Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008165.1 Hibiscus syriacus cultivar Beakdansim tig00110745_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: 2894944
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2696401 original size:18 final size:18
Alignment explanation
Indices: 2696380--2696416 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2696370 GTAATTGGAG
2696380 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
2696398 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
2696416 T
1 T
2696417 ATATATTTCG
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:2696424 original size:24 final size:24
Alignment explanation
Indices: 2696372--2696418 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2696362 TTTCATATGT
* *
2696372 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
2696396 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
2696419 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:2696718 original size:39 final size:39
Alignment explanation
Indices: 2696675--2696758 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
2696665 TCCGATGCTC
*
2696675 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
2696714 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
2696753 ATCAAA
1 ATCAAA
2696759 TCTACAACTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:2697194 original size:23 final size:23
Alignment explanation
Indices: 2697163--2697235 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
2697153 ATAGGTAAAC
*
2697163 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
2697186 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
2697209 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
2697232 ATAT
1 ATAT
2697236 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:2698666 original size:18 final size:21
Alignment explanation
Indices: 2698634--2698676 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
2698624 TATTTTAAAA
2698634 AAAAGTAAACAT-AAATTTT-
1 AAAAGTAAACATAAAATTTTG
*
2698653 AAAA-TAAACCTAAAATTTTG
1 AAAAGTAAACATAAAATTTTG
2698673 AAAA
1 AAAA
2698677 CCTTCATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 11 0.52
20 4 0.19
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (21 bp):
AAAAGTAAACATAAAATTTTG
Found at i:2699363 original size:17 final size:18
Alignment explanation
Indices: 2699332--2699371 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2699322 TTAATATGAG
2699332 TTATTATAAAATATAATT
1 TTATTATAAAATATAATT
* *
2699350 TTATTAT-AATTATATTT
1 TTATTATAAAATATAATT
2699367 TTATT
1 TTATT
2699372 TGTATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATAAAATATAATT
Found at i:2703518 original size:24 final size:25
Alignment explanation
Indices: 2703491--2703592 Score: 102
Period size: 24 Copynumber: 4.2 Consensus size: 25
2703481 TTGATCCTGT
2703491 TTAGTGCATTCGTT-CACTCCAATA
1 TTAGTGCATTCGTTGCACTCCAATA
* * *
2703515 TTAGTGCATTTGTTGCACTCCTATT
1 TTAGTGCATTCGTTGCACTCCAATA
* * *
2703540 TTAGTGCCTT-GTTGCACCCCAACA
1 TTAGTGCATTCGTTGCACTCCAATA
* * *
2703564 ATAGTGCATTCG-TGCACTCCTATG
1 TTAGTGCATTCGTTGCACTCCAATA
2703588 TTAGT
1 TTAGT
2703593 ACCTATGTGT
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
24 43 0.70
25 18 0.30
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (25 bp):
TTAGTGCATTCGTTGCACTCCAATA
Found at i:2703546 original size:49 final size:48
Alignment explanation
Indices: 2703490--2703592 Score: 127
Period size: 49 Copynumber: 2.1 Consensus size: 48
2703480 ATTGATCCTG
* * * *
2703490 TTTAGTGCATTCGTT-CACTCCAATATTAGTGCATTTGTTGCACTCCTAT
1 TTTAGTGCATT-GTTGCACCCCAACAATAGTGCATTCG-TGCACTCCTAT
*
2703539 TTTAGTGCCTTGTTGCACCCCAACAATAGTGCATTCGTGCACTCCTAT
1 TTTAGTGCATTGTTGCACCCCAACAATAGTGCATTCGTGCACTCCTAT
*
2703587 GTTAGT
1 TTTAGT
2703593 ACCTATGTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
48 19 0.40
49 28 0.60
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (48 bp):
TTTAGTGCATTGTTGCACCCCAACAATAGTGCATTCGTGCACTCCTAT
Found at i:2703676 original size:24 final size:24
Alignment explanation
Indices: 2703565--2703680 Score: 72
Period size: 24 Copynumber: 4.8 Consensus size: 24
2703555 ACCCCAACAA
* * * *
2703565 TAGTGCATTCGTGCACTCCTATGT
1 TAGTACATTCGTGTACTCCTGTAT
* *
2703589 TAGTACCTAT-GTGTACTCATGTAT
1 TAGTACAT-TCGTGTACTCCTGTAT
* ** * * *
2703613 AAGTGTATACGTGCACTCATGTAT
1 TAGTACATTCGTGTACTCCTGTAT
* * * *
2703637 TAGTACCTTTGGGTACTCCTGTGT
1 TAGTACATTCGTGTACTCCTGTAT
2703661 TAGTACATTCGTGTACTCCT
1 TAGTACATTCGTGTACTCCT
2703681 AACACTATAT
Statistics
Matches: 65, Mismatches: 25, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
