Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005365.1 Hibiscus syriacus cultivar Beakdansim tig00012196_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: 111857
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:24761 original size:19 final size:18
Alignment explanation
Indices: 24737--24797 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
24727 AAACCGAAAC
24737 CGGTTTTTTCGGTTCGGTT
1 CGGTTTTTTC-GTTCGGTT
*
24756 CGGTTTTTT--TAACGGTT
1 CGGTTTTTTCGT-TCGGTT
*
24773 CGGGTTTTTCGATTCGGTT
1 CGGTTTTTTCG-TTCGGTT
24792 CGGTTT
1 CGGTTT
24798 ATCGGTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.38
19 19 0.56
20 1 0.03
ACGTcount: A:0.05, C:0.15, G:0.30, T:0.51
Consensus pattern (18 bp):
CGGTTTTTTCGTTCGGTT
Found at i:34464 original size:4 final size:4
Alignment explanation
Indices: 34455--34479 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
34445 TCAAACTAAG
34455 CTTT CTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT C
34480 ATGCATTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
CTTT
Found at i:41779 original size:29 final size:30
Alignment explanation
Indices: 41747--41812 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
41737 AGGTCGCTTG
* *
41747 TTAAATACCTAATAAGTCTTTATGTTTTT-
1 TTAAATACCTAATAAATCTTTATATTTTTC
41776 TTAAATACCTAATAAATCTTTATATTTTTC
1 TTAAATACCTAATAAATCTTTATATTTTTC
41806 TTAAATA
1 TTAAATA
41813 ATCTAATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 27 0.79
30 7 0.21
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.50
Consensus pattern (30 bp):
TTAAATACCTAATAAATCTTTATATTTTTC
Found at i:42228 original size:3 final size:3
Alignment explanation
Indices: 42220--42259 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
42210 TAGAATCCAA
42220 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
42260 TGTCTGACTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:43153 original size:2 final size:2
Alignment explanation
Indices: 43146--43170 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43136 ATTGAAACTG
43146 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
43171 ATGGAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44278 original size:3 final size:3
Alignment explanation
Indices: 44270--44305 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
44260 TTGTCCGGGA
44270 TAT TAT TAT TAT TAT TAT TA- TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
44306 ATAATAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:53385 original size:36 final size:36
Alignment explanation
Indices: 53259--53417 Score: 178
Period size: 36 Copynumber: 4.4 Consensus size: 36
53249 GGAGAAAAGT
* * *
53259 CCATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAT
1 CCATCTTAAGCCTTCACCAGAGAATAGTGAAGCAAA
* * *
53295 CAATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAA
1 CCATCTTAAGCCTTCACCAGAGAATAGTGAAGCAAA
* * *
53331 CCATCATAAGTCTTCACCAGAGAGTAGTGAAGCAAA
1 CCATCTTAAGCCTTCACCAGAGAATAGTGAAGCAAA
* *
53367 CCATCTTAAGTCTTCACCA-A-AAGTAGTGAAGCAGAT
1 CCATCTTAAGCCTTCACCAGAGAA-TAGTGAAGCA-AA
*
53403 CCATTTTAAGCCTTC
1 CCATCTTAAGCCTTC
53418 TCAGAAGAGT
Statistics
Matches: 108, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
34 1 0.01
35 11 0.10
36 96 0.89
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (36 bp):
CCATCTTAAGCCTTCACCAGAGAATAGTGAAGCAAA
Found at i:53751 original size:104 final size:104
Alignment explanation
Indices: 53602--54474 Score: 932
Period size: 104 Copynumber: 8.3 Consensus size: 104
53592 GTGAAGCAAA
* * * *
53602 TGAAGATTATTTGAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCATTTGAAGAAGATG-T
1 TGAAGATTGTTCGAGTTCCATACTCCCTA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTT
* *
53666 CTGAGTTCCATACTCCCTAA-AGAGAGGGAGCGAACCCGTT
65 C-GAGTTCTATACTCCCTAAGAAAGAGGGAGCGAACCCGTT
* * * * *
53706 TGAAGATTATTCGAGTTCTATAATTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
