Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001956.1 Hibiscus syriacus cultivar Beakdansim tig00003960_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: 55833
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:554 original size:198 final size:197
Alignment explanation
Indices: 5--862 Score: 1039
Period size: 198 Copynumber: 4.4 Consensus size: 197
1 ATCG
* * * * **
5 GTATAAATATACCGGTTTTATGTGAGAATAAGTCTACATAATGTATCAACACTT-TTTAATTTTG
1 GTATAAATATACCGGTTTTATGAGAGAATAGGTCTA-AAAATGTATCGACACTTGTGGAA-TTTG
* * * * * *
69 TGTCTATACATTTTGTCCAGAATGAATGCCCAAAAAAATGGTGCACGCATAAAGTGTCAATACAT
64 TGTCGATACTTTTTGTCGAGAATGAATGCCC---AAAAGGGTGCACCCATAAAGTGTCGATACAT
* * * * *
134 TTATAAAAAGTATCGATCCCAGAAACATCGAAACTC-ATGATTATAATATAATAGGTAATTTTTC
126 TTTTAAAAAGTATCGATCCCAAAAACATCGAAAC-CGATAATTATAATGTAATAGGTAA-ATTTC
*
198 AATGTAACC
189 AATGTAACA
* * * *
207 GATATAAATATATCGGTTTTAT--GTGAATAGGTCTAAAAATGTATCGACACTTGTGTATTTTGT
1 G-TATAAATATACCGGTTTTATGAGAGAATAGGTCTAAAAATGTATCGACACTTGTGGAATTTGT
*
270 GTCGATACTTTTTGTCTAGAATGAATG-CCATAAAGGGTGCACCCATAAAGTGTCGATACATTTT
65 GTCGATACTTTTTGTCGAGAATGAATGCCCA-AAAGGGTGCACCCATAAAGTGTCGATACATTTT
* **
334 TAAAAAGTGTCGATCCCAAAAACATCGAAATAGATAATTATAATGTAATAGGTAAATTTCAATGT
129 TAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTCAATGT
399 AATCA
194 AA-CA
* * *
404 GTATAAATATACCGATTTTATGAGAGAATAGGTCTAAAAAATATATCGACAGTTGTGGAATTTGT
1 GTATAAATATACCGGTTTTATGAGAGAATAGGTCT-AAAAATGTATCGACACTTGTGGAATTTGT
* *
469 GTCGATACTTTTTGTCGAGAAGGAATGCCCAAAAGGGTGCACCCAT-AAGTGTCGATACTTTTTT
65 GTCGATACTTTTTGTCGAGAATGAATGCCCAAAAGGGTGCACCCATAAAGTGTCGATACATTTTT
533 AAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTCAATGTA
130 AAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTCAATGTA
598 ACCA
195 A-CA
* * * *
602 ATATAAATATA-CGGTTTTATGAGAGAATATGTCTACAAATGTATCGACACTTCTGGAA-TTGTG
1 GTATAAATATACCGGTTTTATGAGAGAATAGGTCTAAAAATGTATCGACACTTGTGGAATTTGTG
*
665 TCGATAC-TTTTGTCGAGAATGAATGCCTAAAA-GGTGCACCCATAAAGTGTCGAT--ATTTTTA
66 TCGATACTTTTTGTCGAGAATGAATGCCCAAAAGGGTGCACCCATAAAGTGTCGATACATTTTTA
* *
726 AAAAGTTTCGATCCCTAAAAATATCGAAACCGATAATTATAATGTAATAGGTAAATTTCCAATGT
131 AAAAGTATCGATCCC-AAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTT-CAATGT
791 AACA
194 AACA
* * * ** * * **
795 TTAT-AA-ATA-CGAG-TATATGAGAAAATAGGTCGCATAA-GTATCGACAATTGTTAAATTTGT
1 GTATAAATATACCG-GTTTTATGAGAGAATAGGTCTAAAAATGTATCGACACTTGTGGAATTTGT
855 GTCGATAC
65 GTCGATAC
863 CATTTTAAAA
Statistics
Matches: 582, Mismatches: 60, Indels: 39
0.85 0.09 0.06
Matches are distributed among these distances:
190 14 0.02
191 34 0.06
192 23 0.04
193 57 0.10
194 41 0.07
195 12 0.02
196 50 0.09
197 100 0.17
198 103 0.18
199 67 0.12
200 47 0.08
201 14 0.02
202 1 0.00
203 19 0.03
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (197 bp):
GTATAAATATACCGGTTTTATGAGAGAATAGGTCTAAAAATGTATCGACACTTGTGGAATTTGTG
TCGATACTTTTTGTCGAGAATGAATGCCCAAAAGGGTGCACCCATAAAGTGTCGATACATTTTTA
AAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTCAATGTAA
CA
Found at i:2328 original size:3 final size:3
Alignment explanation
Indices: 2320--2355 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2310 GGACGATAAA
*
2320 GAT GAT GAT GAT GAT GAT GAT CAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
2356 CTAAACAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:3652 original size:24 final size:25
Alignment explanation
Indices: 3625--3676 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
3615 TTTCAAATTC
*
3625 ATTTTATATGT-AATTGGAGTTTGA
1 ATTTTAAATGTCAATTGGAGTTTGA
* *
3649 A-TTTAAATTTCAATTTGAGTTTGA
1 ATTTTAAATGTCAATTGGAGTTTGA
3673 ATTT
1 ATTT
3677 CAATATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 7 0.30
24 14 0.61
25 2 0.09
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.52