24 64 0.98
25 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.39
Consensus pattern (24 bp):
TAGTACATTCGTGTACTCCTGTAT
Found at i:2705320 original size:14 final size:14
Alignment explanation
Indices: 2705292--2705338 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2705282 AATAATGTTT
*
2705292 TTTAGG-TTTAGGG
1 TTTAGGATTTAAGG
*
2705305 TTTAGGATTTATGG
1 TTTAGGATTTAAGG
*
2705319 TTTAAGATTTAAGG
1 TTTAGGATTTAAGG
2705333 TTTAGG
1 TTTAGG
2705339 TTTTGAGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 6 0.21
14 23 0.79
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (14 bp):
TTTAGGATTTAAGG
Found at i:2705334 original size:28 final size:27
Alignment explanation
Indices: 2705298--2705351 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
2705288 GTTTTTTAGG
*
2705298 TTTAGGGTTTAGGATTTATG-GTTTAAGA
1 TTTAAGGTTTAGG-TTT-TGAGTTTAAGA
2705326 TTTAAGGTTTAGGTTTTGAGTTTAAG
1 TTTAAGGTTTAGGTTTTGAGTTTAAG
2705352 GTAGAGGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 2 0.08
27 10 0.42
28 12 0.50
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (27 bp):
TTTAAGGTTTAGGTTTTGAGTTTAAGA
Found at i:2711197 original size:17 final size:19
Alignment explanation
Indices: 2711161--2711197 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2711151 ATTATGATCT
2711161 AAACAAATATCATTTACAA
1 AAACAAATATCATTTACAA
*
2711180 AAACATATA-CATTT-CAA
1 AAACAAATATCATTTACAA
2711197 A
1 A
2711198 GCACTTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 5 0.29
19 8 0.47
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (19 bp):
AAACAAATATCATTTACAA
Found at i:2717158 original size:276 final size:276
Alignment explanation
Indices: 2716523--2717354 Score: 1477
Period size: 276 Copynumber: 3.0 Consensus size: 276
2716513 GCATTATATA
* * * *
2716523 ACTTGGTAGATGATAGTGTATGCTTACACTTTGGTGTTACATTATTAGAAGCATCAACGAGCATA
1 ACTTGGTAGACGATAGTGTATGCTTACATTTTGGTGTTACATTATTAGAAGCATCAACCAACATA
* * *
2716588 CTAAACTACATGTTTGTGAAAGAAAATAATATGGAAAAGTTAGAAGTTTGTTACCTTTAACTTAA
66 CTAAACTACATGTTTGTAAAAGAAAATAATATGGAAGAGTTAGAAGTTTGTTACCTTTAACTTAC
* * **
2716653 AAGACACAATAACTCTTTTGCTCAACTTTCCATTGTTTTCTTGTTTCTTTTGCTAAAGCTTAATA
131 AAGACACAATAACTCTTGTGCTCAAATTTCCATTGTTTTCTCCTTTCTTTTGCTAAAGCTTAATA
* * * * * *
2716718 GAATCATAAGATTCTAAAAAAATTAAAGAATGTCCAAAATTCTAAAA-CGATTTAATGATATTAA
196 GACTCGTAAGATTCT-AAAATATTAAACAATGCCCAAAATTCTAAAAGC-ATCTAATGATATTAA
*
2716782 AATAAAATTTTCCTTAAT
259 CATAAAATTTTCCTTAAT
2716800 ACTTGGTAGACGATAGTGTATGCTTACATTTTGGTGTTACATTATTAGAAGCATCAACCAACATA
1 ACTTGGTAGACGATAGTGTATGCTTACATTTTGGTGTTACATTATTAGAAGCATCAACCAACATA
2716865 CTAAACTACATGTTTGTAAAAGAAAATAATATGGAAGAGTTAGAAGTTTGTTACCTTTAACTTAC
66 CTAAACTACATGTTTGTAAAAGAAAATAATATGGAAGAGTTAGAAGTTTGTTACCTTTAACTTAC
2716930 AAGACACAATAACTCTTGTGCTCAAATTTCCATTGTTTTCTCCTTTCTTTTGCTAAAGCTTAATA
131 AAGACACAATAACTCTTGTGCTCAAATTTCCATTGTTTTCTCCTTTCTTTTGCTAAAGCTTAATA
2716995 GACTCGTAAGATTCTAAAATATTAAACAATGCCCAAAATTCTAAAAGCATCTAATGATATTAACA
196 GACTCGTAAGATTCTAAAATATTAAACAATGCCCAAAATTCTAAAAGCATCTAATGATATTAACA
2717060 TAAAATTTTCCTTAAT
261 TAAAATTTTCCTTAAT
2717076 ACTTGGTAGACGATAGTGTATGCTTACATTTTGGTGTTACATTATTAGAAGCATCAACCAACATA
1 ACTTGGTAGACGATAGTGTATGCTTACATTTTGGTGTTACATTATTAGAAGCATCAACCAACATA
2717141 CTAAACTACATGTTTGTAAAAGAAAATAATATGGAAGAGTTAGAAGTTTGTTACCTTTAACTTAC
66 CTAAACTACATGTTTGTAAAAGAAAATAATATGGAAGAGTTAGAAGTTTGTTACCTTTAACTTAC
2717206 AAGACACAATAACTCTTGTGCTCAAATTTCCATTGTTTTCTCCTTTCTTTTGCTAAAGCTTAATA
131 AAGACACAATAACTCTTGTGCTCAAATTTCCATTGTTTTCTCCTTTCTTTTGCTAAAGCTTAATA
2717271 GACTCGTAAGATTCTAAAATATTAAACAATGCCCAAAATTCTAAAAGCATCTAATGATATTAACA
196 GACTCGTAAGATTCTAAAATATTAAACAATGCCCAAAATTCTAAAAGCATCTAATGATATTAACA
2717336 TAAAATTTTCCTTAAT
261 TAAAATTTTCCTTAAT
2717352 ACT
1 ACT
2717355 ATAAATGTTT
Statistics
Matches: 536, Mismatches: 18, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
276 338 0.63
277 198 0.37
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (276 bp):
ACTTGGTAGACGATAGTGTATGCTTACATTTTGGTGTTACATTATTAGAAGCATCAACCAACATA
CTAAACTACATGTTTGTAAAAGAAAATAATATGGAAGAGTTAGAAGTTTGTTACCTTTAACTTAC
AAGACACAATAACTCTTGTGCTCAAATTTCCATTGTTTTCTCCTTTCTTTTGCTAAAGCTTAATA
GACTCGTAAGATTCTAAAATATTAAACAATGCCCAAAATTCTAAAAGCATCTAATGATATTAACA
TAAAATTTTCCTTAAT
Found at i:2720281 original size:23 final size:23
Alignment explanation
Indices: 2720253--2720309 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
2720243 TATCCAAGAA
2720253 TGGATGGAATTCAATTCCCTTAT
1 TGGATGGAATTCAATTCCCTTAT
* *
2720276 TGGATGAAATTCAATTCCCTTGT
1 TGGATGGAATTCAATTCCCTTAT
*
2720299 TGGAGGGAATT
