Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006545.1 Hibiscus syriacus cultivar Beakdansim tig00015976_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: 106273
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:732 original size:2 final size:2
Alignment explanation
Indices: 725--787 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
715 ATACCATACA
725 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
*
767 AT AT AT AT CT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
788 CAATAAAGCT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2214 original size:65 final size:63
Alignment explanation
Indices: 2131--2317 Score: 195
Period size: 62 Copynumber: 3.0 Consensus size: 63
2121 TATCAGTCTA
*
2131 CTTTGAGA-TAGTTTCTCTTGAAACAAATATTATTTTCCTTGAGACTGTTTCTTAT-AAA-AGAA
1 CTTTGAGATTA-TTTCTCTTGAAAC--A-ATTATTTTCCTTGAGACTGTTTCTCATGAAACA-AA
2193 CAT
61 CAT
*
2196 CTTTGAGATTATTTCTCTTGAAACACTTATTTTCCTTGAGACTGTTTCTCATGAAACAAACAT
1 CTTTGAGATTATTTCTCTTGAAACAATTATTTTCCTTGAGACTGTTTCTCATGAAACAAACAT
** * ** * * *
2259 C-TTGAGATCGTTTCCCTTGAAACGAATTA-AATCTTTGAGTCTGTTTCTCTTGAAACAAA
1 CTTTGAGATTATTTCTCTTGAAAC-AATTATTTTCCTTGAGACTGTTTCTCATGAAACAAA
2318 ACAAACATCT
Statistics
Matches: 107, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
62 69 0.64
63 14 0.13
64 1 0.01
65 21 0.20
66 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (63 bp):
CTTTGAGATTATTTCTCTTGAAACAATTATTTTCCTTGAGACTGTTTCTCATGAAACAAACAT
Found at i:2272 original size:29 final size:30
Alignment explanation
Indices: 2230--2318 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 30
2220 ACTTATTTTC
* *
2230 CTTGAGA-CTGTTTCTCATGAAACAAACAT
1 CTTGAGATCTGTTTCTCTTGAAACAAAAAT
*
2259 CTTGAGATC-GTTTCCCTTGAAACGAATTAAAT
1 CTTGAGATCTGTTTCTCTTGAAAC-AA--AAAT
2291 CTTTGAG-TCTGTTTCTCTTGAAACAAAA
1 C-TTGAGATCTGTTTCTCTTGAAACAAAA
2319 CAAACATCTT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
29 19 0.38
30 5 0.10
32 8 0.16
33 18 0.36
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (30 bp):
CTTGAGATCTGTTTCTCTTGAAACAAAAAT
Found at i:2305 original size:33 final size:33
Alignment explanation
Indices: 2260--2365 Score: 142
Period size: 33 Copynumber: 3.2 Consensus size: 33
2250 AACAAACATC
2260 TTGAGATCGTTTCCCTTGAAACGAATTAAATCT
1 TTGAGATCGTTTCCCTTGAAACGAATTAAATCT
* * **
2293 TTGAG-TCTGTTTCTCTTGAAACAAAACAAACATCT
1 TTGAGATC-GTTTCCCTTGAAAC-GAATTAA-ATCT
2328 TTGAGATCGTTTCCCTTGAAACGAATTAAATCT
1 TTGAGATCGTTTCCCTTGAAACGAATTAAATCT
2361 TTGAG
1 TTGAG
2366 TATTTCTCTT
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
32 2 0.03
33 27 0.44
34 8 0.13
35 22 0.36
36 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (33 bp):
TTGAGATCGTTTCCCTTGAAACGAATTAAATCT
Found at i:2357 original size:68 final size:66
Alignment explanation
Indices: 2249--2415 Score: 247
Period size: 68 Copynumber: 2.6 Consensus size: 66
2239 GTTTCTCATG
*
2249 AAACAAACATC-TTGAGATCGTTTCCCTTGAAACGAATTAAATCTTTGAGTCTGTTTCTCTTGAA
1 AAACAAACATCTTTGAGATCGTTTCCCTTGAAACGAATTAAATCTTTGAG--TATTTCTCTTGAA
2313 ACA
64 ACA
2316 AAACAAACATCTTTGAGATCGTTTCCCTTGAAACGAATTAAATCTTTGAGTATTTCTCTTGAAAC
1 AAACAAACATCTTTGAGATCGTTTCCCTTGAAACGAATTAAATCTTTGAGTATTTCTCTTGAAAC
2381 A
66 A
* *
2382 AAAC---CATCTTTGAG-TC-ATTCCCTTGAAACAAATT
1 AAACAAACATCTTTGAGATCGTTTCCCTTGAAACGAATT
2416 TTGTCTCTTT
Statistics
Matches: 96, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
61 16 0.17
62 2 0.02
63 10 0.10
66 19 0.20
67 11 0.11
68 38 0.40
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (66 bp):
AAACAAACATCTTTGAGATCGTTTCCCTTGAAACGAATTAAATCTTTGAGTATTTCTCTTGAAAC
A
Found at i:2393 original size:30 final size:31
Alignment explanation
Indices: 2247--2413 Score: 118
Period size: 33 Copynumber: 5.3 Consensus size: 31
2237 CTGTTTCTCA
*
2247 TGAAAC-AAA-CATC-TTGAGATCGTTTCCCT
1 TGAAACAAAACCATCTTTGAG-TCATTTCCCT
* *
2276 TGAAACGAATTAA--ATCTTTGAGTCTGTTTCTCT
1 TGAAAC-AA--AACCATCTTTGAGTC-ATTTCCCT
*
2309 TGAAACAAAACAAACATCTTTGAGATCGTTTCCCT
1 TGAAACAAAAC---CATCTTTGAG-TCATTTCCCT
