Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006595.1 Hibiscus syriacus cultivar Beakdansim tig00016179_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: 55463
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:9124 original size:18 final size:18
Alignment explanation
Indices: 9101--9139 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
9091 TTATTCGCAA
9101 TTTTTGAATTTTTGTATT
1 TTTTTGAATTTTTGTATT
** *
9119 TTTTTGGTTTTTTTTATT
1 TTTTTGAATTTTTGTATT
9137 TTT
1 TTT
9140 CCTTCTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (18 bp):
TTTTTGAATTTTTGTATT
Found at i:12284 original size:16 final size:19
Alignment explanation
Indices: 12247--12286 Score: 59
Period size: 16 Copynumber: 2.3 Consensus size: 19
12237 CATAAATTTA
12247 ATTTTTATTTGTTTATAAT
1 ATTTTTATTTGTTTATAAT
12266 ATTTTTA-TT-TTTA-AAT
1 ATTTTTATTTGTTTATAAT
12282 ATTTT
1 ATTTT
12287 AAATGGCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 4 0.19
18 2 0.10
19 7 0.33
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
ATTTTTATTTGTTTATAAT
Found at i:13419 original size:15 final size:16
Alignment explanation
Indices: 13399--13431 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13389 TAAAATACTA
13399 AATTT-ATTTTTCTTT
1 AATTTAATTTTTCTTT
*
13414 AATTTAATTTTTTTTT
1 AATTTAATTTTTCTTT
13430 AA
1 AA
13432 ATTTTACCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
AATTTAATTTTTCTTT
Found at i:14942 original size:23 final size:23
Alignment explanation
Indices: 14916--14974 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
14906 AAAATTCAAG
*
14916 AGCTCGATTGAAGCTAGTTTTTA
1 AGCTCGATTCAAGCTAGTTTTTA
* *
14939 AGCTCGATTCAAGCTCGTTTTTT
1 AGCTCGATTCAAGCTAGTTTTTA
14962 AGCTCGATTCAAG
1 AGCTCGATTCAAG
14975 ATCGAAGGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (23 bp):
AGCTCGATTCAAGCTAGTTTTTA
Found at i:16227 original size:42 final size:42
Alignment explanation
Indices: 16175--16368 Score: 178
Period size: 42 Copynumber: 4.5 Consensus size: 42
16165 TGCATAACCC
* *
16175 TAAACCCTAAATCCTAAACTATAAACCTTAAATCATATCACA
1 TAAACCCTAAACCCTAAACTCTAAACCTTAAATCATATCACA
* ** *
16217 TAAACTCTAAACCTTAAACCTTAAACTCTAAA-CTCTAACCCATAACACA
1 TAAA--C----CC-TAAACCCTAAACTCTAAACCT-TAAATCATATCACA
* *
16266 TAAACACTAAACCCTAATA-TCTAAACCTTAAATCCTATCACA
1 TAAACCCTAAACCCTAA-ACTCTAAACCTTAAATCATATCACA
* * *
16308 TAAACTCTAAACCCTAAA-TCTTAAATCTTAAATCATATCAAA
1 TAAACCCTAAACCCTAAACTC-TAAACCTTAAATCATATCACA
16350 TAAACCCTAAACCCTAAAC
1 TAAACCCTAAACCCTAAAC
16369 CTTAACACAT
Statistics
Matches: 123, Mismatches: 17, Indels: 23
0.75 0.10 0.14
Matches are distributed among these distances:
41 3 0.02
42 80 0.65
43 4 0.03
44 1 0.01
47 1 0.01
48 4 0.03
49 30 0.24
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (42 bp):
TAAACCCTAAACCCTAAACTCTAAACCTTAAATCATATCACA
Found at i:16248 original size:28 final size:27
Alignment explanation
Indices: 16173--16297 Score: 76
Period size: 28 Copynumber: 4.5 Consensus size: 27
16163 TGTGCATAAC
* *
16173 CCTAAACCCTAAATC-CTAAACTATAAA
1 CCTAAACCTTAAA-CACTAAACTCTAAA
* * *
16200 CCTTAAATCAT-ATCACATAAACTCTAAA
1 CC-TAAACCTTAAACAC-TAAACTCTAAA
*
16228 CCTTAAACCTTAAACTCTAAACTCT-AA
1 CC-TAAACCTTAAACACTAAACTCTAAA
* * *
16255 CCCATAACACATAAACACTAAACCCTAATA
1 CCTA-AAC-CTTAAACACTAAACTCTAA-A
*
16285 TCTAAACCTTAAA
1 CCTAAACCTTAAA
16298 TCCTATCACA
Statistics
Matches: 75, Mismatches: 15, Indels: 15
0.71 0.14 0.14
Matches are distributed among these distances:
26 2 0.03
27 11 0.15
28 52 0.69
29 7 0.09
30 3 0.04
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (27 bp):
CCTAAACCTTAAACACTAAACTCTAAA
Found at i:16290 original size:21 final size:20
Alignment explanation
Indices: 16222--16328 Score: 55
Period size: 21 Copynumber: 5.2 Consensus size: 20
16212 TCACATAAAC
*
16222 TCTAAACCTTAAACCTTAA-A
1 TCTAAACC-TAAACCCTAATA
*
16242 CTCTAAACTCT-AACCCATAACA
1 -TCTAAAC-CTAAACCC-TAATA
16264 -CATAAACACTAAACCCTAATA
1 TC-TAAAC-CTAAACCCTAATA
*
16285 TCTAAACCTTAAATCCT-ATCA
1 TCTAAACC-TAAACCCTAAT-A
16306 -CATAAACTCTAAACCCTAA-A
1 TC-TAAAC-CTAAACCCTAATA
16326 TCT
1 TCT
16329 TAAATCTTAA
Statistics
Matches: 69, Mismatches: 5, Indels: 25
0.70 0.05 0.25
Matches are distributed among these distances:
20 11 0.16
21 48 0.70
22 10 0.14
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (20 bp):
TCTAAACCTAAACCCTAATA
Found at i:16332 original size:21 final size:20
Alignment explanation
Indices: 16231--16325 Score: 61
Period size: 21 Copynumber: 4.5 Consensus size: 20
16221 CTCTAAACCT
* *
16231 TAAACCTTAAACTCTAAACTC
1 TAAACCCTAAAC-ATAAACTC
*
16252 T-AACCCATAACACATAAACAC
1 TAAACCC-TAA-ACATAAACTC
16273 TAAACCCTAATATC-TAAAC-C