1 TGGATGGAATT
2720310 GAAATTTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (23 bp):
TGGATGGAATTCAATTCCCTTAT
Found at i:2720758 original size:220 final size:224
Alignment explanation
Indices: 2720454--2720867 Score: 649
Period size: 220 Copynumber: 1.9 Consensus size: 224
2720444 GATATTCAGG
* * ** *
2720454 TCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCAACCTGAAAATATATATAATTTTACCTTAT
1 TCGGGTCGAGTTCGGGTTTAAGGTGAAAAATAACCAACCCAAAAAAATATATAATTTTACCTTAT
* *
2720519 ATATTTAAGAATAATTACAATAATACCCCTATATATATAA-TTTTTTCAATTAAGTCACTGTTTT
66 ATATTTAAGAAAAATTACAATAATACCCCTATATATATAATTTTTTTCAATTAAGTCAATGTTTT
2720583 TATTGAATAAAAATAATTTTTTTTATTATTTC-G-G-GTCGGGTCGGATTTCTAATTCATATATT
131 TATTGAATAAAAAT-ATTTTTTTTATTATTTCGGCGTGTCGGGTCGGATTTCTAATTCATATATT
2720645 CGGGTCTGGTCGGGTGAAACTTTATTTTGT
195 CGGGTCTGGTCGGGTGAAACTTTATTTTGT
* **
2720675 TCGGGTCGGGTTCGGGTTTAAGGTGAAAAA-AACCGGCCCAAAAAAATATATAATTTTACCTTAT
1 TCGGGTCGAGTTCGGGTTTAAGGTGAAAAATAACCAACCCAAAAAAATATATAATTTTACCTTAT
* *
2720739 ATATTTAGGAAAAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAATGTTTT
66 ATATTTAAGAAAAATTACAATAATACCCCTATATATATAATTTTTTTCAATTAAGTCAATGTTTT
*
2720804 TATTGAATAAAAATATTTTTTTTATTATTTCGTGTCGTGTCGGGTCGGGTTTCTAATTCATATA
131 TATTGAATAAAAATATTTTTTTTATTATTTCG-G-CGTGTCGGGTCGGATTTCTAATTCATATA
2720868 ATGAATAAAA
Statistics
Matches: 174, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
220 82 0.47
221 65 0.37
222 1 0.01
224 1 0.01
225 25 0.14
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (224 bp):
TCGGGTCGAGTTCGGGTTTAAGGTGAAAAATAACCAACCCAAAAAAATATATAATTTTACCTTAT
ATATTTAAGAAAAATTACAATAATACCCCTATATATATAATTTTTTTCAATTAAGTCAATGTTTT
TATTGAATAAAAATATTTTTTTTATTATTTCGGCGTGTCGGGTCGGATTTCTAATTCATATATTC
GGGTCTGGTCGGGTGAAACTTTATTTTGT
Found at i:2721289 original size:18 final size:18
Alignment explanation
Indices: 2721257--2721302 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
2721247 AAATGGAACT
2721257 AGATTCCAA-TTCTTGAC
1 AGATTCCAATTTCTTGAC
2721274 AGATTCCAATTTCTTGAC
1 AGATTCCAATTTCTTGAC
*
2721292 AGATTCAAATT
1 AGATTCCAATT
2721303 CCCTCATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Consensus pattern (18 bp):
AGATTCCAATTTCTTGAC
Found at i:2725768 original size:19 final size:19
Alignment explanation
Indices: 2725742--2725791 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2725732 CAATGATGGG
2725742 AGAGGAGGAAGGAGA-GGA
1 AGAGGAGGAAGGAGACGGA
* * *
2725760 AGAAGGAGGCAGAAGACGGG
1 AG-AGGAGGAAGGAGACGGA
2725780 AGAGGAGGAAGG
1 AGAGGAGGAAGG
2725792 GGAAGGCAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 2 0.08
19 19 0.76
20 4 0.16
ACGTcount: A:0.42, C:0.04, G:0.54, T:0.00
Consensus pattern (19 bp):
AGAGGAGGAAGGAGACGGA
Found at i:2738925 original size:20 final size:20
Alignment explanation
Indices: 2738859--2738928 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 20
2738849 TCTATGTATT
*
2738859 GATACACTATGATAGTGTACC
1 GATACACTCTG-TAGTGTACC
* * * *
2738880 GATGCATTCCTTGAATGTGTATC
1 GATACACT-C-TGTA-GTGTACC
2738903 GATACACTCTGTAGTGTACC
1 GATACACTCTGTAGTGTACC
2738923 GATACA
1 GATACA
2738929 GTCGTCGGGT
Statistics
Matches: 37, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
20 12 0.32
21 9 0.24
22 2 0.05
23 14 0.38
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (20 bp):
GATACACTCTGTAGTGTACC
Found at i:2739369 original size:20 final size:18
Alignment explanation
Indices: 2739320--2739361 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
2739310 TAAATTTCGA
*
2739320 AATTAATGTTTTTATTTT
1 AATTATTGTTTTTATTTT
2739338 AATTATTGTTTTTGA-TTT
1 AATTATTGTTTTT-ATTTT
2739356 AATTAT
1 AATTAT
2739362 GTTGTTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (18 bp):
AATTATTGTTTTTATTTT
Found at i:2739429 original size:13 final size:13
Alignment explanation
Indices: 2739391--2739432 Score: 61
Period size: 12 Copynumber: 3.4 Consensus size: 13
2739381 TATGTATCAT
2739391 AATT-TTTTCAAA
1 AATTGTTTTCAAA
*
2739403 CATTGTTTTC-AA
1 AATTGTTTTCAAA
2739415 AATTGTTTTCAAA
1 AATTGTTTTCAAA
2739428 AATTG
1 AATTG
2739433 CCCATTAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 14 0.54
13 12 0.46
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.48
Consensus pattern (13 bp):
AATTGTTTTCAAA
Found at i:2749828 original size:29 final size:29
Alignment explanation
Indices: 2749796--2749918 Score: 92
Period size: 29 Copynumber: 4.2 Consensus size: 29
2749786 ATACTCATCT
*
2749796 TGATTCTGCATGAGATTACATTC-TCGTCC
1 TGATTCTGCATGGGATTACA-TCATCGTCC
* * *
2749825 TGATTCTCCATGGGATTATATCATTGTCC
1 TGATTCTGCATGGGATTACATCATCGTCC
