Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009374.1 Hibiscus syriacus cultivar Beakdansim tig00113245_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: 62553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:12891 original size:22 final size:22
Alignment explanation
Indices: 12863--12906 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
12853 CTTATTTTTC
*
12863 GATTTTTGTCTCCTTTTATGTG
1 GATTTTTGTCTCATTTTATGTG
*
12885 GATTTTTGTCTTATTTTATGTG
1 GATTTTTGTCTCATTTTATGTG
12907 AAGTATTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.61
Consensus pattern (22 bp):
GATTTTTGTCTCATTTTATGTG
Found at i:17024 original size:39 final size:35
Alignment explanation
Indices: 16983--17137 Score: 129
Period size: 37 Copynumber: 4.2 Consensus size: 35
16973 ATATATACAC
*
16983 ATATATATTATATAGTTTGCAAATTGTTTTTGAAAAT
1 ATATATATTATATAGTTT-AAAATT-TTTTTGAAAAT
* *
17020 ACATATATAATATATAGTTTAAAACATTTTTTG-AAAT
1 --ATATATATTATATAGTTTAAAA-TTTTTTTGAAAAT
*
17057 ATGTATATTATATAGTTTTTAAAATATTTTTTGAAAAT
1 ATATATATTATATAG--TTTAAAAT-TTTTTTGAAAAT
**
17095 -TATATA-TATATAGTTTTTGAAAACGTTTTT-AAAAT
1 ATATATATTATATAG--TTT-AAAATTTTTTTGAAAAT
17130 ATATATAT
1 ATATATAT
17138 ACTTTTGAAA
Statistics
Matches: 99, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
35 18 0.18
36 23 0.23
37 27 0.27
38 13 0.13
39 18 0.18
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (35 bp):
ATATATATTATATAGTTTAAAATTTTTTTGAAAAT
Found at i:17118 original size:74 final size:71
Alignment explanation
Indices: 16983--17137 Score: 172
Period size: 73 Copynumber: 2.1 Consensus size: 71
16973 ATATATACAC
* *
16983 ATATATATTATATAGTTTGCAAATTGTTTTTGAAAATACATATATAATATATAGTTTAAAACATT
1 ATATATATTATATAGTTTGAAAATTGTTTTTGAAAAT--ATATATAATATATAGTTTAAAAC-GT
*
17048 TTTTGAAAT
63 TTTTAAAAT
* *
17057 ATGTATATTATATAGTTTTTAAAATAT-TTTTTGAAAAT-TATAT-ATATATAGTTTTTGAAAAC
1 ATATATATTATATAG-TTTGAAAAT-TGTTTTTGAAAATATATATAATATATAG--TTT-AAAAC
17119 GTTTTTAAAAT
61 GTTTTTAAAAT
17130 ATATATAT
1 ATATATAT
17138 ACTTTTGAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
71 8 0.11
72 5 0.07
73 19 0.27
74 19 0.27
75 18 0.26
76 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (71 bp):
ATATATATTATATAGTTTGAAAATTGTTTTTGAAAATATATATAATATATAGTTTAAAACGTTTT
TAAAAT
Found at i:17168 original size:31 final size:31
Alignment explanation
Indices: 17098--17169 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
17088 TGAAAATTAT
* * * *
17098 ATATATATAGTTTTTGAAAACGTTTTTAAAAT
1 ATATATATA-CTTTTGAAAACGTTATGAAAAC
17130 ATATATATACTTTTGAAAACGTTATGAAAAC
1 ATATATATACTTTTGAAAACGTTATGAAAAC
17161 ACT-TATATA
1 A-TATATATA
17170 ATATATAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 25 0.71
32 10 0.29
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
ATATATATACTTTTGAAAACGTTATGAAAAC
Found at i:17252 original size:27 final size:26
Alignment explanation
Indices: 17169--17256 Score: 81
Period size: 25 Copynumber: 3.3 Consensus size: 26
17159 ACACTTATAT
*
17169 AATATATAATTTTTAAAAACCATTTTGAA
1 AATATATAATTTTTGAAAA-C-TTTT-AA
* * *
17198 AATATAT-TTTTTTGAAAA-TTATAT
1 AATATATAATTTTTGAAAACTTTTAA
*
17222 AATATATAGTTTTTGAAAACGTTTTAA
1 AATATATAATTTTTGAAAAC-TTTTAA
17249 AATATATA
1 AATATATA
17257 TAATATATAC
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
24 8 0.16
25 13 0.27
27 12 0.24
28 9 0.18
29 7 0.14
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (26 bp):
AATATATAATTTTTGAAAACTTTTAA
Found at i:17258 original size:36 final size:36
Alignment explanation
Indices: 17207--17392 Score: 157
Period size: 39 Copynumber: 5.1 Consensus size: 36
17197 AAATATATTT
17207 TTTTGAAAAT-TATATAATATATAGTTTTTGAAAACG
1 TTTT-AAAATATATATAATATATAGTTTTTGAAAACG
*
17243 TTTTAAAATATATATAATATATA-CTTTTGAAAACG
1 TTTTAAAATATATATAATATATAGTTTTTGAAAACG
* * * * *
17278 TTATGAAAACATTTATATAATATATAATTTTTAAAAACC
1 TT-T-TAAA-ATATATATAATATATAGTTTTTGAAAACG
* * * *
17317 ATTTGAAA-ATATATAATATATAGTTTTTTAAAAAAAACA
1 TTTTAAAATATATATAATATATAG-TTTTT---GAAAACG
* *
17356 TTTTAAAA-ATTTATATTATAT-GTTTTTGAAAACG
1 TTTTAAAATATATATAATATATAGTTTTTGAAAACG
17390 TTT
1 TTT
17393 ATATATATTT
Statistics
Matches: 123, Mismatches: 18, Indels: 20
0.76 0.11 0.12
Matches are distributed among these distances:
34 8 0.07
35 31 0.25
36 24 0.20
37 10 0.08
38 17 0.14
39 33 0.27
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
TTTTAAAATATATATAATATATAGTTTTTGAAAACG