1 TGAAGATTGTTCGAGTTCCATACTCCCT-AAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTT
* * *
53771 CAAGTTCTATACTCCCTAGAGAAAGAGGGAGCAAACCCGTA
65 CGAGTTCTATACTCCCTA-AGAAAGAGGGAGCGAACCCGTT
* * * * *
53812 AGAAGAAGATGTTCGAGTTCCATACTCCCTAA-AGAGAGGGAACGAACCCGTTT---GAAGATTT
1 TGAAG-A-TTGTTCGAGTTCCATACTCCCTAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGT
* * *
53873 TCGAGTTGTATACTCCCTAATAAAGAGGGAGCGAACCCGTA
64 TCGAGTTCTATACTCCCTAAGAAAGAGGGAGCGAACCCGTT
* * * *
53914 AGAAGAAGATGTTCGAGTTCCATACTCCCTAA-AGAGAGGGAGCGAACCCGTTTGAAG-A-TTGT
1 TGAAG-A-TTGTTCGAGTTCCATACTCCCTAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGT
* *
53976 TCGAGTTCTATACTTCCTAGAGAAAGAGGGAGCGAACCCGTA
64 TCGAGTTCTATACTCCCTA-AGAAAGAGGGAGCGAACCCGTT
* * *
54018 AGAAGAAGATGTTCGAGTTCCATACTCCCTAA-AGAGAGGGAGCGAACCCGTTT--A-AAGATTG
1 TGAAG-A-TTGTTCGAGTTCCATACTCCCTAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA-TG
*
54079 TTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTT
63 TTCGAGTTCTATACTCCCT-AAGAAAGAGGGAGCGAACCCGTT
* * * * * ** *
54122 TGAAGAAGATGTCCAAGTTCTATACTCCCTAGAGAAAGAGGGAGTGAACCCGTAAGAAGATGATG
1 TGAAG-A-TTGTTCGAGTTCCATACTCCCTA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATG
* *
54187 TTCGAGTTCCATACTCCCTAA-AGAGAGGGAGCGAACCCGTT
63 TTCGAGTTCTATACTCCCTAAGAAAGAGGGAGCGAACCCGTT
* * *
54228 TGAAGATTGTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
1 TGAAGATTGTTCGAGTTCCATACTCCCT-AAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTT
*
54293 CGAGTTCTATACTCCCTAGAGAAAGAGGGAACGAACCCGTT
65 CGAGTTCTATACTCCCTA-AGAAAGAGGGAGCGAACCCGTT
** * * *
54334 TGAAGATT-TTCGAGTTGTATACTCCCTAATAAAGAGGGAGCGAACCCGTTTGCAGAAGAAGTTC
1 TGAAGATTGTTCGAGTTCCATACTCCCTAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * *
54398 GAGTTCTATACTCCCTAAAAAAGAGGAAGCGAACTCGATGGT
66 GAGTTCTATACTCCCTAAGAAAGAGGGAGCGAACCCG-T--T
*
54440 TGAAGATTGTTCGAG-TCTCATACTCTCTGAAGAAA
1 TGAAGATTGTTCGAGTTC-CATACTCCCT-AAGAAA
54475 TAGGAGTAGA
Statistics
Matches: 669, Mismatches: 72, Indels: 52
0.84 0.09 0.07
Matches are distributed among these distances:
102 74 0.11
103 58 0.09
104 330 0.49
105 26 0.04
106 117 0.17
107 19 0.03
108 42 0.06
109 3 0.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (104 bp):
TGAAGATTGTTCGAGTTCCATACTCCCTAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
GAGTTCTATACTCCCTAAGAAAGAGGGAGCGAACCCGTT
Found at i:53950 original size:158 final size:156
Alignment explanation
Indices: 53614--54431 Score: 996
Period size: 158 Copynumber: 5.2 Consensus size: 156
53604 AAGATTATTT
* * * *
53614 GAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCATTTGAAGAAGATG-TCTGAGTTCCATA
1 GAGTTCTATACTCCCTA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC-GAGTTCTATA
* * *
53678 CTCCCTA-A-AGAGAGGGAGCGAACCCGTTTGAAGATTATTCGAGTTCTATAATTCCTGAAGAAA
64 CTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATT-TTCGAGTTCTATACTCCCT-AA-AAA
*
53741 GAGGGAGCGAACCCGTTTGAAGAAGATGTCC
126 GAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * ** *
53772 AAGTTCTATACTCCCTAGAGAAAGAGGGAGCAAACCCGTAAGAAGAAGATGTTCGAGTTCCATAC
1 GAGTTCTATACTCCCTA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATAC
* * *
53837 TCCCTA-A-AGAGAGGGAACGAACCCGTTTGAAGATTTTCGAGTTGTATACTCCCTAATAAAGAG
65 TCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATTTTCGAGTTCTATACTCCCTAA-AAAGAG
**
53900 GGAGCGAACCCGTAAGAAGAAGATGTTC
129 GGAGCGAACCCGTTTGAAGAAGATGTTC
* * *
53928 GAGTTCCATACTCCCTAA-AGAGAGGGAGCGAACCCGTTTGAAG-A-TTGTTCGAGTTCTATACT
1 GAGTTCTATACTCCCTAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATACT
* ** * * *
53990 TCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAGA
66 CCCTAGAGAAAGAGGGAGCGAACCCGT---TTGAAGATTTTCGAGTTCTATACTCCCTAAAAAGA
54055 GGGAGCGAACCCGTTT--A-AAGATTGTTC
128 GGGAGCGAACCCGTTTGAAGAAGA-TGTTC
* * *
54082 GAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCAAGTTCTATAC
1 GAGTTCTATACTCCCT-AAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATAC
* ** * *
54147 TCCCTAGAGAAAGAGGGAGTGAACCCGTAAGAAGATGATGTTCGAGTTCCATACTCCCTAAAGAG
65 TCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAT--T-TTCGAGTTCTATACTCCCTAAAAAG
*
54212 AGGGAGCGAACCCGTTTGAAG-A-TTGTTC
127 AGGGAGCGAACCCGTTTGAAGAAGATGTTC
* *
54240 GAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATAC
1 GAGTTCTATACTCCCT-AAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATAC
* *
54305 TCCCTAGAGAAAGAGGGAACGAACCCGTTTGAAGATTTTCGAGTTGTATACTCCCTAATAAAGAG
65 TCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATTTTCGAGTTCTATACTCCCTAA-AAAGAG
* *
54370 GGAGCGAACCCGTTTGCAGAAGAAGTTC
129 GGAGCGAACCCGTTTGAAGAAGATGTTC
* *
54398 GAGTTCTATACTCCCTAAAAAAGAGGAAGCGAAC
1 GAGTTCTATACTCCCTAAGAAAGAGGGAGCGAAC
54432 TCGATGGTTG
Statistics
Matches: 582, Mismatches: 58, Indels: 41
0.85 0.09 0.06
Matches are distributed among these distances:
152 20 0.03
153 6 0.01
154 58 0.10
155 30 0.05
156 114 0.20
157 59 0.10
158 291 0.50
159 2 0.00
160 2 0.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (156 bp):
GAGTTCTATACTCCCTAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATACT
CCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATTTTCGAGTTCTATACTCCCTAAAAAGAGGG
AGCGAACCCGTTTGAAGAAGATGTTC
Found at i:54453 original size:262 final size:258
Alignment explanation
Indices: 53614--54464 Score: 1119
Period size: 262 Copynumber: 3.3 Consensus size: 258
53604 AAGATTATTT
* * * *
53614 GAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCATTTGAAGAAGA-TG-TCTGAGTTCCAT
1 GAGTTCTATACTCCCTA-AAAAAGAGGGAGCGAACCC--GTGAAGAAGATTGTTC-GAGTTCCAT
* *
53677 ACTCCCTAAAGAGAGGGAGCGAACCCGTTTGAAGATTATTCGAGTTCTATAATTCCTGAAGAAAG
62 ACTCCCTAAAGAGAGGGAGCGAACCCGTTTGAAGATTGTTCGAGTTCTATACTTCCTGAAGAAAG
* *
53742 AGGGAGCGAACCCGTTTGAAGAAGATGTCCAAGTTCTATACTCCCTAGAGAAAGAGGGAGCAAAC
127 AGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAAC
** * * * *
53807 CCGTAAGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAGAGGGAACGAACCCGTTT--GAAGA
192 CCGT---TTGAAGATTTTCGAGTTCTATACTCCCTAAAAAGAGGGAGCGAACCCGTTTGAGAAGA
*
53870 TTTTC
254 TGTTC
* *
53875 GAGTTGTATACTCCCTAATAAAGAGGGAGCGAACCCGTAAGAAGAAGA-TGTTCGAGTTCCATAC
1 GAGTTCTATACTCCCTAAAAAAGAGGGAGCGAACCCGT--GAAGAAGATTGTTCGAGTTCCATAC
53939 TCCCTAAAGAGAGGGAGCGAACCCGTTTGAAGATTGTTCGAGTTCTATACTTCCT-AGAGAAAGA
64 TCCCTAAAGAGAGGGAGCGAACCCGTTTGAAGATTGTTCGAGTTCTATACTTCCTGA-AGAAAGA
** * * *
54003 GGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTCCATACTCCCTA-A-AGAGAGGGAGCGAACC
128 GGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACC
* *
54066 CGTTTAAAGATTGTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA
193 CGTTTGAAGATT-TTCGAGTTCTATACTCCCT-AA-AAAGAGGGAGCGAACCCGTTTG-AGAAGA
*
54131 TGTCC
254 TGTTC
* * *
54136 AAGTTCTATACTCCCTAGAGAAAGAGGGAGTGAACCCGT-AAGAAGATGATGTTCGAGTTCCATA
1 GAGTTCTATACTCCCTA-AAAAAGAGGGAGCGAACCCGTGAAGAAGAT--TGTTCGAGTTCCATA
54200 CTCCCTAAAGAGAGGGAGCGAACCCGTTTGAAGATTGTTCGAGTTCTATACTTCCTGAAGAAAGA
63 CTCCCTAAAGAGAGGGAGCGAACCCGTTTGAAGATTGTTCGAGTTCTATACTTCCTGAAGAAAGA
*
54265 GGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAACGAACC
128 GGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACC
* *
54330 CGTTTGAAGATTTTCGAGTTGTATACTCCCTAATAAAGAGGGAGCGAACCCGTTTGCAGAAGAAG
193 CGTTTGAAGATTTTCGAGTTCTATACTCCCTAA-AAAGAGGGAGCGAACCCGTTTG-AGAAGATG
54395 TTC
256 TTC
* * **
54398 GAGTTCTATACTCCCTAAAAAAGAGGAAGCGAACTCGATGGTTGAAGATTGTTCGAG-TCTCATA
1 GAGTTCTATACTCCCTAAAAAAGAGGGAGCGAACCCG-T-GAAGAAGATTGTTCGAGTTC-CATA
54462 CTC
63 CTC
54465 TCTGAAGAAA
Statistics
Matches: 521, Mismatches: 48, Indels: 41
0.85 0.08 0.07
Matches are distributed among these distances:
255 5 0.01
256 17 0.03
257 2 0.00
258 37 0.07
259 9 0.02
260 139 0.27
261 58 0.11
262 204 0.39
263 19 0.04
264 31 0.06
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (258 bp):