1 TAAACCCTAA-A-CATAAACTC
* *
16293 TTAAATCCTATCACATAAACTC
1 -TAAACCCTA-AACATAAACTC
16315 TAAACCCTAAA
1 TAAACCCTAAA
16326 TCTTAAATCT
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
20 7 0.12
21 42 0.72
22 9 0.16
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAACCCTAAACATAAACTC
Found at i:16339 original size:21 final size:19
Alignment explanation
Indices: 16217--16339 Score: 54
Period size: 21 Copynumber: 5.8 Consensus size: 19
16207 TCATATCACA
*
16217 TAAACTCTAAACCTTAAACCT
1 TAAA-TCTAAA-CTTAAACCC
16238 TAAACTCTAAACTCT-AACCC
1 TAAA-TCTAAACT-TAAACCC
*
16258 ATAACA-CATAAACACTAAACCC
1 -TAA-ATC-TAAAC-TTAAACCC
*
16280 TAATATCTAAACCTTAAATCC
1 TAA-ATCTAAA-CTTAAACCC
*
16301 TATCA-CATAAACTCTAAACCC
1 TA-AATC-TAAACT-TAAACCC
16322 TAAATCTTAAATCTTAAA
1 TAAATC-TAAA-CTTAAA
16340 TCATATCAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 26
0.70 0.08 0.23
Matches are distributed among these distances:
20 11 0.14
21 59 0.74
22 10 0.12
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAATCTAAACTTAAACCC
Found at i:16456 original size:19 final size:19
Alignment explanation
Indices: 16432--16475 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
16422 ACTTGTTTTG
16432 ATATTTTTTAAAATTATCA
1 ATATTTTTTAAAATTATCA
*
16451 ATATTTTTTAAAATTATTA
1 ATATTTTTTAAAATTATCA
16470 ATATTT
1 ATATTT
16476 AAATTGAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTTTTTAAAATTATCA
Found at i:16791 original size:14 final size:14
Alignment explanation
Indices: 16774--16814 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
16764 TTTATTCATC
16774 AATAATGTATTTTT
1 AATAATGTATTTTT
16788 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
16799 AATAATGTAATTTT
1 AATAATGTATTTTT
16813 AA
1 AA
16815 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:16963 original size:16 final size:16
Alignment explanation
Indices: 16942--16972 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
16932 AGTCCATTCG
16942 ATCCGAGTATTTATCA
1 ATCCGAGTATTTATCA
16958 ATCCGAGTATTTATC
1 ATCCGAGTATTTATC
16973 GAGCTAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (16 bp):
ATCCGAGTATTTATCA
Found at i:29115 original size:182 final size:182
Alignment explanation
Indices: 28730--29203 Score: 689
Period size: 182 Copynumber: 2.6 Consensus size: 182
28720 GATCCAAATT
* * * * **
28730 AAAAATGTATCGATCCACAACGATATAACAGGTAAAACTATGACAAAACCAGTATTGAAATGATA
1 AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * * *
28795 AAACCGGTAAAGCGGTACCGAATATATTTAAAGTGTCGGTACTTTAATATAAGGATCGATACTTC
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCAACACTTC
* *
28860 GTTAATTTAAAAGAGAACCAGTTTTAGCGCCTATAAAATGTCGATACTTTCA
131 GTGAATTTAAAAGAGAACCAGTTTTAGCGCCTATAAAATGTCGATACTTTAA
* * *
28912 AAAAATATATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACTGGTATCAAAATGATG
1 AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * *
28977 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGAAACTTT-ATATAAGGATCAACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCAACACTTC
* *
29041 GTGAATTTAAAAGAGAAGCAGTTTTAGCGTCTATAAAATGTCGATACTTTAA
131 GTGAATTTAAAAGAGAACCAGTTTTAGCGCCTATAAAATGTCGATACTTTAA
*
29093 AAAAATGTATCGATCAAACAACGATATAATAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAAATGTATCGATC-AACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
* *
29158 AAAACCGGTAAAATGATATCGGATATATTAAAAGTGTCGATACTTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
29204 CGTAAGTACG
Statistics
Matches: 260, Mismatches: 31, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
181 78 0.30
182 182 0.70
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCAACACTTC
GTGAATTTAAAAGAGAACCAGTTTTAGCGCCTATAAAATGTCGATACTTTAA
Found at i:29147 original size:20 final size:19
Alignment explanation
Indices: 29124--29170 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
29114 CGATATAATA
29124 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
29144 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
29164 GGTAAAA
1 GGTAAAA
29171 TGATATCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:29172 original size:17 final size:19
Alignment explanation
Indices: 29133--29175 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
29123 AGGTAAAAAT
29133 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
29153 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
29170 ATGATA
1 ATGATA
29176 TCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:32087 original size:182 final size:182
Alignment explanation
Indices: 31379--32275 Score: 1559
Period size: 182 Copynumber: 4.9 Consensus size: 182
31369 AGGTAAAAAT
* *