Consensus pattern (25 bp):
ATTTTAAATGTCAATTGGAGTTTGA
Found at i:3665 original size:18 final size:18
Alignment explanation
Indices: 3644--3680 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3634 GTAATTGGAG
3644 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
3662 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
3680 T
1 T
3681 ATAAATTTCG
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:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:3687 original size:24 final size:24
Alignment explanation
Indices: 3636--3688 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3626 TTTTATATGT
* * *
3636 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
3660 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
3684 AATTT
1 AATTT
3689 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:4316 original size:197 final size:198
Alignment explanation
Indices: 3903--4659 Score: 975
Period size: 197 Copynumber: 3.8 Consensus size: 198
3893 AAGTTTCCCG
*
3903 TAAAGTGTCGATACATTTTTAAAAAGTATCGATCCAAAAAATATCGAAACCGAAAATTATAATGT
1 TAAAGTGTCGATACA-TTTTAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAATGT
* * * * *
3968 AATAGGTAAA-TTACAATGTGACCGGTATAAATATACCGATTTTATGTGCAAATAGGTCAGCATA
65 AATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAACATA
* * **** *
4032 AAGTATCGACACCTTTTAAATTTGTGTCGATACTTTTTGTCC-GAACCTTTGCTC-AAC-GAGCT
130 ATGTATCGACA-CTTTTAAATTTGTGTCGATACATTTTGTCCAGAATGAATG-TCAAACAG-GGT
4094 TCACGCA
192 TCACGCA
* * * *
4101 TAAAAGTGTTGATACA-TTTAAAATTGTATCGATCC-AAAAATATCGAAATCGAAAATTATAATG
1 T-AAAGTGTCGATACATTTTAAAA-AGTATCGATCCAAAAAACATCGAAACCGAAAATTATAATG
** *
4164 TAATAGGTAAATTTACAATGTAACTAGTATAAATATACCGGTTTTATGAGAAAATATGT-ATACA
64 TAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCA-ACA
*
4228 TAATGTATCGACACTGTTTAAATTTGTGTCGATACATTTTGTCCATAATGAATGTCAAACAGGGT
128 TAATGTATCGACACT-TTTAAATTTGTGTCGATACATTTTGTCCAGAATGAATGTCAAACAGGGT
* *
4293 GCACACA
192 TCACGCA
4300 T-AAGTGTCGATACATTTT-AAAAGTATCGAT-CACAAAAACATCGAAA-C-AATAATTATAATG
1 TAAAGTGTCGATACATTTTAAAAAGTATCGATCCA-AAAAACATCGAAACCGAA-AATTATAATG
* * * *
4360 TAATAGGTAAATTTACAATGTAACCCGTATAAGTATACCGGTTTTATGAGAAAATAAGTGAACAT
64 TAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAACAT
* * * *
4425 AATGTATCGACACTTTTAGATTTGGGTCGATACATTTTGTCTAGAATGAATG-CAAAAACGGGTT
129 AATGTATCGACACTTTTAAATTTGTGTCGATACATTTTGTCCAGAATGAATGTCAAACA-GGGTT
4489 CACGCA
193 CACGCA
* *
4495 TAAAGTGTCAATACATTTTAAAAAGTATCGATCCAAAAAACATTGAAACCGAAAATTATAATGTA
1 TAAAGTGTCGATACATTTTAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAATGTA
* *
4560 ATAGGTAAATTTACAATGTAACCGGTATAAATATACC-GATTTATGAGAAAATAGGTTAACATAA
66 ATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAACATAA
* * *
4624 TGTATCAACACTTTTAAATTTGTGTTGATACGTTTT
131 TGTATCGACACTTTTAAATTTGTGTCGATACATTTT
4660 TAAATTACGT
Statistics
Matches: 493, Mismatches: 47, Indels: 39
0.85 0.08 0.07
Matches are distributed among these distances:
194 5 0.01
195 47 0.10
196 108 0.22
197 155 0.31
198 147 0.30
199 30 0.06
200 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (198 bp):
TAAAGTGTCGATACATTTTAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAATGTA
ATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAACATAA
TGTATCGACACTTTTAAATTTGTGTCGATACATTTTGTCCAGAATGAATGTCAAACAGGGTTCAC
GCA
Found at i:5839 original size:19 final size:19
Alignment explanation
Indices: 5815--5858 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
5805 AGGGTTGATT
5815 TTGTATAAGATTTATAATG
1 TTGTATAAGATTTATAATG
* *
5834 TTGTATACGATTTATAATT
1 TTGTATAAGATTTATAATG
5853 TTGTAT
1 TTGTAT
5859 GTGAATGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.52
Consensus pattern (19 bp):
TTGTATAAGATTTATAATG
Found at i:8863 original size:200 final size:197