GAGTTCTATACTCCCTAAAAAAGAGGGAGCGAACCCGTGAAGAAGATTGTTCGAGTTCCATACTC
CCTAAAGAGAGGGAGCGAACCCGTTTGAAGATTGTTCGAGTTCTATACTTCCTGAAGAAAGAGGG
AGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
TTGAAGATTTTCGAGTTCTATACTCCCTAAAAAGAGGGAGCGAACCCGTTTGAGAAGATGTTC
Found at i:54728 original size:3 final size:3
Alignment explanation
Indices: 54720--54755 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
54710 TTGTCCGGGA
54720 TAT TAT TAT TAT TAT TAT TA- TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
54756 ATAATAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:58020 original size:2 final size:2
Alignment explanation
Indices: 58013--58044 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
58003 ATAAACCAAA
58013 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
58045 GAATTTGATT
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:65365 original size:12 final size:12
Alignment explanation
Indices: 65348--65373 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
65338 TTATTTGATT
65348 CTAATTATTTAC
1 CTAATTATTTAC
65360 CTAATTATTTAC
1 CTAATTATTTAC
65372 CT
1 CT
65374 TTGGTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (12 bp):
CTAATTATTTAC
Found at i:70115 original size:106 final size:106
Alignment explanation
Indices: 69930--71161 Score: 2108
Period size: 106 Copynumber: 11.6 Consensus size: 106
69920 GAAAAGTTGT
69930 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
69995 GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
66 GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
*
70036 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCGCAACGAAGGATATTGGACTC
1 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
70101 GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
66 GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
*
70142 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCGCAACGAAGGATATTGGACTC
1 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
70207 GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
66 GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
70248 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
70313 GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
66 GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* *
70354 TTGTCAACAAACAACTTCTCAATTTCAGAGCTAATTTCAACTTCACAACGAAGGATATTGGACTT
1 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
* *
70419 GAGACAACGTAAGTTCAACTTCACAACGAAGGGACCGCTGG
66 GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* * * *
70460 TTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
1 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
* * *
70525 CAGACAACGTAAGTTCAACTTCACAACGAAGGGACCGCTGG
66 GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
70566 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
70631 GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
66 GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
70672 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
* *
70737 GAGACAACGTAAGTTCAACTTCACAACGAAGGGACCGCTGG
66 GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* * ** * *
70778 TTGTCAACAAACAATTTCCCAATTTTGGAGCCAATTTCAACTTTACAACGAAGGATATTGAACTC
1 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
* *
70843 CAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGG
66 GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
*
70884 TTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTT
1 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-T
*
70949 C-AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGG
65 CGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
*
70990 TTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
* * * *
71055 CAGACAACACAAGTTCTACTTCACAACGAAGGGACCGCTGG
66 GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* * * * * *
