 22 0.51
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (23 bp):
GGGTATCGGTACATCCTTAACTG
Found at i:242573 original size:43 final size:43
Alignment explanation
Indices: 242512--242604 Score: 168
Period size: 43 Copynumber: 2.2 Consensus size: 43
242502 ATTTAAAGTA
* *
242512 GGTATCGGTACCCTCTATAGGGTATCGGTACATCCTTAACTGG
1 GGTATCGATACCCTCTATAGGGAATCGGTACATCCTTAACTGG
242555 GGTATCGATACCCTCTATAGGGAATCGGTACATCCTTAACTGG
1 GGTATCGATACCCTCTATAGGGAATCGGTACATCCTTAACTGG
242598 GGTATCG
1 GGTATCG
242605 GTATCCACCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (43 bp):
GGTATCGATACCCTCTATAGGGAATCGGTACATCCTTAACTGG
Found at i:245306 original size:32 final size:32
Alignment explanation
Indices: 245270--245385 Score: 153
Period size: 32 Copynumber: 3.6 Consensus size: 32
245260 ATACTAGTAG
*
245270 AGTGTTGCATTCAGATAATTCACAATAGTATC
1 AGTGTTGCATTCAGATAATGCACAATAGTATC
* *
245302 AGTGTTACATTCAGATAATGCACAACAGTATC
1 AGTGTTGCATTCAGATAATGCACAATAGTATC
* *
245334 AGTTTTGCATTAAGATAATGCACAATAG-AGTC
1 AGTGTTGCATTCAGATAATGCACAATAGTA-TC
* *
245366 AATATTGCATTCAGATAATG
1 AGTGTTGCATTCAGATAATG
245386 GACATCAGTG
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
31 1 0.01
32 72 0.99
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (32 bp):
AGTGTTGCATTCAGATAATGCACAATAGTATC
Found at i:245399 original size:32 final size:32
Alignment explanation
Indices: 245272--245422 Score: 146
Period size: 32 Copynumber: 4.7 Consensus size: 32
245262 ACTAGTAGAG
* *
245272 TGTTGCATTCAGATAATTCACAATAGTATCAG
1 TGTTGCATTCAGATAATGCACAATAGTATCAA
* * *
245304 TGTTACATTCAGATAATGCACAACAGTATCAG
1 TGTTGCATTCAGATAATGCACAATAGTATCAA
* *
245336 TTTTGCATTAAGATAATGCACAATAG-AGTCAA
1 TGTTGCATTCAGATAATGCACAATAGTA-TCAA
* * *
245368 TATTGCATTCAGATAATGGAC-ATCAGTGTCAA
1 TGTTGCATTCAGATAATGCACAAT-AGTATCAA
* *
245400 TGTTGTATGT-AGATAATGTACAA
1 TGTTGCAT-TCAGATAATGCACAA
245423 CAATTACAAT
Statistics
Matches: 99, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
31 3 0.03
32 94 0.95
33 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.32
Consensus pattern (32 bp):
TGTTGCATTCAGATAATGCACAATAGTATCAA
Found at i:245414 original size:64 final size:64
Alignment explanation
Indices: 245272--245422 Score: 162
Period size: 64 Copynumber: 2.4 Consensus size: 64
245262 ACTAGTAGAG
* * * * *
245272 TGTTGCATTCAGATAATTCACAATAGTATCAGTGTTACATTCAGATAATGCACAACAGTATCAG
1 TGTTGCATTAAGATAATGCACAATAGTATCAATATTACATTCAGATAATGCACAACAGTATCAA
* * * * *
245336 TTTTGCATTAAGATAATGCACAATAG-AGTCAATATTGCATTCAGATAATGGACATCAGTGTCAA
1 TGTTGCATTAAGATAATGCACAATAGTA-TCAATATTACATTCAGATAATGCACAACAGTATCAA
* *
245400 TGTTGTATGT-AGATAATGTACAA
1 TGTTGCAT-TAAGATAATGCACAA
245423 CAATTACAAT
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
63 1 0.01
64 70 0.97
65 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.32
Consensus pattern (64 bp):
TGTTGCATTAAGATAATGCACAATAGTATCAATATTACATTCAGATAATGCACAACAGTATCAA
Found at i:247710 original size:34 final size:34
Alignment explanation
Indices: 247646--247710 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
247636 ATCCAATCAG
*
247646 ATATCTTTTAATATTTAAATTTAAATAGATAATA
1 ATATCTTTTAATATTAAAATTTAAATAGATAATA
247680 ATATCTTTTAAT-TTGAAATATTTAAA-AGATA
1 ATATCTTTTAATATT-AAA-ATTTAAATAGATA
247711 TATATACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 2 0.07
34 19 0.68
35 7 0.25
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (34 bp):
ATATCTTTTAATATTAAAATTTAAATAGATAATA
Found at i:257426 original size:2 final size:2
Alignment explanation
Indices: 257419--257449 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
257409 ATTTCACATA
257419 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
257450 ATTAAGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:260420 original size:15 final size:15
Alignment explanation
Indices: 260400--260431 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
260390 CATCAAAAGC
260400 ACCATTCATCTTTTG
1 ACCATTCATCTTTTG
260415 ACCATTCATCTTTTG
1 ACCATTCATCTTTTG
260430 AC
1 AC
260432 AGAATTTGAC
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:0.22, C:0.28, G:0.06, T:0.44
Consensus pattern (15 bp):
ACCATTCATCTTTTG
Found at i:260500 original size:14 final size:14
Alignment explanation
Indices: 260481--260539 Score: 82