Alignment explanation
Indices: 8514--9029 Score: 621
Period size: 200 Copynumber: 2.6 Consensus size: 197
8504 ATATAAAGTA
* *
8514 TCGATACATTTATTAAAAT-TATCGATCTCAATAACATCGAAACCGATAATTATAATATAAT-AG
1 TCGATACATTTATT-AAATGTATCGATCCCAA-AACATCGAAACCGATAATTATAATGTAATAAG
** * * *
8577 ATAAATTTACAATGTAATTGGTATAAATATACCGGTTTTATAAGAAAATATGTCAGCATAAAGTA
64 -TAAATTTACAATGT-ACCGGTATAAATATATCGGTTTTATAAGAAAATAGGTCAGAATAAAGTA
* * *
8642 TCGACACCATTTAAATTTGTGTCGATACTTTTTGTCCATAATGAATGTCAAACGGGGTGCACGCA
127 TCGACACCATTTAAATTTGTGTCGATACTTTTT-TCCAGAATGAATGCCAAACGAGGTGCACGCA
8707 TAAAATG
191 TAAAATG
* *
8714 TCGATACATTTATTAAATGTATCGATCCCACAAACATCGAAACCGATAATTACAATGTGATAAGT
1 TCGATACATTTATTAAATGTATCGATCCCA-AAACATCGAAACCGATAATTATAATGTAATAAGT
* * * * *
8779 AAATTTACAATGTACCCGATAGAAATATATCGGTTTTATGATAAAATAGGTCTA-AATAATGTAT
65 AAATTTACAATGTA-CCGGTATAAATATATCGGTTTTATAAGAAAATAGGTC-AGAATAAAGTAT
** * * **
8843 CGACACTTTTTAAGTTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAACGAGGTGCTTGCATA
128 CGACACCATTTAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCCAAACGAGGTGCACGCATA
*
8908 AAGTG
193 AAATG
* * *
8913 TCGATACATTTA--AAATTGTATCGATCCAAAAAACATCGAAATCGATAATTATAATGTAATAAT
1 TCGATACATTTATTAAA-TGTATCGATCC-CAAAACATCGAAACCGATAATTATAATGTAATAAG
* *
8976 TAAATTTGCAATGTTACCGGTATAAATATATCGG-TTTACTTAGAAAATAGGTCA
64 TAAATTTACAATG-TACCGGTATAAATATATCGGTTTTA-TAAGAAAATAGGTCA
9030 ATATAAGCGT
Statistics
Matches: 273, Mismatches: 34, Indels: 21
0.83 0.10 0.06
Matches are distributed among these distances:
197 8 0.03
198 80 0.29
199 51 0.19
200 130 0.48
201 4 0.01
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.33
Consensus pattern (197 bp):
TCGATACATTTATTAAATGTATCGATCCCAAAACATCGAAACCGATAATTATAATGTAATAAGTA
AATTTACAATGTACCGGTATAAATATATCGGTTTTATAAGAAAATAGGTCAGAATAAAGTATCGA
CACCATTTAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCCAAACGAGGTGCACGCATAAAA
TG
Found at i:16079 original size:20 final size:21
Alignment explanation
Indices: 16056--16101 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
16046 TTTGAGTTGA
16056 TTAAAATATGTTT-AAACTAT
1 TTAAAATATGTTTAAAACTAT
* *
16076 TTAAAATGTGTTTAAAACTTT
1 TTAAAATATGTTTAAAACTAT
16097 TTAAA
1 TTAAA
16102 TGTGAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (21 bp):
TTAAAATATGTTTAAAACTAT
Found at i:16163 original size:16 final size:16
Alignment explanation
Indices: 16139--16170 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16129 TGGTACTGTT
16139 CATGATATTGTTCATA
1 CATGATATTGTTCATA
*
16155 CATGGTATTGTTCATA
1 CATGATATTGTTCATA
16171 GTTTGGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (16 bp):
CATGATATTGTTCATA
Found at i:16392 original size:19 final size:19
Alignment explanation
Indices: 16363--16418 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
16353 TAGTGTGTTT
*
16363 AAAAGTTTCGATACTTTTAC
1 AAAA-TTTCGATACTTTCAC
16383 AAAATTTCGATACTTTCAC
1 AAAATTTCGATACTTTCAC
*
16402 AAAATTTCGAAACTTTC
1 AAAATTTCGATACTTTC
16419 TTCGAAGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 30 0.88
20 4 0.12
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (19 bp):
AAAATTTCGATACTTTCAC
Found at i:19292 original size:19 final size:19
Alignment explanation
Indices: 19264--19318 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
19254 TACTGTTCAT
* * *
19264 AGTTTGGAAACTTTGTAAG
1 AGTTTTGAAACTTTGCAAA
*
19283 AGTTTTGAAACTTTACAAA
1 AGTTTTGAAACTTTGCAAA
*
19302 AATTTTGAAACTTTGCA
1 AGTTTTGAAACTTTGCA
19319 CCTAGAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
AGTTTTGAAACTTTGCAAA
Found at i:19449 original size:20 final size:19
Alignment explanation
Indices: 19405--19477 Score: 92
Period size: 20 Copynumber: 3.7 Consensus size: 19
19395 AGTGTGTTTA
* * *
19405 AAAGTTTCGATACTTTCAC