* * *
2749854 TGGTTCTGCATGGGATTATATC-TCCATCC
1 TGATTCTGCATGGGATTACATCAT-CGTCC
* * *
2749883 TAATTC-GACATGGGATTATATC-TCCGTCT
1 TGATTCTG-CATGGGATTACATCAT-CGTCC
2749912 TGATTCT
1 TGATTCT
2749919 ATATGTAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 7
0.79 0.13 0.07
Matches are distributed among these distances:
28 4 0.05
29 73 0.95
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (29 bp):
TGATTCTGCATGGGATTACATCATCGTCC
Found at i:2750707 original size:19 final size:19
Alignment explanation
Indices: 2750685--2750784 Score: 80
Period size: 19 Copynumber: 5.3 Consensus size: 19
2750675 AACTTACAGA
*
2750685 TTTTTATTGACTTAGGGTTT
1 TTTTTAGTGACTTAGGG-TT
*
2750705 TTTTTAGTGAGTTAGGGTT
1 TTTTTAGTGACTTAGGGTT
* * *
2750724 TATTGAGTGACTT-GTAGTT
1 TTTTTAGTGACTTAG-GGTT
** *
2750743 TTTTTAACGAGTTAGGG-T
1 TTTTTAGTGACTTAGGGTT
*
2750761 TTTTAAGTGACTTA-GGTT
1 TTTTTAGTGACTTAGGGTT
2750779 TTTTTA
1 TTTTTA
2750785 ATGAAATATA
Statistics
Matches: 60, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
17 2 0.03
18 18 0.30
19 24 0.40
20 16 0.27
ACGTcount: A:0.19, C:0.04, G:0.24, T:0.53
Consensus pattern (19 bp):
TTTTTAGTGACTTAGGGTT
Found at i:2750770 original size:37 final size:37
Alignment explanation
Indices: 2750692--2750785 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 37
2750682 AGATTTTTAT
** *
2750692 TGACTTAGGGTTTTTTTTAGTGAGTTAGGGTTTATTGAG
1 TGACTTA-GG-TTTTTTTAACGAGTTAGGGTTTATTAAG
2750731 TGACTT-GTAGTTTTTTTAACGAGTTAGGGTTT-TTAAG
1 TGACTTAG--GTTTTTTTAACGAGTTAGGGTTTATTAAG
2750768 TGACTTAGGTTTTTTTAA
1 TGACTTAGGTTTTTTTAA
2750786 TGAAATATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
36 10 0.20
37 11 0.22
38 21 0.43
39 7 0.14
ACGTcount: A:0.20, C:0.04, G:0.26, T:0.50
Consensus pattern (37 bp):
TGACTTAGGTTTTTTTAACGAGTTAGGGTTTATTAAG
Found at i:2751031 original size:112 final size:114
Alignment explanation
Indices: 2750806--2751067 Score: 275
Period size: 112 Copynumber: 2.3 Consensus size: 114
2750796 GTTAGATTTG
* * *
2750806 GGTATAATAATAATTTCAAATGACAGAGAATCTTAATTATTCACGTCATTTTCTTTTCAGTGAAA
1 GGTACAATAATAATTTCAAATAACAGAGAATCTTAAATATTCACGTCATTTTCTTTTCAGTGAAA
* *** * * *
2750871 AATTACATTAAATCAAAACTTCCTTTTTACTGCAAGAGAAATTATATCT
66 AATCACATTAAATCAAAACTTCCTTCACAATGCAAAACAAATTATATCT
* * * *
2750920 GAG-ACAATAATAGTTTCAAATAAC-GA-AATCTTAAATATTCACGTCCTTTTCTTTTTAGTTAA
1 G-GTACAATAATAATTTCAAATAACAGAGAATCTTAAATATTCACGTCATTTTCTTTTCAGTGAA
*
2750982 ACATCAC-TTCAAATCAAAACTTCCTTCACAATG-AATAACAAATGT-TATCT
65 AAATCACATT-AAATCAAAACTTCCTTCACAATGCAA-AACAAAT-TATATCT
* * * *
2751032 GGTACACTAATAATTTTAAATAACAGATAGTCTTAA
1 GGTACAATAATAATTTCAAATAACAGAGAATCTTAA
2751068 CTATACAAGT
Statistics
Matches: 122, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
111 5 0.04
112 85 0.70
113 5 0.04
114 26 0.21
115 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (114 bp):
GGTACAATAATAATTTCAAATAACAGAGAATCTTAAATATTCACGTCATTTTCTTTTCAGTGAAA
AATCACATTAAATCAAAACTTCCTTCACAATGCAAAACAAATTATATCT
Found at i:2753522 original size:16 final size:16
Alignment explanation
Indices: 2753501--2753533 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2753491 ATACCCCTAC
2753501 TTGGATTATCGATACT
1 TTGGATTATCGATACT
2753517 TTGGATTATCGATACT
1 TTGGATTATCGATACT
2753533 T
1 T
2753534 CTTTATTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.45
Consensus pattern (16 bp):
TTGGATTATCGATACT
Found at i:2753984 original size:20 final size:20
Alignment explanation
Indices: 2753961--2754030 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
2753951 GATAACAAGA
2753961 CTTCGGTATGGATACCCAAT
1 CTTCGGTATGGATACCCAAT
** *
2753981 CTTCGGTATAAATA-CCAGCT
1 CTTCGGTATGGATACCCA-AT
*
2754001 CATCTGGTATGGATACCCAAT
1 CTTC-GGTATGGATACCCAAT
2754022 CTTCGGTAT
1 CTTCGGTAT
2754031 AAATACTAGC
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 3 0.08
20 21 0.54
21 12 0.31
22 3 0.08
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (20 bp):
CTTCGGTATGGATACCCAAT
Found at i:2754010 original size:21 final size:21
Alignment explanation
Indices: 2753985--2754066 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
2753975 CCCAATCTTC
2753985 GGTATAAATACCAGCTCATCT
1 GGTATAAATACCAGCTCATCT
** * *
2754006 GGTATGGATACCCA-ATCTTC-
1 GGTATAAATA-CCAGCTCATCT
*
2754026 GGTATAAATACTAGCTCATCT
1 GGTATAAATACCAGCTCATCT
* *
2754047 GGTATAGATACCAACTCATC
1 GGTATAAATACCAGCTCATC
2754067 CAATATGGAT
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
19 2 0.04
20 12 0.26
21 29 0.63
22 3 0.07
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (21 bp):
GGTATAAATACCAGCTCATCT