Found at i:17285 original size:127 final size:121
Alignment explanation
Indices: 17083--17330 Score: 424
Period size: 127 Copynumber: 2.0 Consensus size: 121
17073 TTTTAAAATA
*
17083 TTTTTTGAAAATTATATATATATAGTTTTTGAAAACGTTTTTAAAATATATATATACTTTTGAAA
1 TTTTTTGAAAATTATATATATATAGTTTTTGAAAACGTTTTAAAAATATATATATACTTTTGAAA
17148 ACGTTATGAAAACACTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATAT
66 ACGTTATGAAAACACTTATATAATATATAATTTTTAAAAACCA-TTTGAAAATATAT
17205 TTTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTAAAATATATATAATATATACTTT
1 TTTTTTGAAAATTATAT-ATATATAGTTTTTGAAAACGTTTT-AAA-A-ATAT-ATATATACTTT
*
17270 TGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTGAAAATATAT
61 TGAAAACGTTATGAAAACACTTATATAATATATAATTTTTAAAAACCATTTGAAAATATAT
17331 AATATATAGT
Statistics
Matches: 119, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
122 17 0.14
123 24 0.20
124 2 0.02
125 1 0.01
126 17 0.14
127 58 0.49
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (121 bp):
TTTTTTGAAAATTATATATATATAGTTTTTGAAAACGTTTTAAAAATATATATATACTTTTGAAA
ACGTTATGAAAACACTTATATAATATATAATTTTTAAAAACCATTTGAAAATATAT
Found at i:17295 original size:38 final size:35
Alignment explanation
Indices: 17212--17343 Score: 117
Period size: 35 Copynumber: 3.7 Consensus size: 35
17202 TATTTTTTTG
* *
17212 AAAA-TTATATAATATATAGTTTTTGAAAACGTTTT
1 AAAATTTATATAATATATA-ATTTTGAAAACGTTTA
* *
17247 AAAATATATATAATATATACTTTTGAAAACGTTATGA
1 AAAATTTATATAATATATAATTTTGAAAACGTT-T-A
* * *
17284 AAACATTTATATAATATATAATTTTTAAAAACCATTTG
1 AAA-ATTTATATAATATATAA-TTTTGAAAA-CGTTTA
*
17322 AAAA--TATATAATATATAGTTTT
1 AAAATTTATATAATATATAATTTT
17344 TTAAAAAAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
34 4 0.05
35 30 0.37
36 14 0.17
37 4 0.05
38 18 0.22
39 9 0.11
40 3 0.04
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (35 bp):
AAAATTTATATAATATATAATTTTGAAAACGTTTA
Found at i:17351 original size:37 final size:38
Alignment explanation
Indices: 17207--17387 Score: 105
Period size: 35 Copynumber: 4.9 Consensus size: 38
17197 AAATATATTT
* * *
17207 TTTTGAAAATTATATAATATATAG-TTTTT--GAAAACG
1 TTTT-AAAAATATATAATATATAGTTTTTTAAAAAAACA
* * *
17243 TTTTAAAATATATATAATATATA--CTTTT--GAAAACG
1 TTTTAAAA-ATATATAATATATAGTTTTTTAAAAAAACA
* * *
17278 TTATGAAAACATTTATATAATATATA-ATTTTT-AAAAACCA
1 TT-TTAAAA-A--TATATAATATATAGTTTTTTAAAAAAACA
*
17318 -TTTGAAAATATATAATATATAGTTTTTTAAAAAAAACA
1 TTTTAAAAATATATAATATATAGTTTTTT-AAAAAAACA
* * *
17356 TTTTAAAAATTTATATTATAT-GTTTTTGAAAA
1 TTTTAAAAATATATAATATATAGTTTTTTAAAA
17388 CGTTTATATA
Statistics
Matches: 119, Mismatches: 16, Indels: 19
0.77 0.10 0.12
Matches are distributed among these distances:
35 30 0.25
36 28 0.24
37 5 0.04
38 30 0.25
39 22 0.18
40 4 0.03
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (38 bp):
TTTTAAAAATATATAATATATAGTTTTTTAAAAAAACA
Found at i:17353 original size:39 final size:39
Alignment explanation
Indices: 17291--17387 Score: 105
Period size: 38 Copynumber: 2.6 Consensus size: 39
17281 TGAAAACATT
* * *
17291 TATATAATATATA-ATTTTT--AAAAACCA-TTTGAAAA
1 TATATAATATATAGTTTTTTAAAAAAAACATTTTAAAAA
17326 TATATAATATATAGTTTTTTAAAAAAAACATTTTAAAAA
1 TATATAATATATAGTTTTTTAAAAAAAACATTTTAAAAA
* * *
17365 TTTATATTATAT-GTTTTTGAAAA
1 TATATAATATATAGTTTTTTAAAA
17388 CGTTTATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
35 13 0.25
36 5 0.10
38 17 0.33
39 17 0.33
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.44
Consensus pattern (39 bp):
TATATAATATATAGTTTTTTAAAAAAAACATTTTAAAAA
Found at i:18682 original size:11 final size:11
Alignment explanation
Indices: 18666--18697 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
18656 TATTTTTTCT
18666 TATTTATTTAG
1 TATTTATTTAG
*
18677 TATTTATTTAT
1 TATTTATTTAG
18688 TATTTATTTA
1 TATTTATTTA
18698 ATTTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (11 bp):
TATTTATTTAG
Found at i:18752 original size:3 final size:3
Alignment explanation
Indices: 18746--18780 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
18736 TTATTTACTT
*
18746 TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
18781 TTGATTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:27478 original size:37 final size:35
Alignment explanation
Indices: 27390--27715 Score: 152
Period size: 37 Copynumber: 9.4 Consensus size: 35
27380 TTTTTGACGA
* * *
27390 AATATAATATATAATTTTCAGAAAACGATTTTCGAAAATT