71096 TTGTCAATAAACAA-TTTTCCAGTTTCAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACT
1 TTGTCAACAAACAACTTCT-CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
71160 CG
65 CG
71162 GAACAATACT
Statistics
Matches: 1076, Mismatches: 47, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
105 5 0.00
106 1069 0.99
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
Found at i:74239 original size:21 final size:21
Alignment explanation
Indices: 74199--74236 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
74189 GGTGTGACGA
74199 ATATAATAAAAGAATTAAATT
1 ATATAATAAAAGAATTAAATT
74220 ATATAA-AAAA-AATTAAA
1 ATATAATAAAAGAATTAAA
74237 AATCACAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (21 bp):
ATATAATAAAAGAATTAAATT
Found at i:79990 original size:27 final size:27
Alignment explanation
Indices: 79960--80038 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
79950 TTTTACAACT
*
79960 TAAGGGTATTTTTATAATTTTACCCCA
1 TAAGGGTATTTTCATAATTTTACCCCA
* *
79987 TAAGGGTATTTTCGTAATTTTACCTCA
1 TAAGGGTATTTTCATAATTTTACCCCA
80014 TAAGGGTATTTTCATAATTTTACCC
1 TAAGGGTATTTTCATAATTTTACCC
80039 AACCAAAGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (27 bp):
TAAGGGTATTTTCATAATTTTACCCCA
Found at i:81196 original size:21 final size:20
Alignment explanation
Indices: 81171--81225 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
81161 TTCTTTAAAA
81171 TATAATATTATGAATATATTT
1 TATAATATTA-GAATATATTT
* * *
81192 TATAATTTTAGATTGTATTT
1 TATAATATTAGAATATATTT
*
81212 GATAATATTA-AATA
1 TATAATATTAGAATA
81226 ACATTATAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 2 0.07
20 16 0.59
21 9 0.33
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (20 bp):
TATAATATTAGAATATATTT
Found at i:89584 original size:3 final size:3
Alignment explanation
Indices: 89576--89613 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
89566 ATCTAGTCTT
89576 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
89614 GTAAATAAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:95873 original size:2 final size:2
Alignment explanation
Indices: 95866--95890 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
95856 AAATTTATGT
95866 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
95891 GAATATTTAT
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:106758 original size:24 final size:24
Alignment explanation
Indices: 106731--106776 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
106721 AATGGAACAT
106731 TATACTTATTAAATAAATGATAAC
1 TATACTTATTAAATAAATGATAAC
106755 TATACTTATTAAATAAATGATA
1 TATACTTATTAAATAAATGATA
106777 TAAAGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (24 bp):
TATACTTATTAAATAAATGATAAC
Found at i:107023 original size:2 final size:2
Alignment explanation
Indices: 107016--107043 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
107006 AAATAAATAA
107016 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
107044 GACCAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107041 original size:67 final size:64
Alignment explanation
Indices: 106961--107091 Score: 201
Period size: 67 Copynumber: 2.0 Consensus size: 64
106951 TGTTAAACAA
106961 ATATATATATATAT-GAACAAAAAAAATCAGTTTCCAAGACACATTAAATAAATAAATATATATA
1 ATATATATATATATAG-AC-AAAAAAATCAGTTTCCAAGACACATTAAAT-AA-AAATATATATA
107025 TAT
62 TAT
*
107028 ATATATATATATATATGACCAAAAAATCAGTTTCCAAGACACATTAAATAAAAATATATATATA
1 ATATATATATATATA-GACAAAAAAATCAGTTTCCAAGACACATTAAATAAAAATATATATATA
107092 CGTTTAACAA
Statistics
Matches: 61, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
65 13 0.21
66 2 0.03
67 43 0.70
68 2 0.03
69 1 0.02
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (64 bp):
ATATATATATATATAGACAAAAAAATCAGTTTCCAAGACACATTAAATAAAAATATATATATAT
Found at i:107265 original size:52 final size:51
Alignment explanation
Indices: 107147--107281 Score: 193
