Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004286.1 Hibiscus syriacus cultivar Beakdansim tig00009398_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: 87936
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:3165 original size:58 final size:58
Alignment explanation
Indices: 3067--3181 Score: 194
Period size: 58 Copynumber: 2.0 Consensus size: 58
3057 GAGGTTTTGG
* ** *
3067 GGTTTGAGTATTAAGAATGACAAGGATGTAAGTTTTTAATGTCAAATGATTGAGAATA
1 GGTTCGAGTATTAAGAATGACAAGGATGTAAGCATCTAATGTCAAATGATTGAGAATA
3125 GGTTCGAGTATTAAGAATGACAAGGATGTAAGCATCTAATGTCAAATGATTGAGAAT
1 GGTTCGAGTATTAAGAATGACAAGGATGTAAGCATCTAATGTCAAATGATTGAGAAT
3182 TATCTTTGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.31
Consensus pattern (58 bp):
GGTTCGAGTATTAAGAATGACAAGGATGTAAGCATCTAATGTCAAATGATTGAGAATA
Found at i:4476 original size:88 final size:89
Alignment explanation
Indices: 4323--4497 Score: 271
Period size: 88 Copynumber: 2.0 Consensus size: 89
4313 CCTAACACAC
* * * *
4323 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAATTACCCAAATCATATTAGAGATTTATTATTTCAAATTAATTAAATCTATA
* *
4388 TTT-ATTAATTAGAATTTAATAAT
66 TTTAATTAATTAAAATTAAATAAT
* *
4411 CCTTTTATATCCAAATTACCCAAATCATATTAGAGATTTATTATTTCAAATTAATTAAATTTATA
1 CCTTTTATAGCCAAATTACCCAAATCATATTAGAGATTTATTATTTCAAATTAATTAAATCTATA
4476 TTTAATTAATTAAAATTAAATA
66 TTTAATTAATTAAAATTAAATA
4498 TTTGAGATTA
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
88 62 0.79
89 16 0.21
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAATTACCCAAATCATATTAGAGATTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTAAAATTAAATAAT
Found at i:4507 original size:24 final size:21
Alignment explanation
Indices: 4459--4528 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
4449 TATTATTTCA
*
4459 AATTAATT-AAATTTATATTT
1 AATTAATTAAAATTAATATTT
4479 AATTAATTAAAATTAAATATTT
1 AATTAATTAAAATT-AATATTT
*
4501 GAGATT-ATTAAAA-CATATATTT
1 -A-ATTAATTAAAATTA-ATATTT
4523 AATTAA
1 AATTAA
4529 CTCTAGATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
20 11 0.26
21 8 0.19
22 12 0.29
23 8 0.19
24 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (21 bp):
AATTAATTAAAATTAATATTT
Found at i:10992 original size:42 final size:41
Alignment explanation
Indices: 10911--11011 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 41
10901 AGGTCTTATG
* * * *
10911 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTACA
* * *
10952 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGACTTACA
*
10994 GATGGCCCGAATGACTTA
1 GATGGCCCGAAGGACTTA
11012 TAAATTGTGA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTACA
Found at i:11404 original size:216 final size:215
Alignment explanation
Indices: 10740--11430 Score: 1095
Period size: 216 Copynumber: 3.2 Consensus size: 215
10730 AGGTCTTATG
* *
10740 GATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTATTGATGGCCCGAAGGACTTATAAAT
1 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAAT
** * *
10805 TGTGAAATTTTGAAAATATCATTCTTTGTTTTCAAAAATTTCATCTTC-T--CA-ATTTTTTTTT
66 TGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCTTTTTTT
*
10866 TCATTTTCAAATTCATGTGAAAACATCCTACCCGCAGGTCTTATGGATGGCCCGAAGGACTTATC
131 T-ATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATC
10931 ATCTTGCTCTAAAGGCTTACA
195 ATCTTGCTCTAAAGGCTTACA
*
10952 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTATAAAT
1 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAAT
* * *
11017 TGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTCAAACCATCGTTTTTT
66 TGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCTTTTTTT
* * *
11082 CATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTACGGATGGCCCGAAGGACTTATTA
131 TATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCA
*
11147 TCTTGCTCTAAAGGCTTATA
196 TCTTGCTCTAAAGGCTTACA
* *
11167 GATGACCCGAAGGATTTTAAGCATCATGCTTGAAAGACTTATTGATGGCCCGAAGGACTTATAAA
1 GATGACCCGAAGGA-TTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
* * *
11232 TCGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTT
65 TTGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATC-TTTTT
* * *
11297 TTTATTTTCAAATTCATGTGAAAACATCTTACCCGAAGGTTTTATGGATGGCCTGAAGGACTTAT
129 TTTATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTAT
11362 CATCTTGCTCTAAAGGCTTACA
194 CATCTTGCTCTAAAGGCTTACA
*
11384 GATGACCCGAATGATTTAAGCATCATGCTCAGAAAG-CTTACTGATGG
1 GATGACCCGAAGGATTTAAGCATCATGCTC-GAAAGACTTACTGATGG
11431 ATTTGCTTCA
Statistics
Matches: 438, Mismatches: 34, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
212 108 0.25
215 94 0.21
216 134 0.31
217 102 0.23
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (215 bp):
GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAAT
TGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCTTTTTTT
TATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCA
TCTTGCTCTAAAGGCTTACA
Found at i:11563 original size:36 final size:37
Alignment explanation
Indices: 11426--11612 Score: 209
Period size: 37 Copynumber: 5.1 Consensus size: 37
11416 AAAGCTTACT
*
11426 GATGGATTTGCTTCACTACTTTTCGGTGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
* * * ** *
11463 AATTGATTTGCTTCATTGTTC-TCAGGTGAAGGCCTAA
1 GATGGATTTGCTTCACTACTCTTC-GGTGAAGGCTTAA
* * *
11500 GATGGATTTGCTTCACTATTCTCCGGTGAAGGCTTTA
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
*
11537 GATTGATTT-CTTCACTACTCTTCGGTGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
* * * *
11573 GATGGA-TTACTTCACTACTATTTGGTGAAGACTTAA
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
11609 GATG
1 GATG
11613 AATTGCTCCA
Statistics
Matches: 125, Mismatches: 22, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
35 2 0.02
36 59 0.47
37 63 0.50
38 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (37 bp):
GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
Found at i:17790 original size:21 final size:21
Alignment explanation
Indices: 17766--17877 Score: 154
Period size: 21 Copynumber: 5.3 Consensus size: 21
17756 AATGCAAAGT
*
17766 GGTCTTCATGTCTTTATGAAG
1 GGTCTTCATGTCTTTATGAAC
*
17787 GGTCTTCATGTCTTTATGAAT
1 GGTCTTCATGTCTTTATGAAC
*
17808 GGTCTTCATGTCTTTATGAAT
1 GGTCTTCATGTCTTTATGAAC
**
17829 GGTCTTCATGTCCTTGGTGAAC
1 GGTCTTCATGT-CTTTATGAAC
17851 GGTCTTC-TCGTCTTTATGAAC
1 GGTCTTCAT-GTCTTTATGAAC
17872 GGTCTT
1 GGTCTT
17878 TTTGTCCTTG
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
21 67 0.81
22 16 0.19
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (21 bp):
GGTCTTCATGTCTTTATGAAC
Found at i:17869 original size:43 final size:43
Alignment explanation
Indices: 17766--17889 Score: 162
Period size: 43 Copynumber: 2.9 Consensus size: 43
17756 AATGCAAAGT
* ** *
17766 GGTCTTCATGTCTTTATGAAGGGTCTTCATGT-CTTTATGAAT
1 GGTCTTCATGTCTTTATGAACGGTCTTCATGTCCTTGGTGAAC
*
17808 GGTCTTCATGTCTTTATGAATGGTCTTCATGTCCTTGGTGAAC
1 GGTCTTCATGTCTTTATGAACGGTCTTCATGTCCTTGGTGAAC
**
17851 GGTCTTC-TCGTCTTTATGAACGGTCTTTTTGTCCTTGGT
1 GGTCTTCAT-GTCTTTATGAACGGTCTTCATGTCCTTGGT
17890 ATGACTGTAT
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
42 32 0.44
43 41 0.56
ACGTcount: A:0.15, C:0.18, G:0.23, T:0.45
Consensus pattern (43 bp):
GGTCTTCATGTCTTTATGAACGGTCTTCATGTCCTTGGTGAAC
Found at i:24724 original size:59 final size:60
Alignment explanation
Indices: 24642--24757 Score: 162
Period size: 59 Copynumber: 1.9 Consensus size: 60
24632 ACAAATAGTC
* * *
24642 CCCCAACTATAGGGTGTTACTTTGTCGAGTC-CCCGACTATTAAAAGTTATAAAATGATT
1 CCCCAACTATAGGATGTTACTTTGTCGAGTCTACCGACTATTAAAAGTTACAAAATGATT
* * * *
24701 CCCCGACTATAGGATGTTGCTTTGTTGAGTCTATCGACTATTAAAAGTTACAAAATG
1 CCCCAACTATAGGATGTTACTTTGTCGAGTCTACCGACTATTAAAAGTTACAAAATG
24758 GTCACTCGAC
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 27 0.55
60 22 0.45
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (60 bp):
CCCCAACTATAGGATGTTACTTTGTCGAGTCTACCGACTATTAAAAGTTACAAAATGATT
Found at i:24768 original size:60 final size:59
Alignment explanation
Indices: 24629--24757 Score: 152
Period size: 59 Copynumber: 2.2 Consensus size: 59
24619 AAGGGTAAAA
* * *
24629 TACACAAAT-AGTCCCCCAACTATAGGGTGTTACTTTGTCGAGTCCCCGACTATTAAAAGT
1 TACA-AAATGAGT-CCCCGACTATAGGATGTTACTTTGTCGAGTCACCGACTATTAAAAGT
* * * * *
24689 TATAAAATGATTCCCCGACTATAGGATGTTGCTTTGTTGAGTCTATCGACTATTAAAAGT
1 TACAAAATGAGTCCCCGACTATAGGATGTTACTTTGTCGAGTC-ACCGACTATTAAAAGT
24749 TACAAAATG
1 TACAAAATG
24758 GTCACTCGAC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
59 31 0.53
60 27 0.47
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (59 bp):
TACAAAATGAGTCCCCGACTATAGGATGTTACTTTGTCGAGTCACCGACTATTAAAAGT
Found at i:25464 original size:28 final size:29
Alignment explanation
Indices: 25432--25491 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
25422 TTGTAATAAG
* *
25432 AAGGGA-GAGGTTGAATTTATAAAATTTT
1 AAGGGACGAAGTTGAACTTATAAAATTTT
* *
25460 AAGGGACGAATTTTAACTTATAAAATTTT
1 AAGGGACGAAGTTGAACTTATAAAATTTT
25489 AAG
1 AAG
25492 AGATGAAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (29 bp):
AAGGGACGAAGTTGAACTTATAAAATTTT
Found at i:26335 original size:15 final size:16
Alignment explanation
Indices: 26297--26337 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
26287 ACAGAGCCTC
*
26297 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
26313 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
26329 T-AATCATTC
1 TGAATCATTC
26338 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:27235 original size:22 final size:22
Alignment explanation
Indices: 27193--27235 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
27183 ATTTTAGTAT
* *
27193 ATAGTATATGTTATATATATTA
1 ATAGTATATGTAAAATATATTA