1 AATATAATATATAGTTTT--TAAAAC-ATTTT-TAAAA-T
* *
27430 TATATATTATATAGTTTTTGAAAACATTTTTAAAAT
1 AATATAATATATAGTTTTT-AAAACATTTTTAAAAT
* * *
27466 AGATATAATATATA-ATTTT-GAA-ATATTT---AT
1 A-ATATAATATATAGTTTTTAAAACATTTTTAAAAT
*
27496 -ATAT--TATATAGTTTTTAAAACAATTTTAAAAACT
1 AATATAATATATAGTTTTTAAAAC-ATTTTTAAAA-T
* * *
27530 TATATAATATAGA-TTTTTAAAATATTTTTGAAAAAT
1 AATATAATATATAGTTTTTAAAACATTTTT--AAAAT
* *
27566 TATATAATATATAGTTTTTAAAATATTTTTTGAAAA-
1 AATATAATATATAGTTTTTAAAACA-TTTTT-AAAAT
* * *
27602 CATCT-ATA-ATA-TTTTTAAAACATTTTGAAAACT
1 AATATAATATATAGTTTTTAAAACATTTTTAAAA-T
* * *
27635 -ATATAATGTATAGTTTTGAAAAC-TTTTTTAAA-
1 AATATAATATATAGTTTTTAAAACATTTTTAAAAT
* * *
27667 AATAT-A-ATATAG-TTTAAAAATATTTTTTGAAAT
1 AATATAATATATAGTTTTTAAAACA-TTTTTAAAAT
*
27700 ATATATATTATATAGT
1 A-ATATAATATATAGT
27716 AGTAGTATTA
Statistics
Matches: 223, Mismatches: 33, Indels: 63
0.70 0.10 0.20
Matches are distributed among these distances:
26 6 0.03
27 4 0.02
28 6 0.03
30 13 0.06
31 9 0.04
32 16 0.07
33 23 0.10
34 20 0.09
35 21 0.09
36 36 0.16
37 39 0.17
38 10 0.04
39 5 0.02
40 15 0.07
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (35 bp):
AATATAATATATAGTTTTTAAAACATTTTTAAAAT
Found at i:27535 original size:63 final size:63
Alignment explanation
Indices: 27417--27556 Score: 187
Period size: 63 Copynumber: 2.2 Consensus size: 63
27407 TCAGAAAACG
* *
27417 ATTTTCGAAA-ATTTATATATTATATAGTTTTTGAAAACATTTTTAAAATAGATATAATATATA
1 ATTTT-GAAATATTTATATATTATATAGTTTTTGAAAACATTTTAAAAATAGATATAATATAGA
*
27480 ATTTTGAAATATTTATATATTATATAGTTTTT-AAAACAATTTTAAAAACT-TATATAATATAGA
1 ATTTTGAAATATTTATATATTATATAGTTTTTGAAAAC-ATTTTAAAAA-TAGATATAATATAGA
* *
27543 TTTTTAAAATATTT
1 ATTTTGAAATATTT
27557 TTGAAAAATT
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
62 9 0.13
63 59 0.86
64 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (63 bp):
ATTTTGAAATATTTATATATTATATAGTTTTTGAAAACATTTTAAAAATAGATATAATATAGA
Found at i:27569 original size:36 final size:35
Alignment explanation
Indices: 27481--27715 Score: 163
Period size: 36 Copynumber: 6.7 Consensus size: 35
27471 TAATATATAA
* * *
27481 TTTTGAAATATTTATATATTATATAGTTTTTAAAACAA
1 TTTTGAAA-AATTATATA--ATATAGTTTTTAAAATAT
27519 TTTT-AAAAACTTATATAATATAGATTTTTAAAATAT
1 TTTTGAAAAA-TTATATAATATAG-TTTTTAAAATAT
27555 TTTTGAAAAATTATATAATATATAGTTTTTAAAATATT
1 TTTTGAAAAATTATAT-A-ATATAGTTTTTAAAATA-T
* *
27593 TTTTGAAAACA-TCTAT-A-ATA-TTTTTAAAACA-
1 TTTTGAAAA-ATTATATAATATAGTTTTTAAAATAT
* *
27624 TTTTG-AAAACTATATAATGTATAGTTTTGAAAACT-T
1 TTTTGAAAAATTATATAA--TATAGTTTTTAAAA-TAT
*
27660 TTTT--AAAA--ATATAATATAG-TTTAAAAATATT
1 TTTTGAAAAATTATATAATATAGTTTTTAAAATA-T
* *
27691 TTTTGAAATATATATATTATATAGT
1 TTTTGAAAAAT-TATATAATATAGT
27716 AGTAGTATTA
Statistics
Matches: 163, Mismatches: 11, Indels: 47
0.74 0.05 0.21
Matches are distributed among these distances:
29 2 0.01
30 14 0.09
31 16 0.10
33 19 0.12
34 6 0.04
35 19 0.12
36 35 0.21
37 27 0.17
38 24 0.15
39 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (35 bp):
TTTTGAAAAATTATATAATATAGTTTTTAAAATAT
Found at i:29096 original size:2 final size:2
Alignment explanation
Indices: 29091--29130 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29081 TTTTTCTTTG
29091 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
29131 TTTCTATTTA
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:32770 original size:2 final size:2
Alignment explanation
Indices: 32765--32835 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
32755 TTTGTCATTT
*
32765 TA TA TA TA TT 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
32807 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32836 TCCTCCTGAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34614 original size:14 final size:14
Alignment explanation
Indices: 34595--34646 Score: 77
Period size: 14 Copynumber: 3.7 Consensus size: 14
34585 CGTTCGGTAA
34595 TATGTTCGTTCGTT
1 TATGTTCGTTCGTT
34609 TATGTTCGTTCGTT
1 TATGTTCGTTCGTT
* *
34623 TATGTTCATTCATT
1 TATGTTCGTTCGTT
*
34637 TATGTCCGTT
1 TATGTTCGTT
34647 TATGTGCGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.12, C:0.15, G:0.17, T:0.56
Consensus pattern (14 bp):
TATGTTCGTTCGTT
Found at i:34884 original size:24 final size:24
Alignment explanation
Indices: 34857--34933 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
34847 TTTACGTTCA
*
34857 TTTATGTTCGTTCATTTGTGTTTG
1 TTTATGTTCGTTCATTTGAGTTTG