Found at i:2754013 original size:41 final size:41
Alignment explanation
Indices: 2753965--2754058 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2753955 ACAAGACTTC
2753965 GGTATGGATACCCAATCTTCGGTATAAATACCAGCTCATCT
1 GGTATGGATACCCAATCTTCGGTATAAATACCAGCTCATCT
*
2754006 GGTATGGATACCCAATCTTCGGTATAAATACTAGCTCATCT
1 GGTATGGATACCCAATCTTCGGTATAAATACCAGCTCATCT
*
2754047 GGTATAGATACC
1 GGTATGGATACC
2754059 AACTCATCCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (41 bp):
GGTATGGATACCCAATCTTCGGTATAAATACCAGCTCATCT
Found at i:2755818 original size:18 final size:19
Alignment explanation
Indices: 2755782--2755818 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
2755772 AACCTTCATC
2755782 CACACACATTTCATCTTGT
1 CACACACATTTCATCTTGT
2755801 CACA-ACATTCTCAT-TTGT
1 CACACACATT-TCATCTTGT
2755819 GCATACCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (19 bp):
CACACACATTTCATCTTGT
Found at i:2757439 original size:13 final size:13
Alignment explanation
Indices: 2757421--2757447 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2757411 TTCGAGTACC
2757421 ATAATCAAGTCGT
1 ATAATCAAGTCGT
2757434 ATAATCAAGTCGT
1 ATAATCAAGTCGT
2757447 A
1 A
2757448 ACTCCTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATAATCAAGTCGT
Found at i:2757656 original size:25 final size:25
Alignment explanation
Indices: 2757608--2757658 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2757598 AAGATACTTT
* *
2757608 TTTACCATGTTTATGTTATGTTTTA
1 TTTACCATGTTAATATTATGTTTTA
*
2757633 TTTACCATGTTAATAATTATTTTTTA
1 TTTACCATGTTAAT-ATTATGTTTTA
2757659 ATTGTTTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.59
Consensus pattern (25 bp):
TTTACCATGTTAATATTATGTTTTA
Found at i:2762665 original size:29 final size:29
Alignment explanation
Indices: 2762623--2762692 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
2762613 CCTATGTGGG
*
2762623 CCCTTCCTCTCGTTACACCCTCTCTTCTT
1 CCCTTCCCCTCGTTACACCCTCTCTTCTT
2762652 CCCTTCCCCTCGTTACACCCTCTCTTCTT
1 CCCTTCCCCTCGTTACACCCTCTCTTCTT
2762681 CCCTTCCCCTCG
1 CCCTTCCCCTCG
2762693 AAATCGATGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.06, C:0.53, G:0.04, T:0.37
Consensus pattern (29 bp):
CCCTTCCCCTCGTTACACCCTCTCTTCTT
Found at i:2771342 original size:19 final size:19
Alignment explanation
Indices: 2771303--2771343 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2771293 ATATTTTTTT
2771303 ATATTATAAATTAAATATA
1 ATATTATAAATTAAATATA
*
2771322 ATATT-TAATTTAAATATTA
1 ATATTATAAATTAAATA-TA
2771341 ATA
1 ATA
2771344 GAATAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATTATAAATTAAATATA
Found at i:2774772 original size:16 final size:16
Alignment explanation
Indices: 2774751--2774797 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
2774741 AATTTTTGTC
2774751 TTTAAAATAATTTTAA
1 TTTAAAATAATTTTAA
2774767 TTTAAAATAATTTT--
1 TTTAAAATAATTTTAA
*
2774781 TCTTAAAATTATTTTAA
1 T-TTAAAATAATTTTAA
2774798 ACGACATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 1 0.04
15 12 0.44
16 14 0.52
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAAATAATTTTAA
Found at i:2784821 original size:20 final size:20
Alignment explanation
Indices: 2784796--2784838 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2784786 TCTAAAAGAC
*
2784796 CATTTAGAATCATATAGATG
1 CATTTAGAAGCATATAGATG
* *
2784816 CATTTAGAAGCATTTAGTTG
1 CATTTAGAAGCATATAGATG
2784836 CAT
1 CAT
2784839 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (20 bp):
CATTTAGAAGCATATAGATG
Found at i:2802174 original size:256 final size:257
Alignment explanation
Indices: 2801859--2802325 Score: 792
Period size: 256 Copynumber: 1.8 Consensus size: 257
2801849 CACAAAGGAG
*
2801859 AAAAATACCCACCCAAATACCTAATTATTTTTACAGAAAAACTTGCTTAATATAAAAATATATCA
1 AAAAATACCCACCCAAATACCTAATTATTTTTACAGAAAAACTTGCTTAATACAAAAATATATCA
2801924 AAATATACGTAAACTATTATATGATGCATATAAACGCTATATTACACAATAGTTGTAAATGACAT
66 AAATATACGTAAACTATTATATGATGCATATAAACGCTATATTACACAATAGTTGTAAATGACAT
* * * *
2801989 TTTAAATATTTTA-TATTAGATTGTATTATTTTTTTAAAATACTATTTTTCAAATACGAAAATTG
131 TTTAAATATCTTATTATTAGATCGTATAATTTTTTTAAAATACTATTTTTCAAATACGAAAACTG
*
2802053 TTTTAAAAGTATGTGACATCTCTGATTTATGTTTGGGATCGAATACGGGAAAGGAGTGTTAC
196 TTTTAAAAATATGTGACATCTCTGATTTATGTTTGGGATCGAATACGGGAAAGGAGTGTTAC
* *
2802115 AAAAATACCCATCCAAATACCTAATTATTTTTACATAAAAACTTGCTTAATACAAAAATATATCA
1 AAAAATACCCACCCAAATACCTAATTATTTTTACAGAAAAACTTGCTTAATACAAAAATATATCA
* * * *
2802180 AATTATACTTAAACTATTATATGATGCATATAAACGCTATATTACATATTAGTTGTAAATGACAT
66 AAATATACGTAAACTATTATATGATGCATATAAACGCTATATTACACAATAGTTGTAAATGACAT
* * *