31379 ATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTTGATAATTTATTATAAGTATCGA
1 ATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGA
31444 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
66 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
*
31509 TATCGATCCATAACAATATAACAGGTAAAAATACGACAAAACCGGTCTCGAA
131 TATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAA
* * * *
31561 ATGACAAAACAGGTAAAGCACTACCAGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCAA
1 ATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGA
31626 CACTTTTGGAATTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
66 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
** * *
31690 TATCGATCCATAACAATATAACATATAAAAATATGACAAAAACGGTCTCAAA
131 TATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAA
* *
31742 ATGACAAAACAGGTAAAGCGCTACTGGTTATATTGAAAGTGTCGATAATTTATTATAAGTATCG-
1 ATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGA
**
31806 -ACTTTTGGAA-TTAATAAGAGAAGAAGTTATAGCGCCAATAACTTGTCGATACTTTATAAAAAT
66 CACTTTTGGAATTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAAT
*
31869 GTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAA
130 GTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAA
*
31922 ATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGA
1 ATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGA
*
31987 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTGATAAAAATG
66 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
*
32052 TATCGATCCATAACAATATAACAGGTAATAATATGACAAAACCGGTCTCGAA
131 TATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAA
*
32104 ATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTGTCGA
1 ATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGA
* *
32169 CACTTTTGGAATTTAAATGAGAAGAAGTTATAGCGCCAATAAAATGTCGATACTTTATAAAAATG
66 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
32234 TATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC
131 TATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC
32276 AGGTAAAGCG
Statistics
Matches: 674, Mismatches: 36, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
178 4 0.01
179 18 0.03
180 148 0.22
181 145 0.22
182 355 0.53
183 4 0.01
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (182 bp):
ATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGA
CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
TATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAA
Found at i:32373 original size:162 final size:162
Alignment explanation
Indices: 32104--32436 Score: 569
Period size: 162 Copynumber: 2.1 Consensus size: 162
32094 CGGTCTCGAA
* *
32104 ATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTGTCGA
1 ATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGA
* *
32169 CACTTTTGGAATTTAAATGAGAAGAAGTTATAGCGCCAATAAAATGTCGATACTTTATAAAAATG
66 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGACAATAAAATGTCGATACTTTATAAAAATG
32234 TATCGATCCATAACAATATAACAGGTAAAAAT
131 TATCGATCCATAACAATATAACAGGTAAAAAT
32266 ATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGA
1 ATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGA
* *
32331 CACTTTTGGAA-TTAATAAGAGAAGATGTTATAGCGACAATAAAGTGTCGATACTTTATAAAAAT
66 CACTTTTGGAATTTAA-AAGAGAAGAAGTTATAGCGACAATAAAATGTCGATACTTTATAAAAAT
* *
32395 GTATCGATCCATAATAATATAACATGTAAAAAT
130 GTATCGATCCATAACAATATAACAGGTAAAAAT
*
32428 ATGATAAAA
1 ATGACAAAA
32437 TCGGTCTATA
Statistics
Matches: 161, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
161 4 0.02
162 157 0.98
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.29
Consensus pattern (162 bp):
ATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGA
CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGACAATAAAATGTCGATACTTTATAAAAATG
TATCGATCCATAACAATATAACAGGTAAAAAT
Found at i:34241 original size:22 final size:22
Alignment explanation
Indices: 34198--34260 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
34188 AATAAATAAT
*
34198 ATTATTTATTATAATAACTTAATATA
1 ATTATTT-TTA-AAT-A-TTAAAATA
34224 ATTATTTTTAAATATTAAAATA
1 ATTATTTTTAAATATTAAAATA
*
34246 ATT-TATTT-AATATTA
1 ATTATTTTTAAATATTA
34261 TTTATTTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 7 0.20
21 4 0.11
22 10 0.29
23 1 0.03
24 3 0.09
25 3 0.09
26 7 0.20
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTATTTTTAAATATTAAAATA
Found at i:34263 original size:14 final size:14
Alignment explanation
Indices: 34246--34292 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
34236 TATTAAAATA
34246 ATTTATTTAATATT
1 ATTTATTTAATATT
34260 ATTTATTTCAATATT
1 ATTTATTT-AATATT
*
34275 A-TTATTAAAATATT
1 ATTTATT-TAATATT
34289 ATTT