* * ** ** *
34881 TTTACGTTCGTTGACATCCGTTCG
1 TTTATGTTCGTTCATTTGAGTTTG
*
34905 TTTATGTTAGTTCATTTGAGTTTG
1 TTTATGTTCGTTCATTTGAGTTTG
34929 TTTAT
1 TTTAT
34934 CATTTAAATG
Statistics
Matches: 38, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.13, C:0.12, G:0.19, T:0.56
Consensus pattern (24 bp):
TTTATGTTCGTTCATTTGAGTTTG
Found at i:35922 original size:20 final size:20
Alignment explanation
Indices: 35899--35950 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
35889 AACGCGATCC
35899 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
35919 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
35939 CCAAAATCGCAA
1 CCAGAATCGCAA
35951 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:35967 original size:21 final size:20
Alignment explanation
Indices: 35940--36038 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
35930 AATCAGTTTC
35940 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
35961 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
35982 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
36002 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
36023 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
36039 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:36067 original size:20 final size:20
Alignment explanation
Indices: 36005--36198 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
35995 CGATTTTCCA
* ** *
36005 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
36025 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
36045 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
36065 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
36085 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
36105 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
36125 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
36145 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
36165 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
36186 AAATCGCAACGCG
1 AAATCGCAACGCG
36199 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:36089 original size:60 final size:60
Alignment explanation
Indices: 36005--36198 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
35995 CGATTTTCCA
* ** * *
36005 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
36065 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
36125 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
36186 AAATCGCAACGCG
1 AAATCGCAACGCG
36199 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:36620 original size:33 final size:33
Alignment explanation
Indices: 36581--36651 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
36571 TTCACTTAGA
*
36581 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
36614 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
36647 TTTCA
1 TTTCA
36652 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:36791 original size:14 final size:14
Alignment explanation
Indices: 36772--36826 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
36762 AGAATGACTG
36772 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
36786 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
36805 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
36819 TCGCAACG
1 TCGCAACG
36827 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:36839 original size:33 final size:33
Alignment explanation
Indices: 36772--36842 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
36762 AGAATGACTG
***
36772 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
36805 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
36838 TCGCA
1 TCGCA
36843 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:36860 original size:19 final size:19
Alignment explanation
Indices: 36838--36935 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
36828 GAAACCAAAA
*
36838 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
36857 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
36871 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
36890 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
36904 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
36923 TCGCGTTGCGATT
1 TCGCGTTGCGATT
36936 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:36879 original size:14 final size:14
Alignment explanation
Indices: 36860--36949 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
36850 TTTCATTTCG