2802245 TTTAAATATCTTATTATTAGATCGTATAATTTTTTTTAAATATTGTTTTTCAAATACGAAAACTG
131 TTTAAATATCTTATTATTAGATCGTATAATTTTTTTAAAATACTATTTTTCAAATACGAAAACTG
2802310 TTTTAAAAATATGTGA
196 TTTTAAAAATATGTGA
2802326 TATTAGGGCC
Statistics
Matches: 195, Mismatches: 15, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
256 135 0.69
257 60 0.31
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.38
Consensus pattern (257 bp):
AAAAATACCCACCCAAATACCTAATTATTTTTACAGAAAAACTTGCTTAATACAAAAATATATCA
AAATATACGTAAACTATTATATGATGCATATAAACGCTATATTACACAATAGTTGTAAATGACAT
TTTAAATATCTTATTATTAGATCGTATAATTTTTTTAAAATACTATTTTTCAAATACGAAAACTG
TTTTAAAAATATGTGACATCTCTGATTTATGTTTGGGATCGAATACGGGAAAGGAGTGTTAC
Found at i:2802870 original size:12 final size:10
Alignment explanation
Indices: 2802844--2802872 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2802834 TCACACCAAA
2802844 TTCTCTCAAT
1 TTCTCTCAAT
2802854 TTCTCTCAAT
1 TTCTCTCAAT
2802864 TTCTCTCAA
1 TTCTCTCAA
2802873 ATACTCTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.48
Consensus pattern (10 bp):
TTCTCTCAAT
Found at i:2802879 original size:10 final size:10
Alignment explanation
Indices: 2802840--2802880 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
2802830 TTCATCACAC
2802840 CAAATTCTCT
1 CAAATTCTCT
*
2802850 CAATTTCTCT
1 CAAATTCTCT
*
2802860 CAATTTCTCT
1 CAAATTCTCT
*
2802870 CAAATACTCT
1 CAAATTCTCT
2802880 C
1 C
2802881 TCTGTTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:2802950 original size:17 final size:18
Alignment explanation
Indices: 2802918--2802953 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
2802908 TTTAATATTA
2802918 TTTATTTAAGTATTTTAC
1 TTTATTTAAGTATTTTAC
2802936 TTTATTTAA-TATTTTAC
1 TTTATTTAAGTATTTTAC
2802953 T
1 T
2802954 AATATAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTATTTAAGTATTTTAC
Found at i:2808915 original size:20 final size:21
Alignment explanation
Indices: 2808892--2808934 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
2808882 ATTAATAAGA
2808892 AAAAATAAAA-AAA-ACAACAT
1 AAAAATAAAATAAATA-AACAT
2808912 -AAAATAAAATAAATAAACAT
1 AAAAATAAAATAAATAAACAT
2808932 AAA
1 AAA
2808935 TATGAGGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
19 9 0.45
20 8 0.40
21 3 0.15
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (21 bp):
AAAAATAAAATAAATAAACAT
Found at i:2808917 original size:19 final size:20
Alignment explanation
Indices: 2808871--2808934 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
2808861 ATTTAAAAAA
*
2808871 ATAAAATAACAATTAATAAGA-
1 ATAAAATAA-AATAAATAA-AC
2808892 A-AAAATAAAA-AAA-ACAAC
1 ATAAAATAAAATAAATA-AAC
2808910 ATAAAATAAAATAAATAAAC
1 ATAAAATAAAATAAATAAAC
2808930 ATAAA
1 ATAAA
2808935 TATGAGGACC
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
17 2 0.05
18 4 0.11
19 11 0.30
20 18 0.49
21 2 0.05
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.17
Consensus pattern (20 bp):
ATAAAATAAAATAAATAAAC
Found at i:2810476 original size:23 final size:24
Alignment explanation
Indices: 2810447--2810495 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
2810437 AAGGACATAC
*
2810447 AGTGGTCCTTCGGGAC-ATTTCAT
1 AGTGGTCCTTCGGGACAAATTCAT
2810470 AGTGGTCCTTCGGGACAAATTCAT
1 AGTGGTCCTTCGGGACAAATTCAT
2810494 AG
1 AG
2810496 CCCCTAGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (24 bp):
AGTGGTCCTTCGGGACAAATTCAT
Found at i:2812821 original size:18 final size:18
Alignment explanation
Indices: 2812798--2812850 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
2812788 AGGGATTATC
2812798 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
2812816 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
2812834 AATGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
2812851 AATATTCAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:2825508 original size:52 final size:52
Alignment explanation
Indices: 2825361--2825557 Score: 227
Period size: 52 Copynumber: 3.8 Consensus size: 52
2825351 CGTTCTTGTA
* * * ** *
2825361 CATTCATAGGGGGATTTCATACTCATGCTGCAAATTGGTTCAGTCACTTGCG
1 CATTCATAGGGGGATGTCAAACTGATGCAACAAATTGGTCCAGTCACTTGCG
** **
2825413 CATTCATAGATGG-TGTTGAACTGATGCAACAAATTGGTCCAGTCACTTGCG
1 CATTCATAGGGGGATGTCAAACTGATGCAACAAATTGGTCCAGTCACTTGCG
* * *
2825464 CATTCATAGGGGGATGTCAAACTAATGCAACAAATTGGTCCAGTCGCTTGTG
1 CATTCATAGGGGGATGTCAAACTGATGCAACAAATTGGTCCAGTCACTTGCG
* * *
2825516 CATTCAT-TGCGGAGTGTCAAACTGATGCAGCAAATTGGTCCA
1 CATTCATAGGGGGA-TGTCAAACTGATGCAACAAATTGGTCCA
2825558 ATCCCCCCGC
Statistics
Matches: 122, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
51 45 0.37
52 77 0.63
