Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008480.1 Hibiscus syriacus cultivar Beakdansim tig00111311_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: 2515485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 13
Found at i:2447160 original size:2 final size:2
Alignment explanation
Indices: 2447153--2447179 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2447143 TTAAATTCTA
2447153 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 A
2447180 ATTCTTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2448105 original size:6 final size:6
Alignment explanation
Indices: 2448094--2448123 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2448084 CGTTTTTTCC
*
2448094 CCTAAA CCTAAA CCTAAA CCCAAA CCTAAA
1 CCTAAA CCTAAA CCTAAA CCTAAA CCTAAA
2448124 TTTTTCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.37, G:0.00, T:0.13
Consensus pattern (6 bp):
CCTAAA
Found at i:2448413 original size:30 final size:30
Alignment explanation
Indices: 2448377--2448450 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
2448367 AAAGTCGAAA
*
2448377 TACAAAATGATTAATACAAAAACAAGTTCC
1 TACAAAATGATTAATACAAAAACAAGTACC
*
2448407 TACAAAAGGATTAATACAAAAACAAGTACC
1 TACAAAATGATTAATACAAAAACAAGTACC
2448437 TA-AAGAATGATTAA
1 TACAA-AATGATTAA
2448451 AAAACGTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 2 0.05
30 38 0.95
ACGTcount: A:0.55, C:0.14, G:0.09, T:0.22
Consensus pattern (30 bp):
TACAAAATGATTAATACAAAAACAAGTACC
Found at i:2451419 original size:4 final size:4
Alignment explanation
Indices: 2451407--2451449 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
2451397 TCTCGAACAT
* *
2451407 ATAC TTAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
2451450 TATATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (4 bp):
ATAC
Found at i:2451454 original size:12 final size:12
Alignment explanation
Indices: 2451405--2451456 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
2451395 TCTCTCGAAC
*
2451405 ATATACTTACAT
1 ATATACATACAT
*
2451417 ACATACATACAT
1 ATATACATACAT
*
2451429 ACATACATACAT
1 ATATACATACAT
*
2451441 ATATACATATAT
1 ATATACATACAT
2451453 ATAT
1 ATAT
2451457 TATTATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (12 bp):
ATATACATACAT
Found at i:2452986 original size:24 final size:24
Alignment explanation
Indices: 2452959--2453034 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
2452949 AAATTCATAA
2452959 TTATATTTATAATTTATTATATTT
1 TTATATTTATAATTTATTATATTT
** * *
2452983 TTATATAAATAACTTAATATAAGTTT
1 TTATATTTATAATTTATTAT-A-TTT
*
2453009 CTATTATTTATAATTTATATATATTT
1 TTA-TATTTATAATTTAT-TATATTT
2453035 AATCAAATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
24 16 0.41
25 1 0.03
26 8 0.21
27 11 0.28
28 3 0.08
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (24 bp):
TTATATTTATAATTTATTATATTT
Found at i:2453072 original size:2 final size:2
Alignment explanation
Indices: 2453065--2453091 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2453055 AGTTAACTTT
2453065 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 T
2453092 TTGAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2453247 original size:51 final size:50
Alignment explanation
Indices: 2453166--2453298 Score: 167
Period size: 50 Copynumber: 2.6 Consensus size: 50
2453156 TGAGAGATGT
* * *
2453166 GTGTAAGTATGTATTAAGTGTTACACTTTTTTATTTTATTTACTTACATCG
1 GTGTAAGTATGTGTTAAGTGTTACA-TTTTTTATTTTATTCACTTACACCG
* * * **
2453217 TTGTAAGTATGTGTTAAGTGTTATATTTTTTATTTTATTCATTTATGCCG
1 GTGTAAGTATGTGTTAAGTGTTACATTTTTTATTTTATTCACTTACACCG
*
2453267 GTGTAAGTATGTGTTAAGTGATAACATTTTTT
1 GTGTAAGTATGTGTTAAGTG-TTACATTTTTT
2453299 TAGTATGAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
50 39 0.56
51 31 0.44
ACGTcount: A:0.25, C:0.07, G:0.17, T:0.52
Consensus pattern (50 bp):
GTGTAAGTATGTGTTAAGTGTTACATTTTTTATTTTATTCACTTACACCG
Found at i:2453862 original size:12 final size:12
Alignment explanation
Indices: 2453832--2453864 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2453822 AAATAATAAA
2453832 AATAAAAACAAG
1 AATAAAAACAAG