1 AAAGTTTCAAAACTTTCTC
19424 AAAGTTTCAAAACTTTCTC
1 AAAGTTTCAAAACTTTCTC
19443 AAAAGTTTCAAAACTTTCTTC
1 -AAAGTTTCAAAACTTTC-TC
*
19464 AAAGTTTCGAAACT
1 AAAGTTTCAAAACT
19478 GCATGTGCAG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
19 16 0.33
20 30 0.62
21 2 0.04
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (19 bp):
AAAGTTTCAAAACTTTCTC
Found at i:21023 original size:14 final size:14
Alignment explanation
Indices: 20986--21026 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
20976 GTAAAATAGC
20986 TTTTTAATGTATT-
1 TTTTTAATGTATTA
*
20999 TTTTCAA--TATTA
1 TTTTTAATGTATTA
21011 TTTTTAATGTATTA
1 TTTTTAATGTATTA
21025 TT
1 TT
21027 AATAGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 4 0.17
12 6 0.26
13 6 0.26
14 7 0.30
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (14 bp):
TTTTTAATGTATTA
Found at i:27130 original size:3 final size:3
Alignment explanation
Indices: 27122--27197 Score: 81
Period size: 3 Copynumber: 26.7 Consensus size: 3
27112 TACGATTTTG
* *
27122 TAA TAA TAA TAA CAA TAA TAA T-A TAA CAA TAA T-A TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
27167 T-A TAA T-A TAA TAA TATA CAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA
27198 TAAGAATATA
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
2 10 0.16
3 49 0.80
4 2 0.03
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:27152 original size:8 final size:8
Alignment explanation
Indices: 27122--27207 Score: 68
Period size: 8 Copynumber: 10.2 Consensus size: 8
27112 TACGATTTTG
27122 TAATAATAA
1 TAATAAT-A
*
27131 TAACAATAA
1 TAATAAT-A
27140 TAAT-ATAA
1 TAATAAT-A
*
27148 CAATAATA
1 TAATAATA
27156 TAATAATA
1 TAATAATA
27164 TAATATAATA
1 T-A-ATAATA
27174 TAATAATA
1 TAATAATA
*
27182 T-ACAATAA
1 TAATAAT-A
27190 TAATAATA
1 TAATAATA
*
27198 TAAGAATA
1 TAATAATA
27206 TA
1 TA
27208 GTAAATACAT
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
7 4 0.06
8 35 0.54
9 19 0.29
10 7 0.11
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (8 bp):
TAATAATA
Found at i:27158 original size:5 final size:5
Alignment explanation
Indices: 27139--27200 Score: 53
Period size: 5 Copynumber: 12.8 Consensus size: 5
27129 AATAACAATA
*
27139 ATAAT ATAACA ATAAT AT-A- ATAAT ATAAT ATAAT AT-A- ATAAT ATACA-
1 ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT
27186 ATAAT AATAAT ATAA
1 ATAAT -ATAAT ATAA
27201 GAATATAGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
3 4 0.09
4 5 0.11
5 28 0.60
6 10 0.21
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (5 bp):
ATAAT
Found at i:27509 original size:52 final size:51
Alignment explanation
Indices: 27429--27689 Score: 362
Period size: 52 Copynumber: 5.0 Consensus size: 51
27419 TTTAGAGATA
* ** * *
27429 ATTGAGATAACACAGTTCCTTCACGATGAGAATGTTTGGCTATCTAAGGATG
1 ATTGAGATAACACGGTTCCTTCGTGATGAGACT-TCTGGCTATCTAAGGATG
*
27481 ATTGAGATAACACGATTCCTTCGTGATGAGGACTTCTGGCTATCTAAGGATG
1 ATTGAGATAACACGGTTCCTTCGTGATGA-GACTTCTGGCTATCTAAGGATG
*
27533 ATTGAAATAACACGGTTCCTTCGTGATGAGGACTT-TAGGCTATCTAAGGATG
1 ATTGAGATAACACGGTTCCTTCGTGATGA-GACTTCT-GGCTATCTAAGGATG
27585 ATTGAGATAACACGGTTCCTTCGTGATGAAGACTTCTGGCTATCTAAGGATG
1 ATTGAGATAACACGGTTCCTTCGTGATG-AGACTTCTGGCTATCTAAGGATG
* * * *
27637 ATTGAGAAAAGACGGTTCCTTCGTGATGAGGACATCTGGCTATCAAAGGATG
1 ATTGAGATAACACGGTTCCTTCGTGATGA-GACTTCTGGCTATCTAAGGATG
27689 A
1 A
27690 CTTGGCTCAT
Statistics
Matches: 191, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
51 2 0.01
52 184 0.96
53 5 0.03
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (51 bp):
ATTGAGATAACACGGTTCCTTCGTGATGAGACTTCTGGCTATCTAAGGATG
Found at i:27833 original size:52 final size:52
Alignment explanation
Indices: 27785--28188 Score: 567
Period size: 52 Copynumber: 7.8 Consensus size: 52
27775 ATGATAATAT
* * * *