Period size: 52 Copynumber: 2.6 Consensus size: 51
107137 ATGGCTATTC
* *
107147 TTCCTAAGACACATTAAAC-AA-ATATATATGTATATGAACAAAGAATCAGT
1 TTCC-AAGACACATTAAACAAATATATATATATATATGAACAAAAAATCAGT
**
107197 TTCCAAGACATGTTAAACAAATATATATATATATATGAACAAAAAAATCAGT
1 TTCCAAGACACATTAAACAAATATATATATATATATGAAC-AAAAAATCAGT
*
107249 TTCCAAGACACATTAAATAAATATATATATATA
1 TTCCAAGACACATTAAACAAATATATATATATA
107282 CGTTTAACAA
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
49 12 0.16
50 6 0.08
51 17 0.23
52 40 0.53
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (51 bp):
TTCCAAGACACATTAAACAAATATATATATATATATGAACAAAAAATCAGT
Found at i:107346 original size:188 final size:189
Alignment explanation
Indices: 107028--107579 Score: 972
Period size: 188 Copynumber: 2.9 Consensus size: 189
107018 ATATATATAT
* *
107028 ATATATATATATATATG-ACCAAAAAATCAGTTTCCAAGACACATTAAATAAAAATATATATATA
1 ATATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATATATATATATA
107092 CGTTTAACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAGAC
66 CGTTTAACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAGAC
107157 ACATTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTTAAACAA
131 ACATTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTTAAAC-A
107217 ATATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATATATATATATA
1 ATATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATATATATATATA
*
107282 CGTTTAAC-AA-ATCCAACTAAGCTATATGTTAAACAAATAAATAATAGCTATTCTTCCTAAGAC
66 CGTTTAACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAGAC
107345 ACATTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTTAAACA
131 ACATTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTTAAACA
107404 A-ATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATATATATATATA
1 ATATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAAT-AA-ATATATATATA
* *
107468 TACGTTTAACAAATATCCAACTAAGCTATATGTTAAACAAATAAACAATGGTTATTCTTCCTAAG
64 TACGTTTAACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAG
* *
107533 ACACGTTAAAC-AA-ATATATGTATATGAACAAAGAATCAATTTCCAAG
129 ACACATTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAG
107580 GTAAATGTAC
Statistics
Matches: 350, Mismatches: 8, Indels: 11
0.95 0.02 0.03
Matches are distributed among these distances:
186 48 0.14
187 4 0.01
188 164 0.47
189 23 0.07
190 111 0.32
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (189 bp):
ATATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATATATATATATA
CGTTTAACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAGAC
ACATTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTTAAACA
Found at i:107438 original size:50 final size:49
Alignment explanation
Indices: 107335--107468 Score: 205
Period size: 50 Copynumber: 2.7 Consensus size: 49
107325 ATAGCTATTC
* *
107335 TTCCTAAGACACATTAAACAAATATATATGTATATGAACAAAGAATCAGT
1 TTCC-AAGACACATTAAACAAATATATATATATATGAACAAAAAATCAGT
**
107385 TTCCAAGACATGTTAAACAAATATATATATATATGAACAAAAAAATCAGT
1 TTCCAAGACACATTAAACAAATATATATATATATGAAC-AAAAAATCAGT
*
107435 TTCCAAGACACATTAAATAAATATATATATATAT
1 TTCCAAGACACATTAAACAAATATATATATATAT
107469 ACGTTTAACA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
49 31 0.41
50 45 0.59
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (49 bp):
TTCCAAGACACATTAAACAAATATATATATATATGAACAAAAAATCAGT
Found at i:108803 original size:3 final size:3
Alignment explanation
Indices: 108788--108830 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
108778 TAAACACACT
* *
108788 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
108831 TTTTTTAACC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:109367 original size:91 final size:92
Alignment explanation
Indices: 109201--109367 Score: 266
Period size: 91 Copynumber: 1.8 Consensus size: 92
109191 GTCAAAAAGC
*
109201 TCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTTTCATTATGAACTCTCCATTG
1 TCTTCTCATTATGAACTTCTTCTACCTCTATCGGATGAGTTCTTTTCATTATGAACTCTCCATTG
109266 AAAATATTGATGCGAAGTTGAACAAGT
66 AAAATATTGATGCGAAGTTGAACAAGT
* *
109293 TCTTCTCATTATGAACTTCTTCTATCTC-ATTGGATGAGTTCTTCTT-ATTATGAACTCTCCATT
1 TCTTCTCATTATGAACTTCTTCTACCTCTATCGGATGAGTTCTT-TTCATTATGAACTCTCCATT
* *
109356 GGAAATGTTGAT
65 GAAAATATTGAT
109368 CCATCTCTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
91 41 0.59
92 28 0.41
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.42
Consensus pattern (92 bp):
TCTTCTCATTATGAACTTCTTCTACCTCTATCGGATGAGTTCTTTTCATTATGAACTCTCCATTG
AAAATATTGATGCGAAGTTGAACAAGT
Found at i:109599 original size:331 final size:332
Alignment explanation
Indices: 108998--109693 Score: 1071
Period size: 331 Copynumber: 2.1 Consensus size: 332
108988 CCTTTAGGAC
* * * * *
108998 GAGTTCTTCTCATTATGAACTCTTCA--GGAAATGTTGGTTCACCTCCATCTGTGGTGAATTTGA
1 GAGTTCTTCTTATTATGAACTCTCCATTGGAAATGTTGATCCACCTCCATCTGTGATGAATTTGA
* * *
109061 AAGGAACAAGTTCTTCTCATTATGACTTTCTCCTTTATGATGAGTTCTTCTCATTATGAACTCTT
66 AAGGAACAAGTTCTTCTCATTATGACTTTCTCCTTTAGGACGAGTTATTCTCATTATGAACTCTT
* * * * *
109126 CATTGGAAATGTCGATCCCTCAAGCGAGGTATCACTGATTCGAAATGTCGTGAATCAAGTGATAG
131 CA-TGAAAATATCAATCCCTCAAGCGAGGTATCACTAATTCGAAATGTCATGAATCAAGTGATAG
* *
109191 GTCAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTTTCATTATGAA
195 GTCAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGACGAGTTCTTCTCATTATGAA
*
109256 CTCTCCATTGAAAATATTGATGCGAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTATCTC
260 CTCTCCATTGAAAATATTGATGCGAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTACCTC
109321 AT-T-GGAT
325 -TGTCGGAT
* ** *
109328 GAGTTCTTCTTATTATGAACTCTCCATTGGAAATGTTGATCCATCTCTTTCTGTGATGGATTTGA
1 GAGTTCTTCTTATTATGAACTCTCCATTGGAAATGTTGATCCACCTCCATCTGTGATGAATTTGA
109393 AAGGAACAA-TTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTATTCTCATTATGAACTCT
66 AAGGAACAAGTTCTTCTCATTATG-ACTTTCTCCTTTAGGACGAGTTATTCTCATTATGAACTCT
* *
109457 TC-TGAAAATATCAATCCCTCAAGCGAGGTGTCACTAATTCGAAATGTCATGAATCGAGTGATAG
130 TCATGAAAATATCAATCCCTCAAGCGAGGTATCACTAATTCGAAATGTCATGAATCAAGTGATAG
* *
109521 GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGACGAGTTCTTCTCATTATGA
195 GTC-AAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGACGAGTTCTTCTCATTATGA
* * *
109586 GCTCTCCATTGAAAATGTTGATGCGAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCT
259 ACTCTCCATTGAAAATATTGATGCGAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTACCT
109651 CTGTCGGAT
324 CTGTCGGAT
109660 GAGTTCTTCTTATTATGAACTCTCCATTGGAAAT
1 GAGTTCTTCTTATTATGAACTCTCCATTGGAAAT
109694 ACTGATCCTT
Statistics
Matches: 333, Mismatches: 27, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
330 83 0.25
331 134 0.40
332 116 0.35
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (332 bp):
GAGTTCTTCTTATTATGAACTCTCCATTGGAAATGTTGATCCACCTCCATCTGTGATGAATTTGA
AAGGAACAAGTTCTTCTCATTATGACTTTCTCCTTTAGGACGAGTTATTCTCATTATGAACTCTT
CATGAAAATATCAATCCCTCAAGCGAGGTATCACTAATTCGAAATGTCATGAATCAAGTGATAGG
TCAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGACGAGTTCTTCTCATTATGAAC
TCTCCATTGAAAATATTGATGCGAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTACCTCT
GTCGGAT
Found at i:109628 original size:92 final size:92
Alignment explanation
Indices: 109524--109693 Score: 286
Period size: 92 Copynumber: 1.8 Consensus size: 92
109514 GTGATAGGTC
* *
109524 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGACGAGTTCTTCTCATTATGAGCT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGACGAGTTCTTCTCATTATGAACT
109589 CTCCATTGAAAATGTTGATGCGAAGTT
66 CTCCATTGAAAATGTTGATGCGAAGTT
* * *
109616 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTTATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGACGAGTTCTTCTCATTATGAACT
*
109681 CTCCATTGGAAAT
66 CTCCATTGAAAAT
109694 ACTGATCCTT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
92 72 1.00