*
2453844 AA-CAAAACAAG
1 AATAAAAACAAG
2453855 AATAAAAACA
1 AATAAAAACA
2453865 CAGAGAAGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.76, C:0.12, G:0.06, T:0.06
Consensus pattern (12 bp):
AATAAAAACAAG
Found at i:2453876 original size:23 final size:22
Alignment explanation
Indices: 2453830--2453884 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
2453820 CAAAATAATA
2453830 AAAATAAAAACAAGAACAAAAC
1 AAAATAAAAACAAGAACAAAAC
* *
2453852 AAGAATAAAAACACAG-AGAAGAC
1 AA-AATAAAAACA-AGAACAAAAC
2453875 AAAATAAAAA
1 AAAATAAAAA
2453885 AGAAGAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 10 0.34
23 17 0.59
24 2 0.07
ACGTcount: A:0.75, C:0.11, G:0.09, T:0.05
Consensus pattern (22 bp):
AAAATAAAAACAAGAACAAAAC
Found at i:2454217 original size:18 final size:18
Alignment explanation
Indices: 2454168--2454220 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
2454158 ATAGTAATAT
*
2454168 ATATATATATATAAATAAA
1 ATATATATAAAT-AATAAA
*
2454187 ATA-AAATAAATAATAAA
1 ATATATATAAATAATAAA
2454204 ATATATATAAATAATAA
1 ATATATATAAATAATAA
2454221 TTTGTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 9 0.30
18 18 0.60
19 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATATATATAAATAATAAA
Found at i:2455119 original size:3 final size:3
Alignment explanation
Indices: 2455111--2455150 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
2455101 TTATATTTTA
2455111 ATT ATT ATT ATT -TAT ATT ATT ATT ATT ATTT ATT ATT ATT
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT A-TT ATT ATT ATT
2455151 TACATTTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 29 0.85
4 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:2455134 original size:18 final size:19
Alignment explanation
Indices: 2455111--2455150 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
2455101 TTATATTTTA
2455111 ATTATTATTATTTA-TATT
1 ATTATTATTATTTATTATT
2455129 ATTATTATTATTTATTATT
1 ATTATTATTATTTATTATT
2455148 ATT
1 ATT
2455151 TACATTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTATTATTATTTATTATT
Found at i:2455144 original size:28 final size:26
Alignment explanation
Indices: 2455093--2455152 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 26
2455083 TATTTTGTTC
*
2455093 TATTTATTTTATATTTTAATTATTAT
1 TATTTATATTATATTTTAATTATTAT
*
2455119 TATTTATATTATTATTATTATTTATTAT
1 TATTTATATTA-TATT-TTAATTATTAT
2455147 TATTTA
1 TATTTA
2455153 CATTTCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 10 0.33
27 4 0.13
28 16 0.53
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (26 bp):
TATTTATATTATATTTTAATTATTAT
Found at i:2462699 original size:22 final size:22
Alignment explanation
Indices: 2462674--2462732 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
2462664 ATGTTGTATG
2462674 GTTGAGAGTCTATATTTATTGT
1 GTTGAGAGTCTATATTTATTGT
* *
2462696 GTTGACAGTCTATATTTCTTGT
1 GTTGAGAGTCTATATTTATTGT
2462718 GTTGAGAGTCTATAT
1 GTTGAGAGTCTATAT
2462733 CAAACGGTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.47
Consensus pattern (22 bp):
GTTGAGAGTCTATATTTATTGT
Found at i:2466382 original size:21 final size:22
Alignment explanation
Indices: 2466345--2466386 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2466335 ATGCATAAAG
*
2466345 TCGGATGAAAAATCGATCCGGA
1 TCGGATGAAAAACCGATCCGGA
2466367 TCGGAT-AAAAACCGATCCGG
1 TCGGATGAAAAACCGATCCGG
2466387 TTTTTTCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (22 bp):
TCGGATGAAAAACCGATCCGGA
Found at i:2466682 original size:33 final size:33
Alignment explanation
Indices: 2466635--2466705 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
2466625 ACAAAGTTTA
* *
2466635 CGAT-AATTGAAATACTTAAATACTT-CTAAGTT
1 CGATAAATTCAAATACTTAAAAACTTAC-AAGTT
2466667 CGATAAATTCAAATACTTAAAAACTTACAAGTT
1 CGATAAATTCAAATACTTAAAAACTTACAAGTT
2466700 CGATAA
1 CGATAA
2466706 TTGAAACAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
32 4 0.11
33 30 0.86
34 1 0.03
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.32
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTACAAGTT
Found at i:2466725 original size:21 final size:21