1 ATTT
34293 CTACAACTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 20 0.69
15 9 0.31
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTTATTTAATATT
Found at i:34461 original size:60 final size:59
Alignment explanation
Indices: 34350--34483 Score: 169
Period size: 60 Copynumber: 2.2 Consensus size: 59
34340 AAACTATGAC
* * * * * **
34350 GTCCTAAATTTTTAAACATTCTAATTTCATCCCAAAACTAAGACTCTCATTCTAAATTA
1 GTCCTAAACTTTTCAACATTCCAATTTCACCCCAAAACTAAGAATAGCATTCTAAATTA
* *
34409 GTCCTTAAACTTTTCAACATTCCAATTTCACCCCCAAACTATGAATAGCATTCTAAATTA
1 GTCC-TAAACTTTTCAACATTCCAATTTCACCCCAAAACTAAGAATAGCATTCTAAATTA
34469 GTTCCTAAACTTTTC
1 G-TCCTAAACTTTTC
34484 CATATTCAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 4 0.06
60 57 0.89
61 3 0.05
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (59 bp):
GTCCTAAACTTTTCAACATTCCAATTTCACCCCAAAACTAAGAATAGCATTCTAAATTA
Found at i:34938 original size:34 final size:37
Alignment explanation
Indices: 34884--34957 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 37
34874 TATATTAACT
34884 ATTTATTAAAATAAAAATATTATAT-TA-TATTTTAAA
1 ATTTATT-AAATAAAAATATTATATGTATTATTTTAAA
* * *
34920 ATTTATT-AATAAATATATTTTATGTATTTTTTTAAA
1 ATTTATTAAATAAAAATATTATATGTATTATTTTAAA
34956 AT
1 AT
34958 ATTTATTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 14 0.42
35 2 0.06
36 17 0.52
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (37 bp):
ATTTATTAAATAAAAATATTATATGTATTATTTTAAA
Found at i:36573 original size:31 final size:28
Alignment explanation
Indices: 36522--36578 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
36512 TCTTATGACA
**
36522 TATAAATATATTTTTGAATTTTGAAATAT
1 TATAAATATATTTTCAAATTTT-AAATAT
36551 TATAAATATATATTTACAAATTTTAAAT
1 TATAAATATAT-TTT-CAAATTTTAAAT
36579 TATAATATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.46
30 7 0.29
31 6 0.25
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (28 bp):
TATAAATATATTTTCAAATTTTAAATAT
Found at i:36796 original size:36 final size:35
Alignment explanation
Indices: 36717--37132 Score: 323
Period size: 36 Copynumber: 12.0 Consensus size: 35
36707 TGAAATATAA
* * *
36717 TATATAATCTATAGTTTTTAAAAACATTTTAAAAAAC
1 TATATAATATATAG-TTTTGAAAACATTTT-GAAAAC
36754 TTATATAATATATAGTTTTGAAAACATTTTGAAAACC
1 -TATATAATATATAGTTTTGAAAACATTTTGAAAA-C
* *
36791 TATATAATATATAATTTTTGAAAACATTTTAAAAAC
1 TATATAATATAT-AGTTTTGAAAACATTTTGAAAAC
36827 TTATATAATATATAGTTTTGAAAAC---------A-
1 -TATATAATATATAGTTTTGAAAACATTTTGAAAAC
*
36853 TATATAATATATAATTTTGAAAACATTTTGAAAAC
1 TATATAATATATAGTTTTGAAAACATTTTGAAAAC
* *
36888 ATATATAATATATAATTTTGAAAATATTTTGAAAAC
1 -TATATAATATATAGTTTTGAAAACATTTTGAAAAC
* * * *
36924 ATATATAATATATAGTTTTTAAAA-A-ATTAAAAATA
1 -TATATAATATATAGTTTTGAAAACATTTTGAAAA-C
* *
36959 TATATAATATATAG-TTTGAAAATAATTTTGAAAAAAA
1 TATATAATATATAGTTTTGAAAA-CATTTTG--AAAAC
* *
36996 TATATATTATATAGTTTTGAAAATATTTTTG-AAA-
1 TATATAATATATAGTTTTGAAAACA-TTTTGAAAAC
* *
37030 TATAT--TATATAGTTTTAAAAACAATTTTTAAAA-
1 TATATAATATATAGTTTTGAAAAC-ATTTTGAAAAC
* * *
37063 -ATATATTATATGGTTTTGAAAATAATTTTTGAAAA-
1 TATATAATATATAGTTTTGAAAA-CA-TTTTGAAAAC
* * *
37098 TATATATTATATAATTTTAAAAAACATTTTGAAAA
1 TATATAATATATAGTTTT-GAAAACATTTTGAAAA
37133 ACATTTTTGA
Statistics
Matches: 319, Mismatches: 29, Indels: 63
0.78 0.07 0.15
Matches are distributed among these distances:
25 23 0.07
27 1 0.00
32 23 0.07
33 11 0.03
34 41 0.13
35 22 0.07
36 102 0.32
37 66 0.21
38 30 0.09
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (35 bp):
TATATAATATATAGTTTTGAAAACATTTTGAAAAC
Found at i:36862 original size:23 final size:25
Alignment explanation
Indices: 36816--36878 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
36806 TTTTGAAAAC
* *
36816 ATTTTAAAAACTTATATAATATATA
1 ATTTTGAAAACATATATAATATATA
*
36841 GTTTTGAAAACATATATAATATATA
1 ATTTTGAAAACATATATAATATATA
36866 ATTTTGAAAACAT
1 ATTTTGAAAACAT
36879 TTTGAAAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (25 bp):
ATTTTGAAAACATATATAATATATA
Found at i:36864 original size:98 final size:97
Alignment explanation
Indices: 36749--37052 Score: 328
Period size: 98 Copynumber: 3.1 Consensus size: 97
36739 AACATTTTAA
* * *
36749 AAAACTTATATAATATATAGTTTTGAAAACATTTTGAAAACCTATATAATATATAATTTTTGAAA
1 AAAACATATATAATATATAATTTTGAAAACATTTTGAAAACATATATAATATATAA-TTTTGAAA
*
36814 ACATTTTAAAAACTTATATAATATATAGTTTTG
65 ACATTTTAAAAACATATATAATATATAGTTTTG
36847 AAAACATATATAATATATAATTTTGAAAACATTTTGAAAACATATATAATATATAATTTTGAAAA
1 AAAACATATATAATATATAATTTTGAAAACATTTTGAAAACATATATAATATATAATTTTGAAAA
* * *
36912 TATTTTGAAAACATATATAATATATAGTTTTT
66 CATTTTAAAAACATATATAATATATAGTTTTG
* * * * *