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (92 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGACGAGTTCTTCTCATTATGAACT
CTCCATTGAAAATGTTGATGCGAAGTT
Found at i:110719 original size:8 final size:8
Alignment explanation
Indices: 110708--110799 Score: 59
Period size: 8 Copynumber: 11.5 Consensus size: 8
110698 CCTTTTTCTC
110708 TTTTCATT
1 TTTTCATT
110716 TTTTCA--
1 TTTTCATT
*
110722 -TTTCTTT
1 TTTTCATT
110729 TTTTCA-T
1 TTTTCATT
110736 TTTTCATTTTT
1 TTTTCA---TT
110747 TTTTCATT
1 TTTTCATT
**
110755 TTTTTTTCT
1 TTTTCAT-T
110764 TTTTCATT
1 TTTTCATT
110772 TTTTCATCT
1 TTTTCAT-T
110781 TTTT-ATT
1 TTTTCATT
* *
110788 TGTTCCTT
1 TTTTCATT
110796 TTTT
1 TTTT
110800 TTTTCTTCAA
Statistics
Matches: 65, Mismatches: 9, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
5 4 0.06
7 11 0.17
8 32 0.49
9 11 0.17
11 7 0.11
ACGTcount: A:0.09, C:0.13, G:0.01, T:0.77
Consensus pattern (8 bp):
TTTTCATT
Found at i:110725 original size:13 final size:13
Alignment explanation
Indices: 110709--110758 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
110699 CTTTTTCTCT
110709 TTTCATTTTTTCA
1 TTTCATTTTTTCA
*
110722 TTTCTTTTTTTCA
1 TTTCATTTTTTCA
110735 TTTTTCATTTTTT--
1 --TTTCATTTTTTCA
110748 TTTCATTTTTT
1 TTTCATTTTTT
110759 TTTCTTTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 11 0.33
13 12 0.36
15 10 0.30
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTCATTTTTTCA
Found at i:110748 original size:17 final size:17
Alignment explanation
Indices: 110726--110801 Score: 68
Period size: 18 Copynumber: 4.4 Consensus size: 17
110716 TTTTCATTTC
110726 TTTTTTTCATTTTTCATT
1 TTTTTTTCATTTTTCA-T
*
110744 TTTTTTTCATTTTT-TT
1 TTTTTTTCATTTTTCAT
110760 TTCTTTTTCATTTTTTCA-
1 TT-TTTTTCA-TTTTTCAT
* *
110778 TCTTTTT-ATTTGTTCCT
1 TTTTTTTCATTT-TTCAT
110795 TTTTTTT
1 TTTTTTT
110802 TTCTTCAAGC
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
15 3 0.06
16 7 0.15
17 18 0.38
18 20 0.42
ACGTcount: A:0.08, C:0.12, G:0.01, T:0.79
Consensus pattern (17 bp):
TTTTTTTCATTTTTCAT
Found at i:110749 original size:11 final size:11
Alignment explanation
Indices: 110714--110767 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
110704 TCTCTTTTCA
110714 TTTTTTCATTT
1 TTTTTTCATTT
* *
110725 CTTTTT--TTC
1 TTTTTTCATTT
*
110734 ATTTTTCATTT
1 TTTTTTCATTT
110745 TTTTTTCATTT
1 TTTTTTCATTT
110756 TTTTTTC-TTT
1 TTTTTTCATTT
110766 TT
1 TT
110768 CATTTTTTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
9 7 0.19
10 5 0.14
11 24 0.67
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:110784 original size:28 final size:28
Alignment explanation
Indices: 110700--110798 Score: 110
Period size: 28 Copynumber: 3.4 Consensus size: 28
110690 CAAACCCTCC
*
110700 TTTTTCTCTTTTCATTTTTTCAT-TTCTT
1 TTTTTCT-TTTTCATTTTTTCATCTTTTT
** *
110728 TTTTTCATTTTTCATTTTTTTTTCATTTT
1 TTTTTC-TTTTTCATTTTTTCATCTTTTT
110757 TTTTTCTTTTTCATTTTTTCATCTTTTT
1 TTTTTCTTTTTCATTTTTTCATCTTTTT
110785 ATTTGTTCCTTTTT
1 -TTT-TT-CTTTTT
110799 TTTTTCTTCA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
28 38 0.64
29 13 0.22
30 2 0.03
31 6 0.10
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.77
Consensus pattern (28 bp):
TTTTTCTTTTTCATTTTTTCATCTTTTT
Found at i:110802 original size:56 final size:56
Alignment explanation
Indices: 110700--110808 Score: 134
Period size: 56 Copynumber: 1.9 Consensus size: 56
110690 CAAACCCTCC
* *
110700 TTTTTCTCTTTTCATTTTTTCATTTCTTTTTTTCATTTTTCATTTTTTTTTCATTTT
1 TTTTTCTCTTTTCATTTTTTCATTTCTTTTTTTCACTTTT-ATTTTTTCTTCATTTT
*
110757 TTTTTCT-TTTTCATTTTTTCATCTTTTTATTTGTTC-CTTTT-TTTTTTCTTCA
1 TTTTTCTCTTTTCATTTTTTCAT-TTCTT-TTT-TTCACTTTTATTTTTTCTTCA
110809 AGCATAGTAC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
56 25 0.54
57 11 0.24
58 7 0.15
59 3 0.07
ACGTcount: A:0.08, C:0.15, G:0.01, T:0.76
Consensus pattern (56 bp):
TTTTTCTCTTTTCATTTTTTCATTTCTTTTTTTCACTTTTATTTTTTCTTCATTTT
Done.