Alignment explanation
Indices: 2466700--2466741 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2466690 CTTACAAGTT
*
2466700 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAATTTA
2466721 CGATAATTGAAACAAAATTTA
1 CGATAATTGAAACAAAATTTA
2466742 AAAAGAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (21 bp):
CGATAATTGAAACAAAATTTA
Found at i:2471203 original size:14 final size:14
Alignment explanation
Indices: 2471184--2471288 Score: 67
Period size: 14 Copynumber: 7.6 Consensus size: 14
2471174 TTCAAATAAT
2471184 TTTATGTTCGTTCG
1 TTTATGTTCGTTCG
2471198 TTTATG-T--TT-G
1 TTTATGTTCGTTCG
* * *
2471208 TTTATATTCATTCA
1 TTTATGTTCGTTCG
*
2471222 TTTGTGTTCGTTTACG
1 TTTATGTTCG-TT-CG
* *
2471238 TTCAT-TTATGTTCG
1 TTTATGTT-CGTTCG
*
2471252 TTTATATTCGTTCG
1 TTTATGTTCGTTCG
*
2471266 TTTATGTTCGTTCA
1 TTTATGTTCGTTCG
*
2471280 TTTGTGTTC
1 TTTATGTTC
2471289 ATTTATCATT
Statistics
Matches: 69, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
10 6 0.09
11 3 0.04
13 3 0.04
14 44 0.64
15 8 0.12
16 5 0.07
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.59
Consensus pattern (14 bp):
TTTATGTTCGTTCG
Found at i:2471240 original size:44 final size:44
Alignment explanation
Indices: 2471192--2471277 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
2471182 ATTTTATGTT
* * *
2471192 CGTTCGTTTATGTTTGTTTATATTCATTCATTTGTGTTCGTTTA
1 CGTTCATTTATGTTCGTTTATATTCATTCATTTATGTTCGTTTA
* *
2471236 CGTTCATTTATGTTCGTTTATATTCGTTCGTTTATGTTCGTT
1 CGTTCATTTATGTTCGTTTATATTCATTCATTTATGTTCGTT
2471278 CATTTGTGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.58
Consensus pattern (44 bp):
CGTTCATTTATGTTCGTTTATATTCATTCATTTATGTTCGTTTA
Found at i:2471241 original size:20 final size:20
Alignment explanation
Indices: 2471218--2471255 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2471208 TTTATATTCA
*
2471218 TTCATTTGTGTTCGTTTACG
1 TTCATTTATGTTCGTTTACG
2471238 TTCATTTATGTTCGTTTA
1 TTCATTTATGTTCGTTTA
2471256 TATTCGTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.58
Consensus pattern (20 bp):
TTCATTTATGTTCGTTTACG
Found at i:2471256 original size:10 final size:10
Alignment explanation
Indices: 2471226--2471277 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
2471216 CATTCATTTG
2471226 TGTTCGTTTA
1 TGTTCGTTTA
* *
2471236 CGTTCATTTA
1 TGTTCGTTTA
2471246 TGTTCGTTTATA
1 TGTTCG-TT-TA
2471258 TTCGTTCGTTTA
1 -T-GTTCGTTTA
2471270 TGTTCGTT
1 TGTTCGTT
2471278 CATTTGTGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 19 0.56
11 3 0.09
12 4 0.12
13 3 0.09
14 5 0.15
ACGTcount: A:0.12, C:0.13, G:0.17, T:0.58
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:2471288 original size:24 final size:24
Alignment explanation
Indices: 2471190--2471294 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
2471180 TAATTTTATG
* * *
2471190 TTCGTTCGTTTATGTTTGTTTATA
1 TTCGTTCATTTATGTTCGTTCATA
* *
2471214 TTCATTCATTTGTGTTCGTT--TA
1 TTCGTTCATTTATGTTCGTTCATA
*
2471236 --CGTTCATTTATGTTCGTTTATA
1 TTCGTTCATTTATGTTCGTTCATA
*
2471258 TTCGTTCGTTTATGTTCGTTCAT-
1 TTCGTTCATTTATGTTCGTTCATA
*
2471281 TTGTGTTCATTTAT
1 TT-CGTTCATTTAT
2471295 CATTTTAACA
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
20 16 0.24
22 4 0.06
23 2 0.03
24 44 0.67
ACGTcount: A:0.13, C:0.12, G:0.15, T:0.59
Consensus pattern (24 bp):
TTCGTTCATTTATGTTCGTTCATA
Found at i:2479279 original size:27 final size:27
Alignment explanation
Indices: 2479241--2479305 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
2479231 GGAGTGATCT
2479241 TTCGGGACAAATACAATACATAGGTCC
1 TTCGGGACAAATACAATACATAGGTCC
2479268 TTCGGGACAAATACAATACATAGGTCC
1 TTCGGGACAAATACAATACATAGGTCC
2479295 TTCGGGACAAA
1 TTCGGGACAAA
2479306 ATTTCATAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (27 bp):
TTCGGGACAAATACAATACATAGGTCC
Found at i:2487981 original size:21 final size:21
Alignment explanation
Indices: 2487955--2488017 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
2487945 TTTTGGTGCA
*
2487955 GAGGGAATCGATTCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
* **
2487976 GAGGGAACCGATTCCTCCTTT