27785 GGTTCCTTCACGATGAGCACATCTGGCTATCTAAGGATGATGGAGATAACAC
1 GGTTCCTTCATGATGAGGACTTCTGGCTATCTAAGGATGATTGAGATAACAC
* * * *
27837 GGTTCATTCGTGATGAGGACTTATGGCTATCTAAGAATGATTGAGATAACAC
1 GGTTCCTTCATGATGAGGACTTCTGGCTATCTAAGGATGATTGAGATAACAC
** *
27889 AATTCC-TCAGTGATGAGGACTTCTGGCTATCTAAGGATGATTGAGATAACAT
1 GGTTCCTTCA-TGATGAGGACTTCTGGCTATCTAAGGATGATTGAGATAACAC
* * * * *
27941 GGTTCCTTCGTGAAGAAGACTTCTGGCTATCTAAGGATGATTCAGATAACAT
1 GGTTCCTTCATGATGAGGACTTCTGGCTATCTAAGGATGATTGAGATAACAC
* *
27993 GGTTCCTTCGTGATGAGGACTTCTGGCTATCTAAAGATGATTGAGATAACAC
1 GGTTCCTTCATGATGAGGACTTCTGGCTATCTAAGGATGATTGAGATAACAC
*
28045 GGTTCCTTCGTGATGAGGACTTCTGGCTATCTAAGGATGATTGAGATAACAC
1 GGTTCCTTCATGATGAGGACTTCTGGCTATCTAAGGATGATTGAGATAACAC
** * * *
28097 ACTTCCTTCATGATAAGGACTTCTGACTATCTAAGGATGATTGGGATAACAC
1 GGTTCCTTCATGATGAGGACTTCTGGCTATCTAAGGATGATTGAGATAACAC
*
28149 AGTTCCTTCATGATGAGGACTTCTGGCTATCTAAGGATGA
1 GGTTCCTTCATGATGAGGACTTCTGGCTATCTAAGGATGA
28189 CTTGGCTCCT
Statistics
Matches: 314, Mismatches: 36, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
51 2 0.01
52 310 0.99
53 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (52 bp):
GGTTCCTTCATGATGAGGACTTCTGGCTATCTAAGGATGATTGAGATAACAC
Found at i:28471 original size:82 final size:79
Alignment explanation
Indices: 28346--28525 Score: 191
Period size: 80 Copynumber: 2.2 Consensus size: 79
28336 TCTTTTTACT
* * * * * **
28346 TTCAGGGGATATCAGACTTAATCTGTGCCTCTTTTTCGAGTATTCATATTAATTTTTGAAGATTT
1 TTCAGGGGAGATCAGAC-TAATCTATGCATCTTTTTCGAGTATTCAGA-TAA-ATTTGAAGACGT
28411 ATCTACTCCACTACTCA
63 ATCTACTCCACTACTCA
* *
28428 TTCAGGGGAGATCAGACTAGATCTATGCAAT-TTTTTCGGGTATTCAGATAAATTTGAAGACGTG
1 TTCAGGGGAGATCAGACTA-ATCTATGC-ATCTTTTTCGAGTATTCAGATAAATTTGAAGACGTA
* *
28492 TCTACTCTACTATTCA
64 TCTACTCCACTACTCA
* *
28508 TTCAGAGAAGATCAGACT
1 TTCAGGGGAGATCAGACT
28526 GGATGTGGAT
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
80 39 0.47
81 5 0.06
82 38 0.46
83 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (79 bp):
TTCAGGGGAGATCAGACTAATCTATGCATCTTTTTCGAGTATTCAGATAAATTTGAAGACGTATC
TACTCCACTACTCA
Found at i:28801 original size:37 final size:36
Alignment explanation
Indices: 28570--29012 Score: 609
Period size: 36 Copynumber: 12.2 Consensus size: 36
28560 GGCTTGGATC
* * **
28570 GCTTTGCTTCATTACTCTTCTGTGAAGGCTAGGATT
1 GCTTTGCTTCACTACTCTTCCGTGAAGGCTAAAATT
* * * *
28606 TCTTTGCTTCACTACTTTTCTGTGAAGGCTAAGA-T
1 GCTTTGCTTCACTACTCTTCCGTGAAGGCTAAAATT
* * *
28641 GACTTTGCTTCACTACTCTTTCGTAAAGGCTAAGATT
1 G-CTTTGCTTCACTACTCTTCCGTGAAGGCTAAAATT
*
28678 GCTTTGCTTCACTACTCTTCCGTGAAGGCTAAGATT
1 GCTTTGCTTCACTACTCTTCCGTGAAGGCTAAAATT
** * *
28714 TATTTACTTCACTACTCTTCCGTGAAGGCTAAGATT
1 GCTTTGCTTCACTACTCTTCCGTGAAGGCTAAAATT
* *
28750 GCTTTGCTTTACTACTCTTCCGTGAAGACTAAAAATT
1 GCTTTGCTTCACTACTCTTCCGTGAAGGCT-AAAATT
*
28787 GCTTTGCTTCACTACTCTTCCGTGAAGACTAAAAATT
1 GCTTTGCTTCACTACTCTTCCGTGAAGGCT-AAAATT
*
28824 GCTTTGCTTCACTACTCTTTCGTGAAGGCTAAAATT
1 GCTTTGCTTCACTACTCTTCCGTGAAGGCTAAAATT
*
28860 GCTTTACTTCACTACTCTTCCGTGAAGGCTAAATATT
1 GCTTTGCTTCACTACTCTTCCGTGAAGGCTAAA-ATT
*
28897 GCTTTGCTTCACTACTCTTCTGTGAAGGCTAAAAATT
1 GCTTTGCTTCACTACTCTTCCGTGAAGGCT-AAAATT
*
28934 GCTTTGCTTCACTACTCTTCCATGAAGGCTAAAAATT
1 GCTTTGCTTCACTACTCTTCCGTGAAGGCT-AAAATT
*
28971 GCTTTGCTTCACTACTCTTCCATGAAGGCTAAAATT
1 GCTTTGCTTCACTACTCTTCCGTGAAGGCTAAAATT
29007 GCTTTG
1 GCTTTG
29013 AGAAGAATCT
Statistics
Matches: 373, Mismatches: 29, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
35 1 0.00
36 199 0.53
37 170 0.46
38 3 0.01
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (36 bp):
GCTTTGCTTCACTACTCTTCCGTGAAGGCTAAAATT
Found at i:28861 original size:110 final size:108
Alignment explanation
Indices: 28570--29012 Score: 609
Period size: 110 Copynumber: 4.1 Consensus size: 108