36944 AAAAAATTAAAAATATATATAATATATAGTTTGAAAATAATTTTGAAAAAAATATATATTATATA
1 AAAACA-T----ATATA-AT-ATATA-ATTTTGAAAA-CATTTTG-AAAACATATATAATATATA
* * ** *
37009 GTTTTGAAAATATTTT-TGAA-ATATAT--TATATAGTTTTA
56 ATTTTGAAAACATTTTAAAAACATATATAATATATAGTTTTG
37047 AAAACA
1 AAAACA
37053 ATTTTTAAAA
Statistics
Matches: 179, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
97 42 0.23
98 54 0.30
102 5 0.03
103 18 0.10
104 5 0.03
105 15 0.08
106 8 0.04
107 32 0.18
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (97 bp):
AAAACATATATAATATATAATTTTGAAAACATTTTGAAAACATATATAATATATAATTTTGAAAA
CATTTTAAAAACATATATAATATATAGTTTTG
Found at i:36882 original size:11 final size:11
Alignment explanation
Indices: 36866--36925 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
36856 ATAATATATA
36866 ATTTTGAAAAC
1 ATTTTGAAAAC
36877 ATTTTGAAAAC
1 ATTTTGAAAAC
* *
36888 ATATAT-AATATATA
1 AT-TTTGAA-A-A-C
*
36902 ATTTTGAAAAT
1 ATTTTGAAAAC
36913 ATTTTGAAAAC
1 ATTTTGAAAAC
36924 AT
1 AT
36926 ATATAATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
11 27 0.69
12 4 0.10
13 4 0.10
14 4 0.10
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (11 bp):
ATTTTGAAAAC
Found at i:36896 original size:61 final size:62
Alignment explanation
Indices: 36779--36911 Score: 223
Period size: 61 Copynumber: 2.2 Consensus size: 62
36769 TTTTGAAAAC
* *
36779 ATTTTGAAAACCTATATAATATATAATTTTTGAAAACATTTTAAAAACTTATATAATATATA
1 ATTTTGAAAACATATATAATATATAATTTTTGAAAACATTTTAAAAACATATATAATATATA
* *
36841 GTTTTGAAAACATATATAATATATAA-TTTTGAAAACATTTTGAAAACATATATAATATATA
1 ATTTTGAAAACATATATAATATATAATTTTTGAAAACATTTTAAAAACATATATAATATATA
36902 ATTTTGAAAA
1 ATTTTGAAAA
36912 TATTTTGAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
61 42 0.64
62 24 0.36
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (62 bp):
ATTTTGAAAACATATATAATATATAATTTTTGAAAACATTTTAAAAACATATATAATATATA
Found at i:36899 original size:134 final size:132
Alignment explanation
Indices: 36716--36980 Score: 374
Period size: 134 Copynumber: 2.0 Consensus size: 132
36706 TTGAAATATA
* * * *
36716 ATATATAATCTATAGTTTTTAAAAACATTTTAAAAAACTTATATAATATATAGTTTTGAAAACAT
1 ATATATAATATATAGATTTTAAAAACATTTTAAAAAACATATATAATATATAATTTTGAAAACAT
* *
36781 TTTGAAAACCTATATAATATATAATTTTTGAAAACATTTTAAAAACT-TATATAATATATAGTTT
66 TTTGAAAACATATATAATATATAATTTTT-AAAA-A-ATTAAAAA-TATATATAATATATAG-TT
36845 TGAAAAC
126 TGAAAAC
* * *
36852 ATATATAATATATA-ATTTTGAAAACATTTT-GAAAACATATATAATATATAATTTTGAAAATAT
1 ATATATAATATATAGATTTTAAAAACATTTTAAAAAACATATATAATATATAATTTTGAAAACAT
*
36915 TTTGAAAACATATATAATATATAGTTTTTAAAAAATTAAAAATATATATAATATATAGTTTGAAA
66 TTTGAAAACATATATAATATATAATTTTTAAAAAATTAAAAATATATATAATATATAGTTTGAAA
36980 A
131 A
36981 TAATTTTGAA
Statistics
Matches: 118, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
130 9 0.08
131 21 0.18
132 1 0.01
133 4 0.03
134 56 0.47
135 14 0.12
136 13 0.11
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (132 bp):
ATATATAATATATAGATTTTAAAAACATTTTAAAAAACATATATAATATATAATTTTGAAAACAT
TTTGAAAACATATATAATATATAATTTTTAAAAAATTAAAAATATATATAATATATAGTTTGAAA
AC
Found at i:37033 original size:32 final size:32
Alignment explanation
Indices: 36997--37120 Score: 140
Period size: 34 Copynumber: 3.7 Consensus size: 32
36987 TGAAAAAAAT
*
36997 ATATATTATATAGTTTTGAAAATATTTTTGAA
1 ATATATTATATAGTTTTAAAAATATTTTTGAA
* *
37029 ATATATTATATAGTTTTAAAAACAATTTTTAAAA
1 ATATATTATATAGTTTTAAAAA-TATTTTT-GAA
* *
37063 ATATATTATATGGTTTTGAAAATAATTTTTGAAAA
1 ATATATTATATAGTTTTAAAAAT-ATTTTTG--AA
*
37098 TATATATTATATAATTTTAAAAA
1 -ATATATTATATAGTTTTAAAAA
37121 ACATTTTGAA
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
32 21 0.28
33 6 0.08
34 28 0.37
35 2 0.03
36 19 0.25
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (32 bp):
ATATATTATATAGTTTTAAAAATATTTTTGAA
Found at i:37140 original size:13 final size:12
Alignment explanation
Indices: 37111--37154 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
37101 ATATTATATA
*
37111 ATTTTAAAAAAC
1 ATTTTGAAAAAC
37123 ATTTTGAAAAAC
1 ATTTTGAAAAAC
37135 ATTTTTG-AAAAC
1 A-TTTTGAAAAAC
*
37147 GTTTTGAA
1 ATTTTGAA
37155 CAATATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 5 0.18
12 18 0.64
13 5 0.18
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (12 bp):
ATTTTGAAAAAC
Found at i:38414 original size:15 final size:15
Alignment explanation
Indices: 38394--38424 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
38384 GGTTTTTTTG
38394 TATTTTATTAACATT
1 TATTTTATTAACATT
*
38409 TATTTTCTTAACATT
1 TATTTTATTAACATT
38424 T
1 T
38425 TTTATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTTATTAACATT
Found at i:38435 original size:8 final size:8