1 GAGGGAACCGATTCCCCCCCT
2487997 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
2488018 ACAGGGGAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 18 0.53
22 1 0.03
23 15 0.44
ACGTcount: A:0.21, C:0.35, G:0.25, T:0.19
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:2492601 original size:19 final size:19
Alignment explanation
Indices: 2492577--2492624 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
2492567 TTCAAGGTGT
2492577 ATCGATGCAC-ATGAAGTGC
1 ATCGATGCACTA-GAAGTGC
*
2492596 ATCGATGCACTAGTAGTGC
1 ATCGATGCACTAGAAGTGC
2492615 ATCGATGCAC
1 ATCGATGCAC
2492625 CCCCCTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (19 bp):
ATCGATGCACTAGAAGTGC
Found at i:2496983 original size:64 final size:65
Alignment explanation
Indices: 2496845--2497003 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 65
2496835 TGTTCAGTGT
* * *
2496845 GTATCGATGCA-CAGGAAGTGCATCGATGCA-CCCATTAAAAATGGAAACATCGAATGCAATTAG
1 GTATCGATGCATAAGG-AGTGCATCGATGCACCCCATTAAAAATGAAAACATCGAAGGCAATTAG
*
2496908 T
65 C
* * * ** *
2496909 GCATCAATGCATAAGGAGTGCATCGATGCACCCCCTT-AAAATGAAAACATCGAAGGTGATTTGC
1 GTATCGATGCATAAGGAGTGCATCGATGCACCCCATTAAAAATGAAAACATCGAAGGCAATTAGC
** *
2496973 GTATCGATGCATGTGTAGTGCATCGATGCAC
1 GTATCGATGCATAAGGAGTGCATCGATGCAC
2497004 TTCAAGGGAA
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
64 70 0.90
65 8 0.10
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.23
Consensus pattern (65 bp):
GTATCGATGCATAAGGAGTGCATCGATGCACCCCATTAAAAATGAAAACATCGAAGGCAATTAGC
Found at i:2497417 original size:22 final size:20
Alignment explanation
Indices: 2497396--2497433 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2497386 CTATGTTATG
2497396 ATGAT-ATAAACTATATGAT
1 ATGATAATAAACTATATGAT
*
2497415 ATGATAATAAATTATATGA
1 ATGATAATAAACTATATGA
2497434 ATATAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGATAATAAACTATATGAT
Found at i:2498128 original size:2 final size:2
Alignment explanation
Indices: 2498121--2498171 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2498111 AGGAAAAATG
2498121 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
2498163 AT AT AT AT A
1 AT AT AT AT A
2498172 GGAAGATGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2499623 original size:2 final size:2
Alignment explanation
Indices: 2499616--2499640 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2499606 TAGGTTTTTC
2499616 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 T
2499641 TTATCTTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2500460 original size:37 final size:37
Alignment explanation
Indices: 2500408--2500511 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
2500398 ATTTTCGTCA
*
2500408 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* * *
2500445 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* * * *
2500482 TACTAAGATTTAAATTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
2500512 CCACAAGTAC
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
Found at i:2500907 original size:18 final size:17
Alignment explanation
Indices: 2500868--2500910 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2500858 ATTATATGGA
2500868 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
2500884 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
2500902 TATTATTAT
1 TATTATTAT
2500911 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:2501409 original size:34 final size:36
Alignment explanation
Indices: 2501362--2501433 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
2501352 ATTGGGAGGG
*
2501362 TAGCTTTTCTA-TTT-TTAAGTA-TTTGGTGTATATA
1 TAGCTTTTCTATTTTATTAA-TACTTTGATGTATATA
2501396 TAGCTTATT-TATTTTATTAATACTTTGATGTATATA
1 TAGCTT-TTCTATTTTATTAATACTTTGATGTATATA
2501432 TA
1 TA
2501434 TATTTATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
34 8 0.24
35 7 0.21
36 18 0.55
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.56
Consensus pattern (36 bp):
TAGCTTTTCTATTTTATTAATACTTTGATGTATATA
Found at i:2507232 original size:183 final size:183
Alignment explanation