28560 GGCTTGGATC
* * ** * * *
28570 GCTTTGCTTCATTACTCTTCTGTGAAGGCTAGGATTTCTTTGCTTCACTACTTTTCTGTGAAGGC
1 GCTTTGCTTCACTACTCTTCCGTGAAGGCTAAAATTGCTTTGCTTCACTACTCTTCCGTGAAGGC
* * * *
28635 TAAGA-TGACTTTGCTTCACTACTCTTTCGTAAAGGCTAAGATT
66 TAAAATTG-CTTTGCTTCACTACTCTTCCGTGAAGGCTAAAATT
* ** *
28678 GCTTTGCTTCACTACTCTTCCGTGAAGGCTAAGATTTATTTACTTCACTACTCTTCCGTGAAGGC
1 GCTTTGCTTCACTACTCTTCCGTGAAGGCTAAAATTGCTTTGCTTCACTACTCTTCCGTGAAGGC
* * *
28743 TAAGATTGCTTTGCTTTACTACTCTTCCGTGAAGACTAAAAATT
66 TAAAATTGCTTTGCTTCACTACTCTTCCGTGAAGGCT-AAAATT
* *
28787 GCTTTGCTTCACTACTCTTCCGTGAAGACTAAAAATTGCTTTGCTTCACTACTCTTTCGTGAAGG
1 GCTTTGCTTCACTACTCTTCCGTGAAGGCT-AAAATTGCTTTGCTTCACTACTCTTCCGTGAAGG
*
28852 CTAAAATTGCTTTACTTCACTACTCTTCCGTGAAGGCTAAATATT
65 CTAAAATTGCTTTGCTTCACTACTCTTCCGTGAAGGCTAAA-ATT
* *
28897 GCTTTGCTTCACTACTCTTCTGTGAAGGCTAAAAATTGCTTTGCTTCACTACTCTTCCATGAAGG
1 GCTTTGCTTCACTACTCTTCCGTGAAGGCT-AAAATTGCTTTGCTTCACTACTCTTCCGTGAAGG
*
28962 CTAAAAATTGCTTTGCTTCACTACTCTTCCATGAAGGCTAAAATT
65 CT-AAAATTGCTTTGCTTCACTACTCTTCCGTGAAGGCTAAAATT
29007 GCTTTG
1 GCTTTG
29013 AGAAGAATCT
Statistics
Matches: 302, Mismatches: 28, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
108 88 0.29
109 39 0.13
110 138 0.46
111 37 0.12
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (108 bp):
GCTTTGCTTCACTACTCTTCCGTGAAGGCTAAAATTGCTTTGCTTCACTACTCTTCCGTGAAGGC
TAAAATTGCTTTGCTTCACTACTCTTCCGTGAAGGCTAAAATT
Found at i:29224 original size:62 final size:63
Alignment explanation
Indices: 29145--29300 Score: 244
Period size: 62 Copynumber: 2.5 Consensus size: 63
29135 ATCCACAATA
* *
29145 TTGACTTATCTTCATGAGGAAGTCAAGGATTGACTC-TACTGGGGAGTTAGG-AATAACACAAG
1 TTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCAT-CTGGGGAGTTAGGAAATAACAAAAG
* *
29207 TTGATTTCTCTTCATGAGGAAGTCAAGGATTGGCTCATCTGGGGAGTTAGGAAATAACAAAAG
1 TTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCATCTGGGGAGTTAGGAAATAACAAAAG
*
29270 TTGACTTCTCTTCACGAGGAAGTCAAGGATT
1 TTGACTTCTCTTCATGAGGAAGTCAAGGATT
29301 AACTGTGAGG
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
62 46 0.53
63 40 0.47
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.29
Consensus pattern (63 bp):
TTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCATCTGGGGAGTTAGGAAATAACAAAAG
Found at i:29887 original size:50 final size:50
Alignment explanation
Indices: 29828--29927 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
29818 CACATTCATC
*
29828 CTCTCCTATGGCTTCTGCCTAGATTTCTCAACTAGTGAAGCTCTTTGCAT
1 CTCTCCTATGGCTTCTGCCTAGATTTCTCAACTAGAGAAGCTCTTTGCAT
29878 CTCTCCTATGGCTTCTGCCTAGATTTCTCAACTAGAGAAGCTCTTTGCAT
1 CTCTCCTATGGCTTCTGCCTAGATTTCTCAACTAGAGAAGCTCTTTGCAT
29928 GGTGTTATAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.37
Consensus pattern (50 bp):
CTCTCCTATGGCTTCTGCCTAGATTTCTCAACTAGAGAAGCTCTTTGCAT
Found at i:32871 original size:18 final size:18
Alignment explanation
Indices: 32829--32895 Score: 98
Period size: 18 Copynumber: 3.6 Consensus size: 18
32819 CATTGAACAA
*
32829 TATCGATACTTATGTAAGTAG
1 TATCGATACTGATGT--G-AG
32850 TATCGATACTGATGTGAG
1 TATCGATACTGATGTGAG
32868 TATCGATACTGATGTGAG
1 TATCGATACTGATGTGAG
32886 TATCGATACT
1 TATCGATACT
32896 AAGAGAAAGG
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
18 30 0.67
19 1 0.02
21 14 0.31
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (18 bp):
TATCGATACTGATGTGAG
Found at i:33535 original size:45 final size:45
Alignment explanation
Indices: 33465--33835 Score: 501
Period size: 45 Copynumber: 8.2 Consensus size: 45
33455 TGCAAGTTAG
* ** * * *
33465 ATAAATGAAAATGTATAACAATGCATAATAGGCATGAAAGGATGCC
1 ATAAATG-AAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* * *
33511 ATAAATGAAATCCATAACGGTGCATTATCGACATGAAATGATTCC
1 ATAAATGAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