27215 ATAGTATATGTCAAAAT-TATT
1 ATAGTATATGT-AAAATATATT
27236 TGTAGGTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (22 bp):
ATAGTATATGTAAAATATATTA
Found at i:27871 original size:23 final size:24
Alignment explanation
Indices: 27821--27896 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 24
27811 ATTCTTTTAA
**
27821 TAAATTAAAATAAATTATATATTTT
1 TAAA-TAAAATAAAAAATATATTTT
27846 TAAATAAAATAAAAAATA-ATTTT
1 TAAATAAAATAAAAAATATATTTT
27869 TAAATTAATTTAATAATAAAATATATTT
1 TAAA-TAA---AATAA-AAAATATATTT
27897 AATAAGTTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
23 9 0.21
24 15 0.35
25 4 0.09
27 5 0.12
28 6 0.14
29 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAATAAAATAAAAAATATATTTT
Found at i:27925 original size:21 final size:23
Alignment explanation
Indices: 27878--27931 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 23
27868 TTAAATTAAT
27878 TTAATAATAAAATATATTTAATAAG
1 TTAAT-ATAAAATATATTT-ATAAG
*
27903 TTGATATAAAA-ATATTT-TAAG
1 TTAATATAAAATATATTTATAAG
27924 TTAATATA
1 TTAATATA
27932 TATAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 11 0.41
23 6 0.22
24 6 0.22
25 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.43
Consensus pattern (23 bp):
TTAATATAAAATATATTTATAAG
Found at i:28029 original size:2 final size:2
Alignment explanation
Indices: 28022--28053 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28012 TTTTAAATAA
28022 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
28054 TCTAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32519 original size:2 final size:2
Alignment explanation
Indices: 32512--32545 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
32502 ATACCTTGTT
32512 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
32546 ATAGATTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35306 original size:20 final size:20
Alignment explanation
Indices: 35283--35328 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
35273 ATTCCATAAG
35283 AAAATTAGTGAATAT-TTTTT
1 AAAATT-GTGAATATATTTTT
*
35303 AAAATTTTGAATATATTTTT
1 AAAATTGTGAATATATTTTT
*
35323 TAAATT
1 AAAATT
35329 TAATATTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (20 bp):
AAAATTGTGAATATATTTTT
Found at i:35315 original size:19 final size:20
Alignment explanation
Indices: 35291--35329 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
35281 AGAAAATTAG
35291 TGAATAT-TTTTTAAAATTT
1 TGAATATATTTTTAAAATTT
*
35310 TGAATATATTTTTTAAATTT
1 TGAATATATTTTTAAAATTT
35330 AATATTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TGAATATATTTTTAAAATTT
Found at i:37302 original size:20 final size:19
Alignment explanation
Indices: 37276--37329 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
37266 CCAAAATAAT
*
37276 AAAAATATTATTTTATTCA
1 AAAAATATTATTTAATTCA
*
37295 ATAAAATAATTATTTAATTGA
1 A-AAAAT-ATTATTTAATTCA
*
37316 AAAAATAATATTTA
1 AAAAATATTATTTA
37330 GAGGGATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 8 0.27
20 10 0.33
21 12 0.40
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAAATATTATTTAATTCA
Found at i:37795 original size:23 final size:23
Alignment explanation
Indices: 37769--37816 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
37759 ATAAAGTACA
*
37769 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
37792 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
37815 AT
1 AT
37817 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:38566 original size:18 final size:18
Alignment explanation
Indices: 38543--38579 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38533 CGAAATATAT
38543 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
38561 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
38579 A
1 A
38580 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:38808 original size:23 final size:23
Alignment explanation
Indices: 38782--38846 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
38772 ATGCGAGATA
38782 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
**
38805 GATACCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
38828 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
38847 GTTTACCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:39238 original size:23 final size:23
Alignment explanation
Indices: 39208--39270 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
39198 AATATACCAC
39208 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
39231 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
39254 TACCTATTACATCATAT
1 TACCTATTACATTATAT
39271 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:39943 original size:408 final size:412
Alignment explanation
Indices: 38806--39992 Score: 2133
Period size: 408 Copynumber: 2.9 Consensus size: 412
38796 TATATAAACG
*
38806 ATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGT
1 ATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTTTATTGAAAGTGT
38871 CCATACTTTTTATAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTT
66 CCATACTTTTTATAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTT
38936 TAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCAC-AAAAATTAT
131 TAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTAT
39000 TTGATTGTTTTTATATTTTAT-AAATATTATTTAGAATTTTTAATTTAATAAT-A-ATATACCGT
196 TTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACCGT
39062 AACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAA
261 AACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAA
39127 GATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAGGATAGACA
326 GATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAGGATAGACA
39192 CTTTACAATATACCACTACCTATTACATTATATAAAC
391 CTTTACAATAT--CAC-ACC---T-C--------AAC
39229 GATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTTTATTGAAAGTG
1 -ATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTTTATTGAAAGTG
39294 TCCATACTTTTTATAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTT
65 TCCATACTTTTTATAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTT
39359 TTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTA
130 TTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTA
39424 TTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACCG
195 TTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACCG
39489 TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAA
260 TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAA
39554 AGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGA
325 AGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTAT-AAAAGGATAGA
39619 CACTTTACAATAT-A-A-C-C-AC
389 CACTTTACAATATCACACCTCAAC
39638 -TACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTTTATTGAAAGTGT
1 ATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTTTATTGAAAGTGT
39702 CCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTT
66 CCATACTTTTTAT-AAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTT
39767 TTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTA
130 TTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTA
39832 TTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACCG
195 TTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACCG
39897 TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAA
260 TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAA
39962 AGATAACCTTAAATTAATGTTTTCCACAGTG
325 AGATAACCTTAAATTAATGTTTTCCACAGTG
39993 TCGATATTAA
Statistics
Matches: 756, Mismatches: 1, Indels: 28
0.96 0.00 0.04
Matches are distributed among these distances:
407 77 0.10
408 277 0.37
409 2 0.00
418 1 0.00
423 1 0.00
424 185 0.24
425 30 0.04
426 32 0.04
427 1 0.00
428 126 0.17
429 24 0.03
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (412 bp):
ATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTTTATTGAAAGTGT
CCATACTTTTTATAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTT
TAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTAT
TTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACCGT
AACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAA
GATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAGGATAGACA
CTTTACAATATCACACCTCAAC
Found at i:41750 original size:3 final size:3
Alignment explanation
Indices: 41742--41828 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
41732 ACTTGTTTGG
* * * **
41742 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
41790 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
41829 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:41765 original size:18 final size:18
Alignment explanation
Indices: 41742--41843 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
41732 ACTTGTTTGG
41742 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
41760 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
41778 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
41796 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
41814 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
41832 AGCTTCATCTTC
1 ATCATCATCTTC
41844 TGCGACCGAT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:41809 original size:42 final size:42
Alignment explanation
Indices: 41750--41840 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
41740 GGATCATCAT
*
41750 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
41792 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
41834 CTTCATC
1 CTTCATC
41841 TTCTGCGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:43695 original size:199 final size:200
Alignment explanation
Indices: 43300--44921 Score: 3026
Period size: 199 Copynumber: 8.1 Consensus size: 200
43290 TTTAAATTTG