Indices: 2506924--2507460 Score: 975
Period size: 183 Copynumber: 2.9 Consensus size: 183
2506914 ATTAAATCCG
2506924 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
2506989 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAATTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
2507054 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
2507107 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* * *
2507172 ATAGATTATGTTCAAATTATGACACTGCTCAGATACTTGGAAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAATTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
2507237 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
2507290 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * *
2507355 ATAGATTACATTCAAATCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAATTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* *
2507420 TTGTCAGGTCAAAGACTTTGTGATGAGATGAACCATTCAGT
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
2507461 TAAACCTGAT
Statistics
Matches: 339, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 339 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAATTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:2508657 original size:36 final size:34
Alignment explanation
Indices: 2508617--2508730 Score: 95
Period size: 36 Copynumber: 3.2 Consensus size: 34
2508607 CACTCAAATT
2508617 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACA-A-TTTGTCTCACTTGAGAC
* * ** *
2508653 TGTTTTTCTCTAAAGA-AGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAA-ACA-ATTTGTCTCACTTGAGAC
*
2508689 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-A-ATTTGTCTCACTTGAGAC
*
2508725 CGTTTT
1 TGTTTT
2508731 CACTCGAAAG
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
34 1 0.02
35 4 0.07
36 49 0.80
37 6 0.10
38 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (34 bp):
TGTTTTTCTTAAAACAATTTGTCTCACTTGAGAC
Found at i:2508692 original size:72 final size:76
Alignment explanation
Indices: 2508601--2508762 Score: 219
Period size: 72 Copynumber: 2.2 Consensus size: 76
2508591 ATGCAGATGA
* * *
2508601 TTATTTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
*
2508663 TAAAGAA-G-AT
65 GAAAGAAGGCAT
*
2508673 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCG
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCG
2508737 AAAGAAGGCAT
66 AAAGAAGGCAT
2508748 TTCATTTCACTCAAG
1 TT-ATTTCACTCAAG
2508763 GCTATTTTTT
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
71 1 0.01
72 51 0.65
73 10 0.13
74 1 0.01
75 4 0.05
76 12 0.15
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (76 bp):
TTATTTCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCG
AAAGAAGGCAT
Found at i:2508793 original size:73 final size:71
Alignment explanation
Indices: 2508601--2508796 Score: 166
Period size: 72 Copynumber: 2.7 Consensus size: 71
2508591 ATGCAGATGA
* * * * * * * *
2508601 TTATTTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTTTCTCT
1 TTATTTCACTCAAGA-CTATTTTTCTT-AAACA-AGATTTATCTCGCTTGAGACCGTTTTACTCG
2508664 AAAGAAGAT
63 AAAGAAGAT
* * *
2508673 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGACTATTTTTCTT-AAACAAGATTTATCTCGCTTGAGACCGTTTT-ACTCGA
2508738 AAGAAGGCAT
64 AAGAA-G-AT
* * *
2508748 TTCATTTCACTCAAGGCTATTTTT-TT-AAGAAGATTTATCTTGCTTGAGA
1 TT-ATTTCACTCAAGACTATTTTTCTTAAACAAGATTTATCTCGCTTGAGA
2508797 TTTTCCCTCG
Statistics
Matches: 107, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
71 1 0.01
72 51 0.48
73 30 0.28
74 1 0.01
75 6 0.06
76 18 0.17
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (71 bp):
TTATTTCACTCAAGACTATTTTTCTTAAACAAGATTTATCTCGCTTGAGACCGTTTTACTCGAAA
GAAGAT
Found at i:2508922 original size:39 final size:39
Alignment explanation
Indices: 2508866--2509046 Score: 109
Period size: 39 Copynumber: 4.9 Consensus size: 39
2508856 CCTTGAAATT
* *
2508866 AATTTTTTCTCTCTTGAGATAGTTTCCCTTGAAACAGAA
1 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAGAA
* *
2508905 AATTTTGTCTC-CATTGAGACAGTTTCTCTTGAAACATAA
1 AATTTTGTCTCTC-TTGAGACAGTTTCCCTTGAAACAGAA
* * * *
2508944 ACA--TTG--------AAAACA-TTTCCCTTGAAA-TGAT