Period size: 14 Copynumber: 4.1 Consensus size: 14
260471 GCAATTGGTT
*
260481 TTCTGGAAATTGAA
1 TTCTGGAAAATGAA
260495 TTCTGGAAAATGAA
1 TTCTGGAAAATGAA
**
260509 TTACTGGAATTTGAA
1 TT-CTGGAAAATGAA
260524 TTCTGGAAAATGAA
1 TTCTGGAAAATGAA
260538 TT
1 TT
260540 ACATTTCCGG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 27 0.69
15 12 0.31
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (14 bp):
TTCTGGAAAATGAA
Found at i:260525 original size:29 final size:29
Alignment explanation
Indices: 260483--260541 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
260473 AATTGGTTTT
260483 CTGGAAATTGAATTCTGGAAAATGAATTA
1 CTGGAAATTGAATTCTGGAAAATGAATTA
*
260512 CTGGAATTTGAATTCTGGAAAATGAATTA
1 CTGGAAATTGAATTCTGGAAAATGAATTA
260541 C
1 C
260542 ATTTCCGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.32
Consensus pattern (29 bp):
CTGGAAATTGAATTCTGGAAAATGAATTA
Found at i:260857 original size:26 final size:27
Alignment explanation
Indices: 260806--260857 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
260796 TTATTAATAA
* * *
260806 AAATAAAAATATTGGTATATTTTATTG
1 AAATAAAAATATTGATAAATTATATTG
260833 AAATAAAAATATT-ATAAATTATATT
1 AAATAAAAATATTGATAAATTATATT
260858 AATTATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (27 bp):
AAATAAAAATATTGATAAATTATATTG
Found at i:260937 original size:23 final size:23
Alignment explanation
Indices: 260888--260938 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
260878 GTGTTATATT
**
260888 ATATTTTAAAAATATTAATTATT
1 ATATTTTAAAAATATTAATTAAA
* * *
260911 ATATTTTAAATATGTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
260934 ATATT
1 ATATT
260939 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:260992 original size:27 final size:27
Alignment explanation
Indices: 260951--261031 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
260941 TAGATTATTA
260951 TATTAATATTAAAT-ATATAAATAATAT
1 TATTAATATTAAATAAT-TAAATAATAT
*
260978 TATTAATTATT-AATAATTTAATAATAT
1 TATTAA-TATTAAATAATTAAATAATAT
* ** *
261005 TCTTTCTATGAAATTAA-TAAATAATAT
1 TATTAATATTAAA-TAATTAAATAATAT
261032 AAATTTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
26 3 0.07
27 32 0.73
28 9 0.20
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (27 bp):
TATTAATATTAAATAATTAAATAATAT
Found at i:260994 original size:19 final size:19
Alignment explanation
Indices: 260926--260994 Score: 72
Period size: 19 Copynumber: 3.6 Consensus size: 19
260916 TTAAATATGT
260926 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
260945 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
*
260964 TATATAAATAATATTATTAA
1 T-TATTAATAATATTATTAA
260984 TTATTAATAAT
1 TTATTAATAAT
260995 TTAATAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
18 8 0.19
19 18 0.43
20 9 0.21
22 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:261139 original size:22 final size:22
Alignment explanation
Indices: 261111--261168 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
261101 TTGATTATTT
261111 TATTATAATATTTAAAATATAA
1 TATTATAATATTTAAAATATAA
*
261133 TATTATATTA-TTAGAAATATAA
1 TATTATAATATTTA-AAATATAA
*
261155 TA-AAT-ATATTTAAA
1 TATTATAATATTTAAA
261169 TATTTTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.13
21 8 0.26
22 19 0.61
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTATAATATTTAAAATATAA
Found at i:261171 original size:19 final size:20
Alignment explanation
Indices: 261114--261171 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 20
261104 ATTATTTTAT
*
261114 TATAATAT-TTAAAATATAA
1 TATAATATATTTAAATATAA
* *
261133 TATTATATTATTAGAAATATAA
1 TATAATA-TATT-TAAATATAA
261155 TA-AATATATTTAAATAT
1 TATAATATATTTAAATAT
261172 TTTAATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 12 0.38
20 5 0.16
21 5 0.16
22 10 0.31
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TATAATATATTTAAATATAA
Found at i:263953 original size:17 final size:17
Alignment explanation
Indices: 263933--263971 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
263923 GGAGGTCAAC
*
263933 GGTCAATGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
263950 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
263967 GGTCA
1 GGTCA
263972 GACCGGTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.46, T:0.21
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Done.