* *
43300 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
43365 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
43430 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
43494 AAAAA
196 AAAAA
43499 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
43564 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
43629 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
43694 AAAAA
196 AAAAA
43699 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATT-TCCTCATAAAACCGGTAT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCT-CTCATAAAACCGGTAT
43763 AATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGA
65 AATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGA
* * *
43828 TCGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTTTGGAA
130 TCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAA
43892 AAAAAA
195 AAAAAA
43898 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
43963 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
44027 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
44092 AAAAA
196 AAAAA
* *
44097 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
* *
44162 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
44227 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-AA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
44291 AAAAA
196 AAAAA
44296 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
44361 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
44426 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
44491 AAAAA
196 AAAAA
44496 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
44561 ATTGTACCGGTTAGATTG-AAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *
44625 CGACAC-TTTTTATATATGAATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
44689 AAAAA
196 AAAAA
44694 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
44759 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
44823 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
44888 AAAAA
196 AAAAA
*
44893 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
44922 TGACCCTTAA
Statistics
Matches: 1390, Mismatches: 25, Indels: 16
0.97 0.02 0.01
Matches are distributed among these distances:
198 245 0.18
199 749 0.54
200 396 0.28
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (200 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
AAAAA
Found at i:44096 original size:399 final size:399
Alignment explanation
Indices: 43300--44921 Score: 3038
Period size: 399 Copynumber: 4.1 Consensus size: 399
43290 TTTAAATTTG
*
43300 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
43365 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
43430 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAAA
43495 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
43560 TATAATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTG
43625 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
326 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
43690 GAAAAAAAA
391 GAAAAAAAA
*
43699 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATT-TCCTCATAAAACCGGTAT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCT-CTCATAAAACCGGTAT
43763 AATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGA
65 AATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGA
* *
43828 TCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTTTGGAAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAA
43893 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
*
43958 GTATAATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
260 GTATAATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTT
44022 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
325 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
44087 GGAAAAAAAA
390 GGAAAAAAAA
*
44097 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
44162 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
44227 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-AA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAA
44291 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
44356 GTATAATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTT
260 GTATAATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTT
44421 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
325 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
44486 GGAAAAAAAA
390 GGAAAAAAAA
*
44496 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
44561 ATTGTACCGGTTAGATTG-AAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
44625 CGACACTTTTTATATATGAATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAAA
44690 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
*
44755 TATAATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTG
44819 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
326 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
44884 GAAAAAAAA
391 GAAAAAAAA
*
44893 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
44922 TGACCCTTAA
Statistics
Matches: 1193, Mismatches: 25, Indels: 12
0.97 0.02 0.01
Matches are distributed among these distances:
397 196 0.16
398 476 0.40
399 521 0.44
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (399 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
TATAATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTG
GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
GAAAAAAAA
Found at i:44439 original size:598 final size:596
Alignment explanation
Indices: 43300--44921 Score: 3041
Period size: 598 Copynumber: 2.7 Consensus size: 596
43290 TTTAAATTTG
* *
43300 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
43365 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
43430 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
43495 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
*
43560 TATAATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTG
260 TATAATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
43625 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
324 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
43690 GAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTTCCTCATAAA
389 GAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTTCCTCATAAA
43755 ACCGGTATAATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGA
454 ACCGGTATAATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGA
*
43820 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCAT
519 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCAT
*
43885 TTTGGAAAAAAAA
584 TCTGGAAAAAAAA
43898 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
43963 ATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
66 ATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
44028 GACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 GACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
* *
44093 AAAATATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
44158 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
260 TATAATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
44223 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
324 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
44288 G-AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTA-TTCTCTCATAA
389 GAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTTC-CTCATAA
44351 AACCGGTATAATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATG
453 AACCGGTATAATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATG
*
44416 ATTTTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTC
518 ATTTTGGGATCGACAC-TTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTC
44481 ATTCTGGAAAAAAAA
582 ATTCTGGAAAAAAAA
44496 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
* *
44561 ATTGTACCGGTTAGATTGAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
66 ATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
* * *
44626 GACACTTTTTATATATGAATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAA
131 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAAA
44691 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
196 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
44756 ATAATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
261 ATAATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
44821 ATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGA
326 ATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGA
*
44886 AAAAAAATATCGACACAAACTATATTAGTATCGACA
391 AAAAAAATATCGACACAAACTATATTAGTGTCGACA
44922 TGACCCTTAA
Statistics
Matches: 1002, Mismatches: 18, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
596 112 0.11
597 367 0.37
598 523 0.52
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (596 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAAA
AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
ATAATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGA
AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTTCCTCATAAAAC
CGGTATAATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATT
TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTC
TGGAAAAAAAA
Found at i:45029 original size:19 final size:19
Alignment explanation
Indices: 45002--45046 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
44992 TATTCACATA
*
45002 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
45021 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
45040 AAAATTA
1 AAAATTA
45047 ACTCGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:46869 original size:33 final size:33
Alignment explanation