1 A-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAGAA
** * * * *
2508972 TTTTTTCTCTCTCTTGAGATAGTTTCCCTCGAAATAGAA
1 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAGAA
* *
2509011 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
2509047 TAAACATTGA
Statistics
Matches: 101, Mismatches: 27, Indels: 28
0.65 0.17 0.18
Matches are distributed among these distances:
28 1 0.01
29 13 0.13
30 4 0.04
37 3 0.03
38 15 0.15
39 64 0.63
40 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (39 bp):
AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAGAA
Found at i:2508957 original size:104 final size:104
Alignment explanation
Indices: 2508843--2509163 Score: 504
Period size: 106 Copynumber: 3.1 Consensus size: 104
2508833 ACAGTTTCTC
*
2508843 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCTTGAGATAGTTTCCCTTGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTTGAAACAGAAAAT
*
2508908 TTTGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
2508947 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCTCTTGAGATAGTTTCCCTCGAAATAGAAA
1 TTGAAAACATTTCCCTTGAAATGA-ATTTTT-TCTCTCTTGAGATAGTTTCCCTTGAAACAGAAA
2509012 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
64 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* *
2509053 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTTGAAACAGAAAAT
** *
2509115 TTTGTCTCCCTTGAGACAGGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACA-GTTTCTCTTGAAACATAAACA
2509155 TTGAAAACA
1 TTGAAAACA
2509164 ATTTAACAAA
Statistics
Matches: 201, Mismatches: 13, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
101 21 0.10
102 27 0.13
103 1 0.00
104 48 0.24
105 9 0.04
106 95 0.47
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTTGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:2509109 original size:36 final size:36
Alignment explanation
Indices: 2509062--2509130 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
2509052 ATTGAAAACA
* *
2509062 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGATAG
*
2509098 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGA
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGA
2509131 CAGGTTTCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGATAG
Found at i:2509539 original size:105 final size:106
Alignment explanation
Indices: 2509338--2509584 Score: 415
Period size: 105 Copynumber: 2.3 Consensus size: 106
2509328 ATATCGTGAC
* * * *
2509338 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTC
*
2509403 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGG
*
2509444 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTC
2509508 AATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGG
* *
2509549 ACTTCAGACAACGCAAGTTCAACTTCATAACGAAGG
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGG
2509585 ATATTGGACT
Statistics
Matches: 132, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
105 84 0.64
106 48 0.36
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTC
AATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:2509571 original size:43 final size:43
Alignment explanation
Indices: 2509523--2509627 Score: 174
Period size: 43 Copynumber: 2.4 Consensus size: 43
2509513 CAGAACCAAT
*
2509523 TTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *
2509566 TTCAACTTCATAACGAAGGATATTGGACTCCAGACAATGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
2509609 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
2509628 GACCGCTGCT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:2509686 original size:148 final size:148
Alignment explanation
Indices: 2509418--2509733 Score: 560
Period size: 148 Copynumber: 2.1 Consensus size: 148
2509408 CAGAGCCAAT
2509418 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* *
2509483 CGCTGCTTGTCAACAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTG
66 CGCTGCTTGTCAACAACAACTTCCCAATCTCAGAACCAATTTCAACTTCACAACGAAGGATATTG
* *
2509548 GACTTCAGACAACGCAAG
131 GACTCCAGACAACACAAG
* *
2509566 TTCAACTTCATAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