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (52 bp):
CATTCATAGGGGGATGTCAAACTGATGCAACAAATTGGTCCAGTCACTTGCG
Found at i:2825954 original size:2 final size:2
Alignment explanation
Indices: 2825943--2825994 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
2825933 TTAAAATTGG
2825943 TA TA -A TA TA TA 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 TA TA TA TA TA TA
2825984 TA TA TA TA TA T
1 TA TA TA TA TA T
2825995 TTGGCTCTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2827021 original size:25 final size:25
Alignment explanation
Indices: 2826987--2827040 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
2826977 CACACTAACA
2826987 ACTAGAATCATACTAAAAGTGTATC
1 ACTAGAATCATACTAAAAGTGTATC
2827012 ACTAGAATCATACTAAAAGTGTATC
1 ACTAGAATCATACTAAAAGTGTATC
2827037 ACTA
1 ACTA
2827041 AAATGGTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (25 bp):
ACTAGAATCATACTAAAAGTGTATC
Found at i:2827042 original size:14 final size:14
Alignment explanation
Indices: 2826998--2827043 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
2826988 CTAGAATCAT
2826998 ACTAAAAGTGTATC
1 ACTAAAAGTGTATC
* *
2827012 ACTAGAA-T-CAT-
1 ACTAAAAGTGTATC
2827023 ACTAAAAGTGTATC
1 ACTAAAAGTGTATC
2827037 ACTAAAA
1 ACTAAAA
2827044 TGGTAGATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
11 6 0.24
12 3 0.12
13 3 0.12
14 13 0.52
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (14 bp):
ACTAAAAGTGTATC
Found at i:2827602 original size:22 final size:22
Alignment explanation
Indices: 2827572--2827621 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
2827562 TGAAGGGTCA
* *
2827572 TATCCATACTCTCATGCTATAG
1 TATCAATACTCCCATGCTATAG
2827594 TATCAATACTCCCATGCTATAG
1 TATCAATACTCCCATGCTATAG
2827616 TATCAA
1 TATCAA
2827622 CATTGACTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (22 bp):
TATCAATACTCCCATGCTATAG
Found at i:2831535 original size:20 final size:20
Alignment explanation
Indices: 2831510--2831565 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
2831500 CCACCCCATT
2831510 TGGTATCGATACTCCTTTTG
1 TGGTATCGATACTCCTTTTG
2831530 TGGTATCGATACTCCTTTTG
1 TGGTATCGATACTCCTTTTG
2831550 TGGGTATCGATACTCC
1 T-GGTATCGATACTCC
2831566 CCTTATGGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 21 0.60
21 14 0.40
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.41
Consensus pattern (20 bp):
TGGTATCGATACTCCTTTTG
Found at i:2831557 original size:21 final size:21
Alignment explanation
Indices: 2831511--2831584 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 21
2831501 CACCCCATTT
2831511 GGTATCGATACTCCTTTTGT-
1 GGTATCGATACTCCTTTTGTG
2831531 GGTATCGATACTCCTTTTGTG
1 GGTATCGATACTCCTTTTGTG
** *
2831552 GGTATCGATACTCCCCTTATG
1 GGTATCGATACTCCTTTTGTG
*
2831573 GGTATCAATACT
1 GGTATCGATACT
2831585 GTAATGCCCC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 20 0.41
21 29 0.59
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (21 bp):
GGTATCGATACTCCTTTTGTG
Found at i:2832495 original size:22 final size:22
Alignment explanation
Indices: 2832467--2832533 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
2832457 CCGGTAGGGG
2832467 GTATCGGTACCATAGTAGGGTA
1 GTATCGGTACCATAGTAGGGTA
2832489 GTATCGGTACCATAGTAGGGTA
1 GTATCGGTACCATAGTAGGGTA
** *
2832511 GTATCAATACCATGGTAAGGGTA
1 GTATCGGTACCATAGT-AGGGTA
2832534 TCGATACTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 35 0.85
23 6 0.15
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (22 bp):
GTATCGGTACCATAGTAGGGTA
Found at i:2832609 original size:117 final size:116
Alignment explanation
Indices: 2832389--2832641 Score: 285
Period size: 117 Copynumber: 2.2 Consensus size: 116
2832379 GATACCGATG
** * *
2832389 AGGTAGTATCGGTACCATGGAAAAGGTATCGATACCAAGAAACATCGAATCTAATTTTGGTATCG
1 AGGTAGTATCAATACCATGGAAAAGGTATCGATACCAAGAAACATCGAACCTAATTTTGGTATCA
* * * * * * *
2832454 ATACCGGTAGGGGGTATCGGTACCATAGTAGGGTAGTATCGGTACCATAGT
66 ATACCGGAAGGGGGTATCAGTACCATAGAAGAGAAGTATCAGTACCAGAGT
* * * * * *
2832505 AGGGTAGTATCAATACCATGGTAAGGGTATCGATACTAGGCAACATCGAACCTATTTTTGGTATC
1 A-GGTAGTATCAATACCATGGAAAAGGTATCGATACCAAGAAACATCGAACCTAATTTTGGTATC
* * *
2832570 AATACTC-GAATGGGGTATCAGTACCATAGAATAGAAGTATCAGTACCAGGGT
65 AATAC-CGGAAGGGGGTATCAGTACCATAGAAGAGAAGTATCAGTACCAGAGT
*
2832622 A-GTAGTATCAATACTATGGA
1 AGGTAGTATCAATACCATGGA
2832642 GCCAGAAATA
Statistics
Matches: 113, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
115 17 0.15
116 1 0.01
117 94 0.83
118 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.26
Consensus pattern (116 bp):
AGGTAGTATCAATACCATGGAAAAGGTATCGATACCAAGAAACATCGAACCTAATTTTGGTATCA