Alignment explanation
Indices: 38422--38566 Score: 55
Period size: 8 Copynumber: 17.6 Consensus size: 8
38412 TTTCTTAACA
38422 TTTTTTAT
1 TTTTTTAT
38430 TTTTTTAT
1 TTTTTTAT
*
38438 TATTTTAT
1 TTTTTTAT
***
38446 TTTCAAAT
1 TTTTTTAT
**
38454 TTTAACT-T
1 TTT-TTTAT
38462 TTTTTTAT
1 TTTTTTAT
38470 TTCTATTT-T
1 TT-T-TTTAT
*
38479 TTATTTCAT
1 TT-TTTTAT
38488 TTTTTTAT
1 TTTTTTAT
**
38496 TTTAATAT
1 TTTTTTAT
* *
38504 TCTTCTCA-
1 T-TTTTTAT
*
38512 -ATTTTAT
1 TTTTTTAT
*
38519 TTATTTAT
1 TTTTTTAT
38527 TTTATTTAT
1 TTT-TTTAT
*
38536 TTTGTTAT
1 TTTTTTAT
*
38544 TATTTTATT
1 TTTTTTA-T
38553 TTATTTTAT
1 TT-TTTTAT
38562 TTTTT
1 TTTTT
38567 CTTTTTGTAT
Statistics
Matches: 98, Mismatches: 28, Indels: 22
0.66 0.19 0.15
Matches are distributed among these distances:
6 3 0.03
7 1 0.01
8 62 0.63
9 24 0.24
10 8 0.08
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (8 bp):
TTTTTTAT
Found at i:38445 original size:5 final size:5
Alignment explanation
Indices: 38424--38564 Score: 69
Period size: 5 Copynumber: 26.8 Consensus size: 5
38414 TCTTAACATT
*
38424 TTTTA TTTTT TTATTA TTTTA TTTTCAAA TTTTAA CTTTT- TTTTA TTTCTA
1 TTTTA TTTTA TT-TTA TTTTA TTTT---A TTTT-A -TTTTA TTTTA TTT-TA
* * * *
38475 TTTTTTA TTTCA -TTT- TTTTA TTTTAA TATTC TTCTCAA TTTTA -TTTA
1 --TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TT-T-TA TTTTA TTTTA
*
38522 -TTTA TTTTA -TTTA TTTTG TTATTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTT
38565 TTCTTTTTGT
Statistics
Matches: 107, Mismatches: 12, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
4 21 0.20
5 52 0.49
6 18 0.17
7 8 0.07
8 8 0.07
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:38480 original size:13 final size:13
Alignment explanation
Indices: 38461--38497 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
38451 AATTTTAACT
38461 TTTTTTTATTTC-
1 TTTTTTTATTTCA
38473 TATTTTTTATTTCA
1 T-TTTTTTATTTCA
38487 TTTTTTTATTT
1 TTTTTTTATTT
38498 TAATATTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.04
13 21 0.91
14 1 0.04
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTATTTCA
Found at i:38530 original size:13 final size:13
Alignment explanation
Indices: 38465--38563 Score: 69
Period size: 13 Copynumber: 7.2 Consensus size: 13
38455 TTAACTTTTT
38465 TTTATTTCTATTT-
1 TTTATTT-TATTTA
* *
38478 TTTATTTCATTTT
1 TTTATTTTATTTA
*
38491 TTTATTTTAATATTC
1 TTTATTTT-AT-TTA
38506 TTCTCAATTTTATTTA
1 TT-T--ATTTTATTTA
38522 TTTATTTTATTTA
1 TTTATTTTATTTA
*
38535 TTT-TGTTA-TTA
1 TTTATTTTATTTA
38546 TTTTATTTTATTTTA
1 -TTTATTTTA-TTTA
38561 TTT
1 TTT
38564 TTTCTTTTTG
Statistics
Matches: 70, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
11 3 0.04
12 11 0.16
13 31 0.44
14 5 0.07
15 8 0.11
16 5 0.07
17 2 0.03
18 5 0.07
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:38548 original size:11 final size:10
Alignment explanation
Indices: 38424--38564 Score: 69
Period size: 11 Copynumber: 13.4 Consensus size: 10
38414 TCTTAACATT
*
38424 TTTTATTTTT
1 TTTTATTTTA
38434 TTATTATTTTA
1 TT-TTATTTTA
38445 TTTTCAAATTTTAA
1 TTTT---ATTTT-A
38459 CTTTT-TTTTA
1 -TTTTATTTTA
38469 TTTCTATTTTTTA
1 TTT-TA--TTTTA
*
38482 TTTCA-TTT-
1 TTTTATTTTA
38490 TTTTATTTTAA
1 TTTTATTTT-A
* * *
38501 TATTCTTCTCAA
1 TTTTATT-T-TA
38513 TTTTA-TTTA
1 TTTTATTTTA
38522 -TTTATTTTA
1 TTTTATTTTA
*
38531 -TTTATTTTG
1 TTTTATTTTA
38540 TTATTATTTTA
1 TT-TTATTTTA
38551 TTTTATTTTA
1 TTTTATTTTA
38561 TTTT
1 TTTT
38565 TTCTTTTTGT
Statistics
Matches: 102, Mismatches: 11, Indels: 36
0.68 0.07 0.24
Matches are distributed among these distances:
8 8 0.08
9 22 0.22
10 20 0.20
11 28 0.27
12 6 0.06
13 13 0.13
14 1 0.01
15 4 0.04
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.74
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:38573 original size:34 final size:33
Alignment explanation
Indices: 38512--38582 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 33
38502 ATTCTTCTCA
38512 ATTTTATTTATTTATTTTATTTATTTTGT-TATT
1 ATTTTATTTATTTATTTTATTTATTTTGTATA-T
38545 ATTTTATTTTATTTTATTTT-TTCT-TTTTGTATAT
1 ATTTTA-TTTA-TTTATTTTATT-TATTTTGTATAT
38579 ATTT
1 ATTT
38583 CACCATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
33 6 0.18
34 17 0.50
35 11 0.32
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.76
Consensus pattern (33 bp):
ATTTTATTTATTTATTTTATTTATTTTGTATAT
Found at i:39668 original size:16 final size:16
Alignment explanation
Indices: 39631--39668 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
39621 TCTCACTAAC
39631 TTTTTCCTTTCATTTT
1 TTTTTCCTTTCATTTT
39647 TGTTTT-CTTTCATTTT
1 T-TTTTCCTTTCATTTT
39663 ATTTTT
1 -TTTTT