*
2344 TGAAACGAATTAA--ATCTTTGAGT-ATTTCTCT
1 TGAAAC-AA--AACCATCTTTGAGTCATTTCCCT
2375 TGAAACAAAACCATCTTTGAGTCA-TTCCCT
1 TGAAACAAAACCATCTTTGAGTCATTTCCCT
2405 TGAAACAAA
1 TGAAACAAA
2414 TTTTGTCTCT
Statistics
Matches: 115, Mismatches: 5, Indels: 35
0.74 0.03 0.23
Matches are distributed among these distances:
28 2 0.02
29 6 0.05
30 28 0.24
31 14 0.12
32 8 0.07
33 29 0.25
35 22 0.19
36 4 0.03
38 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.34
Consensus pattern (31 bp):
TGAAACAAAACCATCTTTGAGTCATTTCCCT
Found at i:2690 original size:20 final size:20
Alignment explanation
Indices: 2665--2732 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
2655 TCCCCCGACC
2665 AGCCGTCCTCATCACGTAGG
1 AGCCGTCCTCATCACGTAGG
* * **
2685 AGCCGT-GTCATCCCAGATAACA
1 AGCCGTCCTCATCAC-G-T-AGG
2707 AGCCGTCCTCATCACGTAGG
1 AGCCGTCCTCATCACGTAGG
*
2727 AACCGT
1 AGCCGT
2733 GTTATCACCT
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
19 6 0.17
20 13 0.37
21 2 0.06
22 8 0.23
23 6 0.17
ACGTcount: A:0.25, C:0.34, G:0.22, T:0.19
Consensus pattern (20 bp):
AGCCGTCCTCATCACGTAGG
Found at i:2811 original size:128 final size:127
Alignment explanation
Indices: 2483--2823 Score: 361
Period size: 130 Copynumber: 2.6 Consensus size: 127
2473 AACCATTATC
* * ** *
2483 CCTAAAGATGGTCAGTCATCCTCATCACGTAGAAACTGTGTCATCCTTGATCAGACCTCCTCATC
1 CCTAAAGATGGCCAG-CATCCTCATCACGTAGAAACCGTGTCATCCCCGACCAGACCTCCTCATC
* * *
2548 ACGTAGGAGCCGTGTCACTACTAGAACCAGCCGTCCTCATCGCGTAGAAACCGTGTTATCACATT
65 ACGTAGGAGCCGTGTCACTACCAGAACAAGCCGTCCTCATCACGTAGAAACCGTGTTAT-ACA-T
* * *
2613 CCTAAAGATGGCCAGAACTCTTCATCACGTATG--AGCGTGTCATCCCCCGACCAG-CCGTCCTC
1 CCTAAAGATGGCCAGCA-TCCTCATCACGTA-GAAACCGTGTCAT-CCCCGACCAGACC-TCCTC
* *
2675 ATCACGTAGGAGCCGTGTCA-TCCCAGATAACAAGCCGTCCTCATCACGTAGGAACCGTGTTAT-
62 ATCACGTAGGAGCCGTGTCACTACCAG--AACAAGCCGTCCTCATCACGTAGAAACCGTGTTATA
2738 CA-
125 CAT
* ** * ** *
2740 CCTATAGATTTCCTGCCATCCTCATCGTGTAGAAACCGTGTCATCACCCGACCAGATCTCCTCAT
1 CCTAAAGATGGCCAG-CATCCTCATCACGTAGAAACCGTGTCATC-CCCGACCAGACCTCCTCAT
2805 CACGTAGGAGCCGTGTCAC
64 CACGTAGGAGCCGTGTCAC
2824 CCCTTTAATA
Statistics
Matches: 176, Mismatches: 23, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
126 1 0.01
127 22 0.12
128 44 0.25
129 18 0.10
130 58 0.33
131 33 0.19
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (127 bp):
CCTAAAGATGGCCAGCATCCTCATCACGTAGAAACCGTGTCATCCCCGACCAGACCTCCTCATCA
CGTAGGAGCCGTGTCACTACCAGAACAAGCCGTCCTCATCACGTAGAAACCGTGTTATACAT
Found at i:5290 original size:24 final size:24
Alignment explanation
Indices: 5262--5319 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
5252 TGTTAAAATG
* *
5262 ATAAACGAACACAAGCGAATGTAC
1 ATAAACGAACACAAACGAATGGAC
* *
5286 GTAAATGAACACAAACGAATGGAC
1 ATAAACGAACACAAACGAATGGAC
5310 ATAAACGAAC
1 ATAAACGAAC
5320 TAACATAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.52, C:0.19, G:0.17, T:0.12
Consensus pattern (24 bp):
ATAAACGAACACAAACGAATGGAC
Found at i:7161 original size:71 final size:71
Alignment explanation
Indices: 7069--7204 Score: 191
Period size: 71 Copynumber: 1.9 Consensus size: 71
7059 AATATAACTG
* * *
7069 TGTCCAACTTCAACTGGACTTGACTGCTAGCTGATTTATTATTTGTTTCTTTTATCATGGAGCAT
1 TGTCCAACTTCAACTGCACTTGACTGCTAGCTGATTTACTATTTGTTTCGTTTATCATGGAGCAT
7134 TAAATA
66 TAAATA
* * * * * *
7140 TGTCTAACTTCAATTGCACTTGGCTTCTATCTGATTTACTATTTGTTTCGTTTATTATGGAGCAT
1 TGTCCAACTTCAACTGCACTTGACTGCTAGCTGATTTACTATTTGTTTCGTTTATCATGGAGCAT
7205 GCCGATGGAT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
71 56 1.00
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (71 bp):
TGTCCAACTTCAACTGCACTTGACTGCTAGCTGATTTACTATTTGTTTCGTTTATCATGGAGCAT
TAAATA
Found at i:8212 original size:189 final size:194
Alignment explanation
Indices: 7760--8338 Score: 579
Period size: 189 Copynumber: 3.0 Consensus size: 194
7750 TTTATAACTT
* *
7760 TTATTGTGACTAAA-AAGTTTTGTTACAATTTGTTATTGTGAAAGAATA--ATTTTTGCCACAAT
1 TTATTGTAACTAAATAA-ATTTGTTACAATTTGTTATTGTGAAAGAATATTATTTTT--CACAA-
* * *