*
2509631 CGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
66 CGCTGCTTGTCAACAACAACTTCCCAATCTCAGAACCAATTTCAACTTCACAACGAAGGATATTG
2509696 GACTCCAGACAACACAAG
131 GACTCCAGACAACACAAG
*
2509714 TTCAACTTCACGACGAAGGA
1 TTCAACTTCACAACGAAGGA
2509734 CCGCTGCTTG
Statistics
Matches: 159, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
148 159 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (148 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
CGCTGCTTGTCAACAACAACTTCCCAATCTCAGAACCAATTTCAACTTCACAACGAAGGATATTG
GACTCCAGACAACACAAG
Found at i:2509785 original size:104 final size:104
Alignment explanation
Indices: 2509566--2510010 Score: 630
Period size: 104 Copynumber: 4.3 Consensus size: 104
2509556 ACAACGCAAG
* **
2509566 TTCAACTTCATAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGAC
2509631 CGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAAT
66 CGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCAAT
2509671 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAA-GGAC
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGAC
2509735 CGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAAT
66 CGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCAAT
* ** * *
2509775 TTTAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTCCACGACGAAGAGAC
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGAC
* *
2509840 CGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGAGTCAAT
66 CGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCAAT
* * * *
2509875 TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAAATTCACAACGAAGGGAC
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGAC
* * * **
2509940 GGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAAT
66 CGCTGCTTGTCAAC-AACAACTTCCCAATT-CAGAGCCAAT
* *
2509981 TTCAACTTCACGACGGAGGATATTGGACTC
1 TTCAACTTCACAACGAAGGATATTGGACTC
2510011 GGAACAATGC
Statistics
Matches: 306, Mismatches: 27, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
100 78 0.25
101 4 0.01
102 3 0.01
103 4 0.01
104 103 0.34
105 78 0.25
106 36 0.12
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (104 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGAC
CGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCAAT
Found at i:2509807 original size:209 final size:206
Alignment explanation
Indices: 2509566--2510010 Score: 662
Period size: 209 Copynumber: 2.1 Consensus size: 206
2509556 ACAACGCAAG
* * *
2509566 TTCAACTTCATAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTCCACGACGAAGAGAC
2509631 CGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
66 CGCTGCTTGTCAACAA-AA-TT-CC-AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
* *
2509696 GACTCCAGACAACACAAGTTCAACTTCACGACGAA-GGACCGCTGCTTGTCAAC-AACAACTTCC
126 GACTCCAGACAACACAAGTTCAAATTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCC
2509759 CAA-TCTCAGAGCCAAT
191 CAATTC-CAGAGCCAAT
*
2509775 TTTAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTCCACGACGAAGAGAC
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTCCACGACGAAGAGAC
* * *
2509840 CGCTGCTTGTCAACAAAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTC
66 CGCTGCTTGTCAACAAAATTCCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
* * * * **
2509905 GAGACAACACAAGTTCAAATTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTT
131 CAGACAACACAAGTTCAAATTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCCCAATT
2509970 CCAGAGCCAAT
196 CCAGAGCCAAT
* *
2509981 TTCAACTTCACGACGGAGGATATTGGACTC
1 TTCAACTTCACAACGAAGGATATTGGACTC
2510011 GGAACAATGC
Statistics
Matches: 215, Mismatches: 18, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
204 66 0.31
205 18 0.08
206 48 0.22
207 4 0.02
208 2 0.01
209 77 0.36
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (206 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTCCACGACGAAGAGAC
CGCTGCTTGTCAACAAAATTCCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
CAGACAACACAAGTTCAAATTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCCCAATT
CCAGAGCCAAT
Found at i:2511019 original size:3 final size:3