39669 TCATTTACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.08, C:0.13, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTTCCTTTCATTTT
Found at i:44655 original size:83 final size:84
Alignment explanation
Indices: 44390--44881 Score: 637
Period size: 83 Copynumber: 5.8 Consensus size: 84
44380 TCCCAACCTA
* **
44390 TTACAGTATAGCTCAAGGCGAGAAGGATTATCTATCAAC-AAAACCTTCGAGTTCGATTCCATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATTCCATTC
*
44454 AGCTCAAGGGCAGCCAAAT
66 AGCTCAAGGGCATCCAAAT
* ** * * * *
44473 TTAGATTATAGTTCAAGGCGAGAAGGGTTATCTATCAACAAAAATCTTCGAGTTCGATTCCATTA
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATTCCATTC
* *
44538 AGCTCAAGTGCAGCCAAAT
66 AGCTCAAGGGCATCCAAAT
* * * * *
44557 TTACAGCATAACTCAAGGCGAGAATGGCTATCTATCAACAAAAATCTTAGAGTT-TATTCCATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATTCCATTC
*
44621 AGCTCAAGTGCATCCAAAT
66 AGCTCAAGGGCATCCAAAT
*
44640 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTCCGAGTTCGATTCCATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATTCCATTC
*
44705 AGCTCAAGGGCATATCAAAT
66 AGCTCAAGGGCAT-CCAAAT
* * ** *
44725 TTAAAGCATAGCTCAAAGGCGAGAAGGGATATCTGCCAACAAAAACCTTCGAGTTTGATTCCATT
1 TTACAGCATAGCTC-AAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATTCCATT
* * *
44790 CTGCTCAAAGGCATATCAAAT
65 CAGCTCAAGGGCAT-CCAAAT
* * * *
44811 TTATAGCATAGCTCAAGGCGAGAAGGGCTATCTTTCAACAAAAAACTATCGAGTTCAATTCCATT
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCT-TCGAGTTCGATTCCATT
44876 CAGCTC
65 CAGCTC
44882 GATGACATAT
Statistics
Matches: 362, Mismatches: 42, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
83 110 0.30
84 108 0.30
85 47 0.13
86 97 0.27
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (84 bp):
TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATTCCATTC
AGCTCAAGGGCATCCAAAT
Found at i:44677 original size:167 final size:166
Alignment explanation
Indices: 44390--44881 Score: 628
Period size: 167 Copynumber: 2.9 Consensus size: 166
44380 TCCCAACCTA
* *
44390 TTACAGTATAGCTCAAGGCGAGAAGGATTATCTATCAAC-AAAACCTTCGAGTTCGATTCCATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGA-TATCTATCAACAAAAACCTTCGAGTT-TATTCCATTC
* * ** * * *
44454 AGCTCAAGGGCAGCCAAATTTAGATTATAGTTCAAGGCGAGAAGGGTTATCTATCAACAAAAATC
64 AGCTCAA-GGCATCCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAAAC
* * *
44519 TTCGAGTTCGATTCCATTAAGCTCAAGTGCA-GCCAAAT
128 TTCGAGTTCGATTCCATTCAGCTCAAGGGCATACCAAAT
* * * *
44557 TTACAGCATAACTCAAGGCGAGAATGGCTATCTATCAACAAAAATCTTAGAGTTTATTCCATTCA
1 TTACAGCATAGCTCAAGGCGAGAA-GGATATCTATCAACAAAAACCTTCGAGTTTATTCCATTCA
*
44622 GCTCAAGTGCATCCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCT
65 GCTCAAG-GCATCCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAAACT
* *
44687 CCGAGTTCGATTCCATTCAGCTCAAGGGCATATCAAAT
129 TCGAGTTCGATTCCATTCAGCTCAAGGGCATACCAAAT
* **
44725 TTAAAGCATAGCTCAAAGGCGAGAAGGGATATCTGCCAACAAAAACCTTCGAGTTTGATTCCATT
1 TTACAGCATAGCTC-AAGGCGAGAA-GGATATCTATCAACAAAAACCTTCGAGTTT-ATTCCATT
* * * *
44790 CTGCTCAAAGGCATATCAAATTTATAGCATAGCTCAAGGCGAGAAGGGCTATCTTTCAACAAAAA
63 CAGCTC-AAGGCAT-CCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAA
*
44855 ACTATCGAGTTCAATTCCATTCAGCTC
126 ACT-TCGAGTTCGATTCCATTCAGCTC
44882 GATGACATAT
Statistics
Matches: 283, Mismatches: 33, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
166 1 0.00
167 126 0.45
168 31 0.11
169 35 0.12
170 17 0.06
171 52 0.18
172 21 0.07
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (166 bp):
TTACAGCATAGCTCAAGGCGAGAAGGATATCTATCAACAAAAACCTTCGAGTTTATTCCATTCAG
CTCAAGGCATCCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAAACTTC
GAGTTCGATTCCATTCAGCTCAAGGGCATACCAAAT
Found at i:45584 original size:32 final size:33
Alignment explanation
Indices: 45548--45631 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 33
45538 AAAAATCAGT
*
45548 TTTTG-AAA-TATAATATATAGTTTTTGAAAACA
1 TTTTGAAAACTAT-ATATATAGTTTTTAAAAACA
45580 TTTTGAAAACTTATATATATAGTTTTTAAAAACA
1 TTTTGAAAAC-TATATATATAGTTTTTAAAAACA
*
45614 TTTTAAAAAACT-TATATA
1 TTTT-GAAAACTATATATA
45632 ATATTGAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
32 5 0.11
33 9 0.20
34 24 0.52
35 8 0.17
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (33 bp):
TTTTGAAAACTATATATATAGTTTTTAAAAACA
Found at i:45603 original size:34 final size:35
Alignment explanation
Indices: 45560--45631 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 35
45550 TTGAAATATA
* *
45560 ATATATAGTTTTTGAAAACATTTT-GAAAACTTAT
1 ATATATAGTTTTTAAAAACATTTTAAAAAACTTAT
45594 ATATATAGTTTTTAAAAACATTTTAAAAAACTTAT
1 ATATATAGTTTTTAAAAACATTTTAAAAAACTTAT
45629 ATA
1 ATA
45632 ATATTGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 23 0.66