7822 TTTTTATAATGAGAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGTCACAAT
62 TTTTT-T-ATGAGAAATTAAAATTTGTCATAAATTATTATTTTGATTAAATAAATTTGTCACAA-
* *
7887 TTTTTATTTTGACAAAATATTAGGACGAAATAAATTTGACATAACTTTTTACTTTGACTAAATTT
124 TTCTTATTTTGACAAAATATTAGGACGAAATAAATTTGACATAACATTTTACTTTGACTAAATTT
*
7952 AACGTG
189 AACATG
* * * * * * *
7958 TTATTGTGACTAAATCATTTTGTTGCAATTTATTATTGTGAAAGAATATTACTTGTCACAATTTT
1 TTATTGTAACTAAATAAATTTGTTACAATTTGTTATTGTGAAAGAATATTATTTTTCACAATTTT
* *
8023 TTATGAGAAATTAAAATTTGTCATAAATTATTATTTTGATTAAATAAATTT-TTAGAA-TCTT-T
66 TTATGAGAAATTAAAATTTGTCATAAATTATTATTTTGATTAAATAAATTTGTCACAATTCTTAT
* *
8085 TTTGACAAAATATT-GTGAC-AAATAAATTTGGCATAA-ATTTTATTTTGACTAAATTT-ACTAT
131 TTTGACAAAATATTAG-GACGAAATAAATTTGACATAACATTTTACTTTGACTAAATTTAAC-AT
8146 G
194 G
* * *
8147 TTGTTGTAACTAAATAAATTTGTTACAATTTGTTATTGTAAAAGAATATTATTTTTCATAATTTT
1 TTATTGTAACTAAATAAATTTGTTACAATTTGTTATTGTGAAAGAATATTATTTTTCACAA-TTT
* * * * * * * * * ** * *
8212 TTATATTGAGGAATTAATATTTATTATAATTTGTTATTATAACTATTTAAATTTGTCATAATTTA
65 TT-TA-TGAGAAATTAAAATTTGTCATAAATTATTATTTTGATTAAATAAATTTGTCACAA-TTC
* ** * ** *
8277 TTATTTTGAGAAAATATTTTGACTAAATAAA-TTGACATAATTTTTTA-TTTAACTAAATTTAA
127 TTATTTTGACAAAATATTAGGACGAAATAAATTTGACATAACATTTTACTTTGACTAAATTTAA
8339 TTTTTTATTT
Statistics
Matches: 321, Mismatches: 44, Indels: 33
0.81 0.11 0.08
Matches are distributed among these distances:
188 2 0.01
189 71 0.22
190 22 0.07
191 20 0.06
192 40 0.12
193 4 0.01
194 4 0.01
195 49 0.15
196 38 0.12
197 18 0.06
198 48 0.15
199 1 0.00
200 4 0.01
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (194 bp):
TTATTGTAACTAAATAAATTTGTTACAATTTGTTATTGTGAAAGAATATTATTTTTCACAATTTT
TTATGAGAAATTAAAATTTGTCATAAATTATTATTTTGATTAAATAAATTTGTCACAATTCTTAT
TTTGACAAAATATTAGGACGAAATAAATTTGACATAACATTTTACTTTGACTAAATTTAACATG
Found at i:8429 original size:21 final size:21
Alignment explanation
Indices: 8400--8440 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
8390 ATTTTATTTA
* *
8400 AATTTGTTATTATAACTAAAT
1 AATTGGTTATGATAACTAAAT
8421 AATTGGTTATGATAACTAAA
1 AATTGGTTATGATAACTAAA
8441 AATATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (21 bp):
AATTGGTTATGATAACTAAAT
Found at i:9631 original size:13 final size:13
Alignment explanation
Indices: 9613--9672 Score: 57
Period size: 13 Copynumber: 4.2 Consensus size: 13
9603 ACCGGTCATA
*
9613 ACCCGACCCGTTT
1 ACCCGACCCGTTG
*
9626 ACCCGACCAGTTG
1 ACCCGACCCGTTG
9639 ACCCGACCCGACCCGTTG
1 A-----CCCGACCCGTTG
9657 ACCCGACCCGTTG
1 ACCCGACCCGTTG
9670 ACC
1 ACC
9673 GTTGACCAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 27 0.69
18 12 0.31
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.15
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:9648 original size:31 final size:31
Alignment explanation
Indices: 9613--9672 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
9603 ACCGGTCATA
*
9613 ACCCGACCCGTTTACCCGACCAGTTGACCCG
1 ACCCGACCCGTTGACCCGACCAGTTGACCCG
*
9644 ACCCGACCCGTTGACCCGACCCGTTGACC
1 ACCCGACCCGTTGACCCGACCAGTTGACC
9673 GTTGACCAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.15
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCAGTTGACCCG
Found at i:9649 original size:18 final size:18
Alignment explanation
Indices: 9626--9666 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
9616 CGACCCGTTT
9626 ACCCGACCAGTTGACCCG
1 ACCCGACCAGTTGACCCG
*
9644 ACCCGACCCGTTGACCCG
1 ACCCGACCAGTTGACCCG
9662 ACCCG
1 ACCCG
9667 TTGACCGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.10
Consensus pattern (18 bp):
ACCCGACCAGTTGACCCG
Found at i:12173 original size:17 final size:17
Alignment explanation
Indices: 12153--12193 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
12143 CTGTTCTGAT
*
12153 TTCTGATCTGGATTCTG
1 TTCTGATCTGAATTCTG
12170 TTCTGATCTGAATTCTG
1 TTCTGATCTGAATTCTG
*
12187 TTTTGAT
1 TTCTGAT
12194 TTCTGATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.51
Consensus pattern (17 bp):
TTCTGATCTGAATTCTG
Found at i:12186 original size:12 final size:12