Indices: 46832--46897 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
46822 CATCTTAATA
*
46832 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
46865 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
46898 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:49040 original size:24 final size:24
Alignment explanation
Indices: 49003--49055 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
48993 CCGTTCTATC
49003 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
49027 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
49051 TATTT
1 TATTT
49056 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:49217 original size:17 final size:18
Alignment explanation
Indices: 49195--49236 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
49185 ATATATCCGG
*
49195 TATCATTT-TACCGTTTT
1 TATCATTTATACCGGTTT
49212 TATCATTTGATACCGGTTT
1 TATCATTT-ATACCGGTTT
49231 TATCAT
1 TATCAT
49237 ATTTTTACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
19 14 0.64
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:49393 original size:20 final size:20
Alignment explanation
Indices: 49367--49412 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
49357 CACTTTTAAA
49367 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
49386 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
49407 TTTACC
1 TTTACC
49413 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:58990 original size:32 final size:35
Alignment explanation
Indices: 58935--59007 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 35
58925 AATATATTAA
*
58935 AATTTTAAAATAATTAAAATAATAT-ATTTATTAT
1 AATTTTAAAATAATTAAAATAATATGATTTATAAT
* *
58969 -ATTTTAAAA-AGTTAAATTAATATGATTTATAAT
1 AATTTTAAAATAATTAAAATAATATGATTTATAAT
59002 AATTTT
1 AATTTT
59008 TATGTTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 12 0.35
33 17 0.50
34 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (35 bp):
AATTTTAAAATAATTAAAATAATATGATTTATAAT
Found at i:59053 original size:23 final size:23
Alignment explanation
Indices: 59007--59051 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
58997 ATAATAATTT
59007 TTATGTTTTAATAATATAAAATA
1 TTATGTTTTAATAATATAAAATA
*
59030 TTAT-TTTTAA-AATATTAAATA
1 TTATGTTTTAATAATATAAAATA
59051 T
1 T
59052 ATATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 6 0.29
23 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTATGTTTTAATAATATAAAATA
Found at i:59055 original size:2 final size:2
Alignment explanation
Indices: 59048--59076 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59038 AAAATATTAA
59048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59077 AATTAATCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66492 original size:17 final size:17
Alignment explanation
Indices: 66460--66504 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
66450 AGAAATATGT
*
66460 CTGGTGGGTCACCAGTTG
1 CTGGCGGGT-ACCAGTTG
66478 CTGGCGGGTACCAGTTG
1 CTGGCGGGTACCAGTTG
66495 CTGGCGGGTA
1 CTGGCGGGTA
66505 TGTGAGGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.11, C:0.22, G:0.42, T:0.24
Consensus pattern (17 bp):
CTGGCGGGTACCAGTTG
Found at i:73112 original size:19 final size:20
Alignment explanation
Indices: 73088--73134 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
73078 CTTCTATTTT
*
73088 TAATAA-AATTAGCCCTAAA
1 TAATAATAATTAACCCTAAA
*
73107 TAATAATACTTAACCCTAAA
1 TAATAATAATTAACCCTAAA
73127 TAAGTAAT
1 TAA-TAAT
73135 GAAAAATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.25
20 14 0.58
21 4 0.17
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.30
Consensus pattern (20 bp):
TAATAATAATTAACCCTAAA
Found at i:73554 original size:28 final size:28
Alignment explanation
Indices: 73500--73555 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
73490 GGTATTATTT
* *
73500 TAAAATTTATATTTTTATATTTTTTTTA
1 TAAAATTGATATTTTTATATTTATTTTA
*
73528 TAAAATTGAT-TTTTTGTATTATATTTTA
1 TAAAATTGATATTTTTATATT-TATTTTA
73556 GGTATAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (28 bp):
TAAAATTGATATTTTTATATTTATTTTA
Found at i:74269 original size:2 final size:2
Alignment explanation
Indices: 74262--74338 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
74252 TTGGTTCTCA
*
74262 AT AT AT AT AT TT 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
74304 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
74339 AATGAGTTGT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:81881 original size:14 final size:14
Alignment explanation
Indices: 81859--81900 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
81849 CATATCATAA
*
81859 CAACCAAAATCCAT
1 CAACTAAAATCCAT
81873 CAACTAAAATCCAT
1 CAACTAAAATCCAT
81887 CAACTAAAATCCAT
1 CAACTAAAATCCAT
81901 TAAGTCATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (14 bp):
CAACTAAAATCCAT
Done.