*
33556 ATAAATGAAATGTATAACGGTGCATTATC-AGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGA-CATGAAAGGATGCC
* *
33601 ATAAATGAAATGCATAATGGTGCATTATCGACATTAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* *
33646 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATTCC
1 ATAAATGAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* * *
33691 ATAAATGAAATGCATAATGGTGCATTATCGACATGAAATGATACC
1 ATAAATGAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* * * * *
33736 ATAAATAAAATACATAACGATGCATTATCGGCATGAAATGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
**
33781 ATAAATGAAATGCATAACGGTGCATTATCGACATGAAAGGATGAA
1 ATAAATGAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
33826 ATAAATGAAA
1 ATAAATGAAA
33836 ATAAAGTTTA
Statistics
Matches: 286, Mismatches: 37, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
44 1 0.00
45 277 0.97
46 8 0.03
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (45 bp):
ATAAATGAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
Found at i:39156 original size:45 final size:45
Alignment explanation
Indices: 39099--39704 Score: 748
Period size: 45 Copynumber: 13.4 Consensus size: 45
39089 TGCAAGTTGG
* ** * * * *
39099 ATAAATGAAAATGTATAACAATGCATAATAGGCATGAAAAGTTGCC
1 ATAAATG-AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
39145 ATAAATGAAATGCATAATGGTGCATTATCGACATGAAAGGTTTCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
39190 ATAAATTAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
39235 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATTCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
39280 GTAAA-GAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATG-AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
** * * * *
39325 GCAAATGAAATGCATAACAGTGCATTATCAGAATGAAATGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
39370 ATAAATGAAATGCATAACGATGAATTATCGGCAAGAAAGG-TTCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
39414 ATAAATGAAATGCATAACGGTACATTGTCGGCATGAAAGGATGCT
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
**
39459 ATAAATGAAATGTGTAACGGTGCATTATCGGCATGAAAGGAGTGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGA-TGCC
* * *
39505 ATAAATGAAATGCATAACAGTGCATTATCGACATGAAAGGATTCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
39550 ATAAATGAAATGCATAATGGTGCATTATCGACATGAAATGATACC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
39595 ATAAATAAAATACATAACGATGCATTATCGGCATGAAATGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
** * **
39640 ATAAATGAAATGCATAAATGTGCATTATCGACATGAAAGGATGAA
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
39685 ATAAATGAAAATACATAACG
1 ATAAATG-AAATGCATAACG
39705 ATAATGCATG
Statistics
Matches: 483, Mismatches: 72, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
44 39 0.08
45 387 0.80
46 57 0.12
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.24
Consensus pattern (45 bp):
ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:44028 original size:13 final size:13
Alignment explanation
Indices: 43992--44032 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
43982 ATTTATGAAG
*
43992 ATATTGATAATTC
1 ATATTGATAATTT
44005 ATATT-AT-ATTT
1 ATATTGATAATTT
*
44016 ATTTTGATAATTT
1 ATATTGATAATTT
44029 ATAT
1 ATAT
44033 ATTTATTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 7 0.30
12 4 0.17
13 12 0.52
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (13 bp):
ATATTGATAATTT
Found at i:44035 original size:21 final size:23
Alignment explanation
Indices: 43995--44040 Score: 69
Period size: 21 Copynumber: 2.0 Consensus size: 23
43985 TATGAAGATA
43995 TTGATAATTCATATTATATTTATT
1 TTGATAATT-ATATTATATTTATT
44019 TTGATAATT-TA-TATATTTATT
1 TTGATAATTATATTATATTTATT
44040 T
1 T