Alignment explanation
Indices: 12136--12175 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
12126 GATACATTAC
12136 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
12148 CTGATTTCTGAT
1 CTGAATTCTGTT
*
12160 CTGGATTCTGTT
1 CTGAATTCTGTT
12172 CTGA
1 CTGA
12176 TCTGAATTCT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.47
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:12186 original size:24 final size:23
Alignment explanation
Indices: 12116--12180 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
12106 TCCGACTTGA
* * * *
12116 ATTCTGTTCTGATACATTACCTGA
1 ATTCTGTTCTGATTC-TGATCTGG
12140 ATTCTGTTCTGATTTCTGATCTGG
1 ATTCTGTTCTGA-TTCTGATCTGG
12164 ATTCTGTTCTGA-TCTGA
1 ATTCTGTTCTGATTCTGA
12181 ATTCTGTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.14
24 29 0.81
25 2 0.06
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.46
Consensus pattern (23 bp):
ATTCTGTTCTGATTCTGATCTGG
Found at i:13580 original size:3 final size:3
Alignment explanation
Indices: 13572--13613 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
13562 TTTCTTAAGA
13572 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13614 TAAAGCATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:14002 original size:75 final size:75
Alignment explanation
Indices: 13878--14026 Score: 201
Period size: 75 Copynumber: 2.0 Consensus size: 75
13868 ATTTATGGTA
* * *
13878 TCAAAACAAAATGATAAAATGGTACATATACTATTTACGGTAACAATACTACTTAGTATAGTAGT
1 TCAAAACAAAATGATAAAATGATACATATACTATATACGATAACAATACTACTTAGTATAGTAGT
13943 ACCAATACTG
66 ACCAATACTG
* * * * *
13953 TCAAAACAAAATGCTAAAATGATACCA-ATATTATATACGATATCGATACTACTTAGTGTAGTAG
1 TCAAAACAAAATGATAAAATGATA-CATATACTATATACGATAACAATACTACTTAGTATAGTAG
*
14017 TACCTATACT
65 TACCAATACT
14027 CTTAGTGGTG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
75 62 0.97
76 2 0.03
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.30
Consensus pattern (75 bp):
TCAAAACAAAATGATAAAATGATACATATACTATATACGATAACAATACTACTTAGTATAGTAGT
ACCAATACTG
Found at i:14040 original size:21 final size:23
Alignment explanation
Indices: 13996--14047 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
13986 TATACGATAT
13996 CGATACTACTTAGTGTAGTAGTAC
1 CGATACTACTTAGTG-AGTAGTAC
* *
14020 CTATACT-CTTAGTG-GTGGTAC
1 CGATACTACTTAGTGAGTAGTAC
14041 CGATACT
1 CGATACT
14048 GCCTTTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 12 0.48
23 7 0.28
24 6 0.24
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (23 bp):
CGATACTACTTAGTGAGTAGTAC
Found at i:15163 original size:31 final size:31
Alignment explanation
Indices: 15125--15248 Score: 239
Period size: 31 Copynumber: 4.0 Consensus size: 31
15115 ATAATTCGGC
15125 AGAGCTATTGATTATTGTACCTTAAAACTCA
1 AGAGCTATTGATTATTGTACCTTAAAACTCA
15156 AGAGCTATTGATTATTGTACCTTAAAACTCA
1 AGAGCTATTGATTATTGTACCTTAAAACTCA
15187 AGAGCTATTGATTATTGTACCTTAAAACTCA
1 AGAGCTATTGATTATTGTACCTTAAAACTCA
*
15218 AGAGCTATTGACTATTGTACCTTAAAACTCA
1 AGAGCTATTGATTATTGTACCTTAAAACTCA
15249 TACTGTGTAT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 92 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (31 bp):
AGAGCTATTGATTATTGTACCTTAAAACTCA
Found at i:21789 original size:30 final size:30
Alignment explanation
Indices: 21730--21815 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 30
21720 TCGATATTTC
* **
21730 ATCTAAAATTTAAGGGTAAAAATCTTATTCT
1 ATCTAAAATTT-AGGGTAAAATTAATATTCT
*
21761 ATCTAAAATTTAGGGTTAAATTAATATTCT
1 ATCTAAAATTTAGGGTAAAATTAATATTCT
*
21791 ATCTAAATTTTAGGAGTAAAATTAA
1 ATCTAAAATTTAGG-GTAAAATTAA
21816 AAATTAACTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
30 28 0.58
31 20 0.42
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (30 bp):
ATCTAAAATTTAGGGTAAAATTAATATTCT
Found at i:22255 original size:20 final size:21
Alignment explanation
Indices: 22232--22280 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
22222 GTTTCCAAAT
* *
22232 TCGCAACGCGAATTT-GTAAA
1 TCGCAACACGAATTTAGAAAA
22252 TCGCAACACGAATTTAGAAAA