36860 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
36874 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
36893 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
36907 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
36924 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
36940 CGTTGCGATT
1 CGTTGCGATT
36950 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:36885 original size:33 final size:33
Alignment explanation
Indices: 36843--36957 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
36833 CAAAATCGCA
36843 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
36876 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
36909 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
36942 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
36958 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:38982 original size:93 final size:93
Alignment explanation
Indices: 38650--39119 Score: 912
Period size: 92 Copynumber: 5.1 Consensus size: 93
38640 TAGATTGCTT
38650 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATT-TTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38714 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38742 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38806 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38833 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38898 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38926 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38991 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
39019 AGTAAATTTGTTCGGTTGCTGCC-ATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
39083 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
39111 AGTAAATTT
1 AGTAAATTT
39120 ATCCATTCAA
Statistics
Matches: 375, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
91 72 0.19
92 160 0.43
93 143 0.38
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:39202 original size:19 final size:19
Alignment explanation
Indices: 39162--39290 Score: 98
Period size: 19 Copynumber: 7.3 Consensus size: 19
39152 TAGTTTACTT
* *
39162 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
39182 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
39201 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
39220 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
* **
39234 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
39253 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
39267 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
39286 TCGCA
1 TCGCA
39291 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:39245 original size:33 final size:32
Alignment explanation
Indices: 39198--39290 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
39188 CGCGAAACCA
39198 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAATGAAAATCGCAACGAC
*
39230 AGAATCGCAATGCGAAATGAAAATCGCAACGAC
1 A-AATCGCAACGCGAAATGAAAATCGCAACGAC
**
39263 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAATGAAAATCGCA
39291 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 2 0.04
33 53 0.96
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (32 bp):
AAATCGCAACGCGAAATGAAAATCGCAACGAC
Found at i:39308 original size:19 final size:19
Alignment explanation
Indices: 39286--39420 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
39276 GAAACCAAAA
*
39286 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
39305 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
39321 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
39338 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
39354 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
39371 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
39390 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
39410 TCGTGTTGCGA
1 TCGCGTTGCGA
39421 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:39327 original size:14 final size:14
Alignment explanation
Indices: 39308--39364 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
39298 TTTCATTTCG
39308 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
39322 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
39339 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
39355 CGTTGCGATT
1 CGTTGCGATT
39365 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:39333 original size:33 final size:33
Alignment explanation