44041 CATATATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.50
22 2 0.09
24 9 0.41
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (23 bp):
TTGATAATTATATTATATTTATT
Found at i:44677 original size:14 final size:14
Alignment explanation
Indices: 44658--44687 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
44648 TTTAAATTTT
*
44658 TTAAAATTACATTA
1 TTAAAAATACATTA
44672 TTAAAAATACATTA
1 TTAAAAATACATTA
44686 TT
1 TT
44688 GATGAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:45041 original size:11 final size:10
Alignment explanation
Indices: 45015--45046 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
45005 CTGGTTCACT
45015 GGTTCAACCG
1 GGTTCAACCG
45025 GGTTCAACCG
1 GGTTCAACCG
45035 CGGTTCAACCG
1 -GGTTCAACCG
45046 G
1 G
45047 ATTTTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.19, C:0.31, G:0.31, T:0.19
Consensus pattern (10 bp):
GGTTCAACCG
Found at i:45849 original size:30 final size:30
Alignment explanation
Indices: 45813--45937 Score: 205
Period size: 30 Copynumber: 4.2 Consensus size: 30
45803 AGAGAACCGG
45813 CGGTTCACACTGGTTTTGCCGGTTTTCAGC
1 CGGTTCACACTGGTTTTGCCGGTTTTCAGC
* *
45843 CGGTTCACACTGGTTTTTCCGGTTTTCAGT
1 CGGTTCACACTGGTTTTGCCGGTTTTCAGC
**
45873 CGGTTCACACTGGTTTTTTCGGTTTTCAGC
1 CGGTTCACACTGGTTTTGCCGGTTTTCAGC
*
45903 CGGTTCACCCTGGTTTTGCCGGTTTTCAGC
1 CGGTTCACACTGGTTTTGCCGGTTTTCAGC
45933 CGGTT
1 CGGTT
45938 TTACCTGTTC
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 88 1.00
ACGTcount: A:0.09, C:0.26, G:0.26, T:0.40
Consensus pattern (30 bp):
CGGTTCACACTGGTTTTGCCGGTTTTCAGC
Found at i:45936 original size:11 final size:11
Alignment explanation
Indices: 45892--45939 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 11
45882 CTGGTTTTTT
45892 CGGTTTTCAGC
1 CGGTTTTCAGC
*
45903 CGG--TTCACC
1 CGGTTTTCAGC
45912 CTGGTTTT--GC
1 C-GGTTTTCAGC
45922 CGGTTTTCAGC
1 CGGTTTTCAGC
45933 CGGTTTT
1 CGGTTTT
45940 ACCTGTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
9 12 0.40
10 4 0.13
11 12 0.40
12 2 0.07
ACGTcount: A:0.06, C:0.27, G:0.27, T:0.40
Consensus pattern (11 bp):
CGGTTTTCAGC
Found at i:46827 original size:23 final size:23
Alignment explanation
Indices: 46794--46861 Score: 100
Period size: 23 Copynumber: 2.9 Consensus size: 23
46784 ACTTTGTGGG
* *
46794 CGAGTTCGAGCTTGAATCGAGTT
1 CGAGTTTGAGCTTCAATCGAGTT
46817 CGAGTTTGAGCTTCAATCGAGTT
1 CGAGTTTGAGCTTCAATCGAGTT
*
46840 CGAGTTTCGAGCTTCAGTCGAG
1 CGAGTTT-GAGCTTCAATCGAG
46862 CTCTTGAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 28 0.68
24 13 0.32
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (23 bp):
CGAGTTTGAGCTTCAATCGAGTT
Found at i:50346 original size:2 final size:2
Alignment explanation
Indices: 50339--50374 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
50329 TTAAAGGTTG
50339 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
50375 TGATCACCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52313 original size:85 final size:85
Alignment explanation
Indices: 52209--52392 Score: 262
Period size: 85 Copynumber: 2.2 Consensus size: 85
52199 AAATTAAAAA
* * *
52209 CGTTGGAACTCGTCACGTCGAGGTGACAAGTTCCTTTGGTTTCAATTATATAGT-CGTTTAGATT
1 CGTTGGAACTCGTCACGTCGAGCTGACAAGTTACTTTGGTTTCAAATATATA-TACGTTTAGATT
*
52273 TGAAAAATAGTTGTTGGTAGC
65 TGAAAAATAGTTGTTGCTAGC
*** *
52294 CGTTGGAACTCGTCACGTCGAGCTGGTGAGTTATTTTGGTTTCAAATATATATACGTTTAGATTT
1 CGTTGGAACTCGTCACGTCGAGCTGACAAGTTACTTTGGTTTCAAATATATATACGTTTAGATTT
52359 GAAAAATAGTTGTTGCTAGC
66 GAAAAATAGTTGTTGCTAGC
* *
52379 CATTAGAACTCGTC
1 CGTTGGAACTCGTC
52393 GTGTGGGCTT
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
84 1 0.01
85 87 0.99
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (85 bp):
CGTTGGAACTCGTCACGTCGAGCTGACAAGTTACTTTGGTTTCAAATATATATACGTTTAGATTT
GAAAAATAGTTGTTGCTAGC
Done.