1 TCGCAACACGAATTTAGAAAA
22273 TCGCAACA
1 TCGCAACA
22281 AAGAAGTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.20
Consensus pattern (21 bp):
TCGCAACACGAATTTAGAAAA
Found at i:22350 original size:20 final size:20
Alignment explanation
Indices: 22287--22385 Score: 128
Period size: 20 Copynumber: 5.0 Consensus size: 20
22277 AACAAAGAAG
* *
22287 TCAAATTCGCAACATTGAATT
1 TCAAATTTGCAAC-TCGAATT
22308 TCAAATTTGCAACT-GAATT
1 TCAAATTTGCAACTCGAATT
*
22327 TCAAATTTGCAACTCGATTT
1 TCAAATTTGCAACTCGAATT
*
22347 TCAAATTTGCAACTCGATTT
1 TCAAATTTGCAACTCGAATT
* *
22367 TCAAATTCGCAACACGAAT
1 TCAAATTTGCAACTCGAAT
22386 ATAATTTCGC
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
19 19 0.26
20 41 0.57
21 12 0.17
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.34
Consensus pattern (20 bp):
TCAAATTTGCAACTCGAATT
Found at i:23384 original size:24 final size:24
Alignment explanation
Indices: 23337--23386 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
23327 TCAAAATTTA
*
23337 ATCTTGGTCAATACCCGGACTTTG
1 ATCTTGGTCAATACCCAGACTTTG
* *
23361 ATCTTGGTCAATACTCAGATTTTG
1 ATCTTGGTCAATACCCAGACTTTG
23385 AT
1 AT
23387 GATGTTTCAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (24 bp):
ATCTTGGTCAATACCCAGACTTTG
Found at i:26085 original size:20 final size:20
Alignment explanation
Indices: 26062--26108 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
26052 ATCGCAACGT
* *
26062 GAATTTGACTTTCGCGTTGC
1 GAATTTGACTTTCACATTGC
*
26082 GAATATT-ATTTTCACATTGC
1 GAAT-TTGACTTTCACATTGC
26102 GAATTTG
1 GAATTTG
26109 TACCTTCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.09
20 18 0.82
21 2 0.09
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (20 bp):
GAATTTGACTTTCACATTGC
Found at i:26237 original size:63 final size:64
Alignment explanation
Indices: 26159--26315 Score: 262
Period size: 64 Copynumber: 2.5 Consensus size: 64
26149 TTGAATAAAC
26159 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAATAATTCTTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
* * *
26222 AACAAATCAACTTTTACAAATCAATGAAACAAGCAAAAAATAATTCTTATTTTCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
*
26286 AACAAATCAACTTTTACAAATAAATGTAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAA
26316 ATTCAATTAA
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
63 33 0.38
64 51 0.59
65 3 0.03
ACGTcount: A:0.51, C:0.17, G:0.03, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
Found at i:27708 original size:21 final size:21
Alignment explanation
Indices: 27684--27841 Score: 210
Period size: 21 Copynumber: 7.5 Consensus size: 21
27674 AATCGATCTT
* * *
27684 TTGAACGGTGGGAGGGACCTC
1 TTGAACGATGAGAGGGGCCTC
27705 TTGAACGATGAGAGGGGCCTC
1 TTGAACGATGAGAGGGGCCTC
* *
27726 TTGAACGGTGGGAGGGGCCTC
1 TTGAACGATGAGAGGGGCCTC
27747 TTGAACGATGAGAGGGGCCTC
1 TTGAACGATGAGAGGGGCCTC
* *
27768 TTGAACGGTGGGAGGGGCCTC
1 TTGAACGATGAGAGGGGCCTC
27789 TTGAACGATGAGAGGGGCCTC
1 TTGAACGATGAGAGGGGCCTC
*
27810 TTGAACGAT-AGGAGGTGCCTC
1 TTGAACGATGA-GAGGGGCCTC
* *
27831 TTAAATGATGA
1 TTGAACGATGA
27842 CAGGTGCATC
Statistics
Matches: 121, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
20 1 0.01
21 119 0.98
22 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.39, T:0.21
Consensus pattern (21 bp):
TTGAACGATGAGAGGGGCCTC
Found at i:27747 original size:42 final size:42
Alignment explanation
Indices: 27684--27841 Score: 262
Period size: 42 Copynumber: 3.8 Consensus size: 42
27674 AATCGATCTT
*
27684 TTGAACGGTGGGAGGGACCTCTTGAACGATGAGAGGGGCCTC
1 TTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGGGCCTC
27726 TTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGGGCCTC
1 TTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGGGCCTC
27768 TTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGGGCCTC
1 TTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGGGCCTC
* * * * *
27810 TTGAACGATAGGAGGTGCCTCTTAAATGATGA
1 TTGAACGGTGGGAGGGGCCTCTTGAACGATGA
27842 CAGGTGCATC
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 110 1.00