35 12 0.34
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (35 bp):
ATATATAGTTTTTAAAAACATTTTAAAAAACTTAT
Found at i:45681 original size:51 final size:53
Alignment explanation
Indices: 45582--45688 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
45572 TGAAAACATT
*
45582 TTGAAAACTTATATATATAGTTTTTAAAAACATTTTAAAAAACTTATATAATA
1 TTGAAAACATATATATATAGTTTTTAAAAACATTTTAAAAAACTTATATAATA
45635 TTGAAAACATATATATATAG-TTTTAAAAACATTTTAAAAAACTATATATAATA
1 TTGAAAACATATATATATAGTTTTTAAAAACATTTTAAAAAACT-TATATAATA
45688 T
1 T
45689 ATAGTTTTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
52 23 0.44
53 29 0.56
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (53 bp):
TTGAAAACATATATATATAGTTTTTAAAAACATTTTAAAAAACTTATATAATA
Found at i:45697 original size:38 final size:39
Alignment explanation
Indices: 45643--45723 Score: 114
Period size: 38 Copynumber: 2.1 Consensus size: 39
45633 TATTGAAAAC
*
45643 ATAT-ATATATAGTTTTAAAA-ACATTTT-AAAAAACTAT
1 ATATAATATATAGTTTTAAAATA-ATTTTGAAAAAAATAT
*
45680 ATATAATATATAGTTTTAAAATATTTTTGAAAAAAATAT
1 ATATAATATATAGTTTTAAAATAATTTTGAAAAAAATAT
45719 ATATA
1 ATATA
45724 TAGTTTTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
37 4 0.10
38 20 0.51
39 15 0.38
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (39 bp):
ATATAATATATAGTTTTAAAATAATTTTGAAAAAAATAT
Found at i:45728 original size:34 final size:33
Alignment explanation
Indices: 45638--45830 Score: 167
Period size: 34 Copynumber: 5.6 Consensus size: 33
45628 TATAATATTG
* * * *
45638 AAAACATATATATATAGTTTTAAAAACATTTTAA
1 AAAAAATATATATATAGTTTTGAAAATATTTT-T
45672 AAAACTATATATAATATATAGTTTT-AAAATATTTTT
1 AAAA--A-ATAT-ATATATAGTTTTGAAAATATTTTT
45708 GAAAAAAATATATATATAGTTTTGAAAATATTTTT
1 --AAAAAATATATATATAGTTTTGAAAATATTTTT
* * * * *
45743 TATATATAT-TATATAGTTTTAAAAACAATTTTT
1 AAAAAATATATATATAGTTTTGAAAA-TATTTTT
* * *
45776 -GAAAATATATTACATGGTTTTGAAAATATTTTT
1 AAAAAATATA-TATATAGTTTTGAAAATATTTTT
45809 AAAAAATATATTATATAGTTTT
1 AAAAAATATA-TATATAGTTTT
45831 TTTTAAAAAT
Statistics
Matches: 130, Mismatches: 18, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
32 20 0.15
33 18 0.14
34 47 0.36
35 15 0.12
36 1 0.01
37 13 0.10
38 16 0.12
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.45
Consensus pattern (33 bp):
AAAAAATATATATATAGTTTTGAAAATATTTTT
Found at i:45760 original size:66 final size:67
Alignment explanation
Indices: 45677--45830 Score: 197
Period size: 66 Copynumber: 2.3 Consensus size: 67
45667 TTTAAAAAAC
* * *
45677 TATATATAATATATAGTTTT-AAAA-TATTTTTGAAAAAAATATATATATAGTTTTGAAAATATT
1 TATATATATTATATAGTTTTAAAAACAATTTTTG-AAAAAATAT-TACATAGTTTTGAAAATATT
45740 TTT-
64 TTTA
* *
45743 TATATATATTATATAGTTTTAAAAACAATTTTTGAAAATATATTACATGGTTTTGAAAATATTTT
1 TATATATATTATATAGTTTTAAAAACAATTTTTGAAAAAATATTACATAGTTTTGAAAATATTTT
45808 TAA
66 T-A
* *
45811 AAAATATATTATATAGTTTT
1 TATATATATTATATAGTTTT
45831 TTTTAAAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
66 40 0.52
67 12 0.16
68 25 0.32
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.48
Consensus pattern (67 bp):
TATATATATTATATAGTTTTAAAAACAATTTTTGAAAAAATATTACATAGTTTTGAAAATATTTT
TA
Found at i:47033 original size:15 final size:15
Alignment explanation
Indices: 47015--47045 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
47005 TCGGGTTTTG
47015 TATTTTATTAACATT
1 TATTTTATTAACATT
*
47030 TATTTTCTTAACATT
1 TATTTTATTAACATT
47045 T
1 T
47046 TTTAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTTATTAACATT
Found at i:47100 original size:12 final size:13
Alignment explanation
Indices: 47073--47103 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
47063 AAAATTAAAT
47073 TTTTTTCTTTCTA
1 TTTTTTCTTTCTA
47086 TTTTTTCTTTC-A
1 TTTTTTCTTTCTA
47098 TTTTTT
1 TTTTTT
47104 ATTTTAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTCTTTCTA
Found at i:47253 original size:19 final size:19
Alignment explanation
Indices: 47225--47267 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
47215 AAAGATGAAT
*
47225 AATTTGAATTGAAACTTT-A
1 AATTTCAATTGAAA-TTTCA
*
47244 AATTTCAATTTAAATTTCA
1 AATTTCAATTGAAATTTCA
47263 AATTT
1 AATTT
47268 TCGCAATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (19 bp):
AATTTCAATTGAAATTTCA
Found at i:51933 original size:22 final size:22
Alignment explanation
Indices: 51908--51950 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
51898 CGGACCATTT
* *
51908 GAATTCATTTGAAGACGATCGG
1 GAATTAATTTGAAGACAATCGG
*
51930 GAATTAATTTGGAGACAATCG
1 GAATTAATTTGAAGACAATCG
51951 TGCTCAATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.28
Consensus pattern (22 bp):
GAATTAATTTGAAGACAATCGG
Done.