Indices: 39291--39383 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
39281 CAAAATCGCA
*
39291 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
39324 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
39357 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
39384 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:41269 original size:38 final size:38
Alignment explanation
Indices: 41226--41298 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
41216 AATTGATTGT
*
41226 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
41264 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
41299 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:41285 original size:19 final size:19
Alignment explanation
Indices: 41221--41285 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
41211 AGTTTAATTG
*
41221 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
41240 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
41258 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
41278 ATTGATTT
1 ATTGATTT
41286 GTAAAAGATG
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:41299 original size:14 final size:14
Alignment explanation
Indices: 41280--41315 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
41270 ATTGTTTAAT
41280 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
41294 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
41308 TGATTTGT
1 TGATTTGT
41316 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:41444 original size:19 final size:19
Alignment explanation
Indices: 41428--41528 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
41418 AAAAATGACT
41428 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
41447 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
41466 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
41480 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
41498 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
41518 ATCGCAATGCG
1 ATCGCAATGCG
41529 TTTATAATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 12 0.16
19 34 0.47
20 12 0.16
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:41581 original size:19 final size:19
Alignment explanation
Indices: 41557--41863 Score: 351
Period size: 19 Copynumber: 17.4 Consensus size: 19
41547 GATTATCTCG
41557 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41576 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41595 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
41609 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41628 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
41647 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
41666 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
41685 TTGCGA--TT-ATGTCTG--
1 TTGCGATTTTCATTTC-GCA
41700 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41718 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
41737 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
41751 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41770 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
41789 TTGCGATTCTCA---CG--
1 TTGCGATTTTCATTTCGCA
41803 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
41823 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
41837 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
41856 TTGCGATT
1 TTGCGATT
41864 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 11, Indels: 56
0.79 0.03 0.18
Matches are distributed among these distances:
14 37 0.15
15 2 0.01
16 26 0.10
17 23 0.09
18 5 0.02
19 144 0.58
20 12 0.05
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:41694 original size:142 final size:137
Alignment explanation
Indices: 41525--41863 Score: 513
Period size: 142 Copynumber: 2.4 Consensus size: 137
41515 AAAATCGCAA
41525 TGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTT-TAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
*
41589 TTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
65 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
*
41654 TTTCATTTCGTAT
130 TCTCA---CG--T
*
41667 TGCGATTTTAATTTCGCATTGCGATTATGTCTGTT-CGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTTTAATTTCGCATTGCGATTATCTC-GTTGCGATTTTCATTTCGCATTGCGATTTTCAT
41731 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
65 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
41796 TCTCACGT