ACGTcount: A:0.22, C:0.18, G:0.39, T:0.21
Consensus pattern (42 bp):
TTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGGGCCTC
Found at i:28215 original size:63 final size:62
Alignment explanation
Indices: 28138--28277 Score: 158
Period size: 63 Copynumber: 2.2 Consensus size: 62
28128 TAGAGCGGCT
* * *
28138 ACCTCATCACGTAAAGTA-GATACCTCACCACGTAGCGCACCATTGTCATCGCGTAAAACATCC
1 ACCTCACCACGTAAAG-ACG-TACCTCACCACGTAGCCCACCATTGTCATCACGTAAAACATCC
* * *
28201 ACCTCACCATGTAAAGACCGTACCTCATCACGTAGCCCACCATTGTCTTCACGTAAAACA-CC
1 ACCTCACCACGTAAAGA-CGTACCTCACCACGTAGCCCACCATTGTCATCACGTAAAACATCC
* *
28263 GACCTTATCACGTAA
1 -ACCTCACCACGTAA
28278 CTCCCCTAAC
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
62 3 0.05
63 61 0.94
64 1 0.02
ACGTcount: A:0.31, C:0.34, G:0.13, T:0.21
Consensus pattern (62 bp):
ACCTCACCACGTAAAGACGTACCTCACCACGTAGCCCACCATTGTCATCACGTAAAACATCC
Found at i:28291 original size:63 final size:63
Alignment explanation
Indices: 28161--28292 Score: 140
Period size: 63 Copynumber: 2.1 Consensus size: 63
28151 AAGTAGATAC
* * * * * *
28161 CTCACCACGTAGCGCACCATTGTCATCGCGTAAAACATCCACCTCACCATGTAAAGACCGTAC
1 CTCATCACGTAGCCCACCATTGTCATCACGTAAAACATCCACCTCACCACGTAAAGACCCTAA
* * * ***
28224 CTCATCACGTAGCCCACCATTGTCTTCACGTAAAACA-CCGACCTTATCACGTAACTCCCCTAA
1 CTCATCACGTAGCCCACCATTGTCATCACGTAAAACATCC-ACCTCACCACGTAAAGACCCTAA
28287 CTCATC
1 CTCATC
28293 CTGTGGAGGT
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
62 2 0.04
63 54 0.96
ACGTcount: A:0.29, C:0.38, G:0.11, T:0.22
Consensus pattern (63 bp):
CTCATCACGTAGCCCACCATTGTCATCACGTAAAACATCCACCTCACCACGTAAAGACCCTAA
Found at i:29980 original size:20 final size:20
Alignment explanation
Indices: 29955--30008 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
29945 AGTAGTTTTT
*
29955 GAAAATTAAATTCGCAATGC
1 GAAAATTAAATTCGCAACGC
* *
29975 GAAAATGAAAATCGCAACGC
1 GAAAATTAAATTCGCAACGC
*
29995 G-AAACTAAATTCGC
1 GAAAATTAAATTCGC
30009 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.19
Consensus pattern (20 bp):
GAAAATTAAATTCGCAACGC
Found at i:30046 original size:20 final size:20
Alignment explanation
Indices: 30004--30046 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
29994 CGAAACTAAA
* * *
30004 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGAATTTAAGT
*
30024 TTCGTGTTGCGAATTTAAGT
1 TTCGCGTTGCGAATTTAAGT
30044 TTC
1 TTC
30047 AAAAACTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.16, G:0.21, T:0.49
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTAAGT
Found at i:30612 original size:20 final size:19
Alignment explanation
Indices: 30568--30612 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
30558 CTTCTGTGTA
*
30568 GCGATTTCAAATTTGCATT
1 GCGATTTCAAATTCGCATT
* *
30587 GAGATTTACAAATTCGCGTT
1 GCGATTT-CAAATTCGCATT
30607 GCGATT
1 GCGATT
30613 CACGTTGCGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (19 bp):
GCGATTTCAAATTCGCATT
Found at i:30641 original size:20 final size:20
Alignment explanation
Indices: 30610--30667 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
30600 TCGCGTTGCG
*
30610 ATTCACGTTGCGAATTTGGAA
1 ATTCGCGTTGCGAATTTGG-A
* *
30631 ATT-GGGTTGCGAAATTGGA
1 ATTCGCGTTGCGAATTTGGA
*
30650 GTTCGCGTTGCGAATTTG
1 ATTCGCGTTGCGAATTTG
30668 TTGGTCATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 3 0.10
20 24 0.80
21 3 0.10
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.34
Consensus pattern (20 bp):
ATTCGCGTTGCGAATTTGGA
Found at i:33192 original size:98 final size:99
Alignment explanation
Indices: 32997--33211 Score: 344
Period size: 98 Copynumber: 2.2 Consensus size: 99
32987 ATTTTTTTCA
* * *
32997 AAAC-TTAAGTATGGTTTAGGTACTAAACGTTTTTAGTACCTAGACTTTCATTTTTTTTATCAAA
1 AAACTTTAAGTATGATTTAGGTACTAAACGTATTTAGTACCTAGACTTT-ATATTTTTTATCAAA
*
33061 ACTTAATGGTGGGGTACTAAAATGAAACAAAAACT
65 ACTTAATGGTAGGGTACTAAAATGAAACAAAAACT
*
33096 AAACTTTAAGTATGATTTAGGTACTAAACGTATTTGGTACCTAGACTTT-TATTTTTTATCAAAA
1 AAACTTTAAGTATGATTTAGGTACTAAACGTATTTAGTACCTAGACTTTATATTTTTTATCAAAA