Alignment explanation
Indices: 2510995--2511089 Score: 51
Period size: 3 Copynumber: 32.3 Consensus size: 3
2510985 TTTTATTCAT
* *
2510995 TTA TTT TTA TTA TTCA -TG TTA TTA TTA TTA -TA TGTA TATA TATA TATA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA T-TA T-TA T-TA T-TA
* * *
2511043 TTA AT- TTA TT- TCA TTA TTA TT- TTA CTA -TA TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2511086 TTA T
1 TTA T
2511090 ATATATATAA
Statistics
Matches: 73, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
2 10 0.14
3 48 0.66
4 15 0.21
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2511022 original size:18 final size:17
Alignment explanation
Indices: 2510983--2511025 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2510973 TATATATGGA
2510983 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
2510999 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
2511017 TATTATTAT
1 TATTATTAT
2511026 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:2511064 original size:11 final size:11
Alignment explanation
Indices: 2510983--2511089 Score: 63
Period size: 12 Copynumber: 8.7 Consensus size: 11
2510973 TATATATGGA
2510983 TATTTTATTCATT
1 TATTTTATT-A-T
2510996 TATTTTTATTAT
1 TA-TTTTATTAT
*
2511008 TCATGTTATTAT
1 T-ATTTTATTAT
*
2511020 TATTATATGTAT
1 TATTTTAT-TAT
2511032 ATATATATATATTAATT
1 -TAT-T-T-TATT-A-T
*
2511049 TATTTCATTAT
1 TATTTTATTAT
*
2511060 TATTTTACTA-
1 TATTTTATTAT
2511070 TATTTTATTAT
1 TATTTTATTAT
2511081 TATTATTAT
1 TATT-TTAT
2511090 ATATATATAA
Statistics
Matches: 75, Mismatches: 8, Indels: 23
0.71 0.08 0.22
Matches are distributed among these distances:
10 9 0.12
11 18 0.24
12 19 0.25
13 10 0.13
14 9 0.12
15 2 0.03
16 7 0.09
17 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:2511073 original size:21 final size:21
Alignment explanation
Indices: 2511013--2511093 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 21
2511003 ATTATTCATG
* *
2511013 TTATTATTATTATATGTAT-A
1 TTATTATTATTATATATTTCA
*
2511033 -TATATATATATTAATTTATTTCA
1 TTAT-TAT-TATT-ATATATTTCA
*
2511056 TTATTATT-TTACTATATTTTA
1 TTATTATTATTA-TATATTTCA
2511077 TTATTATTATTATATAT
1 TTATTATTATTATATAT
2511094 ATATAAATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
19 3 0.06
20 4 0.08
21 26 0.53
22 9 0.18
23 4 0.08
24 3 0.06
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (21 bp):
TTATTATTATTATATATTTCA
Found at i:2511298 original size:25 final size:25
Alignment explanation
Indices: 2511269--2511319 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
2511259 TAACTTTATA
2511269 TTTA-TATTATT-TTTA-TATTTTT
1 TTTATTATTATTATTTATTATTTTT
2511291 TTTATTATTATTATTTATTATTTTT
1 TTTATTATTATTATTTATTATTTTT
2511316 TTTA
1 TTTA
2511320 AAAAAAACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 4 0.15
23 7 0.27
24 4 0.15
25 11 0.42
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTATTATTATTATTTATTATTTTT
Found at i:2512435 original size:15 final size:15
Alignment explanation
Indices: 2512412--2512444 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2512402 CGTAGGACTC
2512412 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
2512427 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
2512442 CTA
1 CTA
2512445 TTATACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:2512568 original size:29 final size:29
Alignment explanation
Indices: 2512529--2512667 Score: 226
Period size: 29 Copynumber: 4.8 Consensus size: 29
2512519 TTTTATATGT
2512529 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
* *
2512557 TCATTTAGCTCATGTAATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
2512586 TCATATAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
2512615 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
2512644 TCATGTAGCTCATGTTATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
2512668 ATATCACATA
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 6 0.06
29 92 0.89
30 5 0.05
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.46
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Done.