130 TCTCACGT
* * * *
41804 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTAATTT-CGCATTGCGATTATC-TCGTTGCGATTTTCATTTCGCATTGCGATT
41864 GTATTTTCCG
Statistics
Matches: 184, Mismatches: 8, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
137 17 0.09
138 35 0.19
139 3 0.02
142 123 0.67
143 6 0.03
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (137 bp):
TGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
CTCACGT
Found at i:41797 original size:52 final size:52
Alignment explanation
Indices: 41557--41835 Score: 345
Period size: 52 Copynumber: 5.2 Consensus size: 52
41547 GATTATCTCG
*
41557 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
41609 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
41666 TTGCGATTTTAATTTCGCATTGCGATTATGTCTGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
41718 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
41770 TTGCGATTTTCATTTCGCATTGCGATTCTCACGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
41823 TTGCGATTTTCAT
1 TTGCGATTTTCAT
41836 GTTGGGATTT
Statistics
Matches: 211, Mismatches: 8, Indels: 15
0.90 0.03 0.06
Matches are distributed among these distances:
51 3 0.01
52 151 0.72
53 19 0.09
54 6 0.03
55 8 0.04
57 24 0.11
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:44184 original size:12 final size:12
Alignment explanation
Indices: 44167--44191 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44157 TCTTCGGGGA
44167 CTTTTTCTTCTT
1 CTTTTTCTTCTT
44179 CTTTTTCTTCTT
1 CTTTTTCTTCTT
44191 C
1 C
44192 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:44400 original size:24 final size:24
Alignment explanation
Indices: 44366--44412 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
44356 CTGAAACATC
44366 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
44390 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
44413 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:45114 original size:20 final size:20
Alignment explanation
Indices: 45086--45454 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
45076 AAATTTCAGT
* * * *
45086 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
45106 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
45126 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
45146 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
45166 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
45186 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
45206 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
45226 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
45246 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
45266 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
45286 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
45306 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
45326 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
45346 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
45366 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
45386 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
45406 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
45426 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
45446 GTTGCGATT
1 GTTGCGATT
45455 ATGGAAATCG
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:50867 original size:34 final size:34
Alignment explanation
Indices: 50824--50932 Score: 182
Period size: 34 Copynumber: 3.2 Consensus size: 34
50814 TAATTAATGC
*
50824 ATTTGAAGAATTAACGATTGAATGATTAAGAATAA
1 ATTT-AAGAATTAACGATCGAATGATTAAGAATAA
50859 ATTTAAGAATTAACGATCGAATGATTAAGAATAA
1 ATTTAAGAATTAACGATCGAATGATTAAGAATAA
* *
50893 ATTTAAGAATTAACAATCGAATGATTAATAATAA
1 ATTTAAGAATTAACGATCGAATGATTAAGAATAA
50927 ATTTAA
1 ATTTAA
50933 TGTTTATTTA
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
34 67 0.94
35 4 0.06
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (34 bp):
ATTTAAGAATTAACGATCGAATGATTAAGAATAA
Found at i:53002 original size:18 final size:20
Alignment explanation
Indices: 52963--53002 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
52953 ATACATTATT
*
52963 AATATAATAATGTTTCTATA
1 AATATAATAATGTTTATATA
52983 AATAT-ATAAT-TTTATATA
1 AATATAATAATGTTTATATA
53001 AA
1 AA
53003 GCTATAATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 5 0.26
20 5 0.26
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
AATATAATAATGTTTATATA
Done.