33160 CTTAATGGTAGGGTACTAAAATGAAACAAAAACT
66 CTTAATGGTAGGGTACTAAAATGAAACAAAAACT
* *
33194 AAACTTAAAGTATTATTT
1 AAACTTTAAGTATGATTT
33212 TGAAAAAAAT
Statistics
Matches: 108, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
98 63 0.58
99 4 0.04
100 41 0.38
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (99 bp):
AAACTTTAAGTATGATTTAGGTACTAAACGTATTTAGTACCTAGACTTTATATTTTTTATCAAAA
CTTAATGGTAGGGTACTAAAATGAAACAAAAACT
Found at i:35028 original size:20 final size:20
Alignment explanation
Indices: 35003--35056 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
34993 AGTAGTTTTT
*
35003 GAAAATTAAATTCGCAATGC
1 GAAAATTAAATTCGCAACGC
* *
35023 GAAAATGAAAATCGCAACGC
1 GAAAATTAAATTCGCAACGC
*
35043 G-AAACTAAATTCGC
1 GAAAATTAAATTCGC
35057 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.19
Consensus pattern (20 bp):
GAAAATTAAATTCGCAACGC
Found at i:35094 original size:20 final size:20
Alignment explanation
Indices: 35052--35094 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
35042 CGAAACTAAA
* * *
35052 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGAATTTAAGT
*
35072 TTCGTGTTGCGAATTTAAGT
1 TTCGCGTTGCGAATTTAAGT
35092 TTC
1 TTC
35095 AAAAACTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.16, G:0.21, T:0.49
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTAAGT
Found at i:35446 original size:22 final size:22
Alignment explanation
Indices: 35416--35466 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
35406 GATGGAGATA
* *
35416 GACGAATTTCGTCAGAGATGGG
1 GACGGATTTCATCAGAGATGGG
35438 GACGGATTTCATCAGAGATGGG
1 GACGGATTTCATCAGAGATGGG
35460 GACGGAT
1 GACGGAT
35467 GACGCCGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.14, G:0.37, T:0.22
Consensus pattern (22 bp):
GACGGATTTCATCAGAGATGGG
Found at i:38250 original size:98 final size:99
Alignment explanation
Indices: 38055--38269 Score: 344
Period size: 98 Copynumber: 2.2 Consensus size: 99
38045 TTTTTTTTCA
* * *
38055 AAAC-TTAAGTATGGTTTAGGTACTAAACGTTTTTAGTACCTAGACTTTCATTTTTTTTATCAAA
1 AAACTTTAAGTATGATTTAGGTACTAAACGTATTTAGTACCTAGACTTT-ATATTTTTTATCAAA
*
38119 ACTTAATGGTGGGGTACTAAAATGAAACAAAAACT
65 ACTTAATGGTAGGGTACTAAAATGAAACAAAAACT
*
38154 AAACTTTAAGTATGATTTAGGTACTAAACGTATTTGGTACCTAGACTTT-TATTTTTTATCAAAA
1 AAACTTTAAGTATGATTTAGGTACTAAACGTATTTAGTACCTAGACTTTATATTTTTTATCAAAA
38218 CTTAATGGTAGGGTACTAAAATGAAACAAAAACT
66 CTTAATGGTAGGGTACTAAAATGAAACAAAAACT
* *
38252 AAACTTAAAGTATTATTT
1 AAACTTTAAGTATGATTT
38270 TGAAAAAAAT
Statistics
Matches: 108, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
98 63 0.58
99 4 0.04
100 41 0.38
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (99 bp):
AAACTTTAAGTATGATTTAGGTACTAAACGTATTTAGTACCTAGACTTTATATTTTTTATCAAAA
CTTAATGGTAGGGTACTAAAATGAAACAAAAACT
Found at i:40087 original size:20 final size:20
Alignment explanation
Indices: 40062--40115 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
40052 AGTAGTTTTT
*
40062 GAAAATTAAATTCGCAATGC
1 GAAAATTAAATTCGCAACGC
* *
40082 GAAAATGAAAATCGCAACGC
1 GAAAATTAAATTCGCAACGC
*
40102 G-AAACTAAATTCGC
1 GAAAATTAAATTCGC
40116 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.19
Consensus pattern (20 bp):
GAAAATTAAATTCGCAACGC
Found at i:40153 original size:20 final size:20
Alignment explanation
Indices: 40111--40153 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
40101 CGAAACTAAA
* * *
40111 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGAATTTAAGT
*
40131 TTCGTGTTGCGAATTTAAGT
1 TTCGCGTTGCGAATTTAAGT
40151 TTC
1 TTC
40154 AAAAACTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.16, G:0.21, T:0.49
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTAAGT
Found at i:40505 original size:22 final size:22
Alignment explanation
Indices: 40475--40525 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
40465 GATGGAGATA
* * *
40475 GACGAATTTCGTCGGAGATGGG
1 GACGGATTTCATCAGAGATGGG
40497 GACGGATTTCATCAGAGATGGG
1 GACGGATTTCATCAGAGATGGG
40519 GACGGAT
1 GACGGAT
40526 GACGCCGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.14, G:0.39, T:0.22
Consensus pattern (22 bp):
GACGGATTTCATCAGAGATGGG
Found at i:40727 original size:20 final size:19
Alignment explanation
Indices: 40683--40727 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
40673 CTTCTGTGTA
*
40683 GCGATTTCAAATTTGCATT
1 GCGATTTCAAATTCGCATT
* *
40702 GAGATTTACAAATTCGCGTT
1 GCGATTT-CAAATTCGCATT
40722 GCGATT
1 GCGATT
40728 CACGTTGCGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (19 bp):
GCGATTTCAAATTCGCATT
Found at i:43304 original size:98 final size:99
Alignment explanation
Indices: 43110--43325 Score: 337
Period size: 98 Copynumber: 2.2 Consensus size: 99
43100 ATTTTTTTCA
* * *
43110 AAAC-TTAAGTATGGTTTAGGTACTAAACGTTTTTAGTACCTAGACTTTCATTTTTTTTTATCAA
1 AAACTTTAAGTATGATTTAGGTACTAAAAGTATTTAGTACCTAGACTTTCA--TTTTTTTATCAA
*
43174 AACTTAATGGTGGGGTACTAAAATGAAACAAAAACT
64 AACTTAATGGTAGGGTACTAAAATGAAACAAAAACT
*
43210 AAACTTTAAGTATGATTTAGGTACTAAAAGTATTTGGTACCTAGACTTTCA-TTTTTTATCAAAA
1 AAACTTTAAGTATGATTTAGGTACTAAAAGTATTTAGTACCTAGACTTTCATTTTTTTATCAAAA
43274 CTTAATGGTAGGGTACTAAAATGAAACAAAAACT
66 CTTAATGGTAGGGTACTAAAATGAAACAAAAACT
* *
43308 AAACTTAAAGTATTATTT
1 AAACTTTAAGTATGATTT
43326 TGAAAAAAAT
Statistics
Matches: 108, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
98 62 0.57
100 4 0.04
101 42 0.39
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (99 bp):
AAACTTTAAGTATGATTTAGGTACTAAAAGTATTTAGTACCTAGACTTTCATTTTTTTATCAAAA
CTTAATGGTAGGGTACTAAAATGAAACAAAAACT
Found at i:51631 original size:2 final size:2
Alignment explanation
Indices: 51624--51653 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
51614 CCGTCGAAAT
51624 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51654 ATGTTTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53790 original size:51 final size:51
Alignment explanation
Indices: 53714--53815 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
53704 GATATATAAA
53714 TAATGCATTAATCATATAAATATTATATATTACTAGAAACATACAGTCGTT
1 TAATGCATTAATCATATAAATATTATATATTACTAGAAACATACAGTCGTT
53765 TAATGCATTAATCATATAAATATTATATATTACTAGAAACATACAGTCGTT
1 TAATGCATTAATCATATAAATATTATATATTACTAGAAACATACAGTCGTT
53816 CCTTCCACTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (51 bp):
TAATGCATTAATCATATAAATATTATATATTACTAGAAACATACAGTCGTT
Found at i:57862 original size:22 final size:22
Alignment explanation
Indices: 57837--57878 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
57827 CAATTCATTT
57837 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
57859 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
57879 CCAACACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:59920 original size:19 final size:18
Alignment explanation
Indices: 59896--59934 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
59886 CATGTACAAA
* *
59896 TATTTTCTTTATTTTTTTT
1 TATTTT-TTTACTCTTTTT
59915 TATTTTTTTACTCTTTTT
1 TATTTTTTTACTCTTTTT
59933 TA
1 TA
59935 ATTAAAAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (18 bp):
TATTTTTTTACTCTTTTT
Found at i:60195 original size:2 final size:2
Alignment explanation
Indices: 60190--60214 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60180 GGAAACAATT
60190 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
60215 TATCATTGAG
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:63157 original size:36 final size:36
Alignment explanation
Indices: 63115--63190 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
63105 TTATAGCTAA
*
63115 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
63151 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
63187 AAAA
1 AAAA
63191 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:89119 original size:3 final size:3
Alignment explanation
Indices: 89111--89146 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
89101 TATTTATTTA
89111 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
89147 TGTTTCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.