ATACCGGAAGGGGGTATCAGTACCATAGAAGAGAAGTATCAGTACCAGAGT
Found at i:2833025 original size:54 final size:54
Alignment explanation
Indices: 2832954--2833549 Score: 777
Period size: 54 Copynumber: 11.3 Consensus size: 54
2832944 TTACCAAATA
* * *
2832954 GGCATTAAGTGTGCATTTCACGGAATTCATCTTATGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* ** * *
2833008 GGCACTAAGAGTGCATTTCAAAGAATTCAACCTACGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
2833062 -G-AC--A-----CTTTTCACGGAATTCATCCTAAGTGGATGAATAATCGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
2833107 GGCACTAAGAGTGCATTTCACGGAATTCATCATATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
2833161 GGCACTTAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAATCATTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
2833215 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACAGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
2833269 AGCACTAAGTGTGCATTTCACGG-A---ATCCTATGTGGATGAATTATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
2833319 GTCACTAAGTGTCCATTTCACGGAATTCATCCTATGTGGATTAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
2833373 GACACTAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
2833427 GGCACTAAATATGCATTTCACGGAATTCATCCTCTGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
2833481 GGCACTAAATGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACCATTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
2833535 GGCACTATGTGTGCA
1 GGCACTAAGTGTGCA
2833550 AAGCACGAAA
Statistics
Matches: 470, Mismatches: 59, Indels: 26
0.85 0.11 0.05
Matches are distributed among these distances:
45 34 0.07
46 1 0.00
47 2 0.00
49 1 0.00
50 44 0.09
51 1 0.00
52 2 0.00
53 2 0.00
54 383 0.81
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:2833388 original size:212 final size:210
Alignment explanation
Indices: 2832959--2833541 Score: 725
Period size: 212 Copynumber: 2.8 Consensus size: 210
2832949 AAATAGGCAT
* *
2832959 TAAGTGTGCATTTCACGGAATTCATCTTATGTGGATGAATAACTGTTTCGGCACTAAGAGTGCAT
1 TAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACT-TTT-GGCACTAAGTGTGCAT
** * * *
2833024 TTCAAAGAATTCAACCTACGTGGATGAATAACCGTTTCG-AC--A----CTTTTCACGGAATTCA
64 TTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGCACTAATGTGCATTTCACGGAA-T-A
* * *
2833082 TCCTAAGTGGATGAATAATCGTTTTGGCACTAAGAGTGCATTTCACGGAATTCATCATATGTGGA
127 TCCTATGTGGATGAATAATCGTTTCGGCACTAAGAGTCCATTTCACGGAATTCATCATATGTGGA
*
2833147 TGAATAACCGTTTCGGCAC
192 TGAATAACCGTTTCGACAC
* * *
2833166 TTAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAATCATTTTGGCACTAAGTGTGCAT
1 TAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAA-C-TTTTGGCACTAAGTGTGCAT
*
2833231 TTCACGGAATTCATCCTATGTGGATGAATAACAGTTTCAGCACTAAGTGTGCATTTCACGG-A-A
64 TTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC-GCACTAA-TGTGCATTTCACGGAATA
* * * *
2833294 TCCTATGTGGATGAATTATCGTTTCGTCACTAAGTGTCCATTTCACGGAATTCATCCTATGTGGA
127 TCCTATGTGGATGAATAATCGTTTCGGCACTAAGAGTCCATTTCACGGAATTCATCATATGTGGA
*
2833359 TTAATAACCGTTTCGACAC
192 TGAATAACCGTTTCGACAC
* * *
2833378 TAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACCGTTTCGGCACTAAATATGCAT
1 TAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAA-C-TTTTGGCACTAAGTGTGCAT
* *
2833443 TTCACGGAATTCATCCTCTGTGGATGAATAACCGTTTCGGCACTAAATGTGCATTTCATGGAATT
64 TTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC-GCACT-AATGTGCATTTCACGGAA-T
* * *
2833508 CATCCTATGTGGATGAATAACCATTTTGGCACTA
126 -ATCCTATGTGGATGAATAATCGTTTCGGCACTA
2833542 TGTGTGCAAA
Statistics
Matches: 324, Mismatches: 36, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
207 87 0.27
208 5 0.02
209 3 0.01
211 1 0.00
212 187 0.58
213 3 0.01
215 1 0.00
216 37 0.11
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (210 bp):
TAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACTTTTGGCACTAAGTGTGCATTT
CACGGAATTCATCCTATGTGGATGAATAACCGTTTCGCACTAATGTGCATTTCACGGAATATCCT
ATGTGGATGAATAATCGTTTCGGCACTAAGAGTCCATTTCACGGAATTCATCATATGTGGATGAA
TAACCGTTTCGACAC
Found at i:2833549 original size:266 final size:266
Alignment explanation
Indices: 2832954--2833528 Score: 799
Period size: 266 Copynumber: 2.2 Consensus size: 266
2832944 TTACCAAATA
* * * * * *
2832954 GGCATTAAGTGTGCATTTCACGGAATTCATCTTATGTGGATGAATAACTGTTTCGGCACTAAGAG
1 GGCACTAAATGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACAGTTTCAGCACTAAGTG
** * * * *
2833019 TGCATTTCAAAGAATTCAACCTACGTGGATGAATAACCGTTTCG--AC--A-----CTTTTCACG
66 TGCATTTCACGGAA-T---CCTATGTGGATGAATTATCGTTTCGTCACTAAGTGTCCATTTCACG
* * *
2833075 GAATTCATCCTAAGTGGATGAATAATCGTTTTGGCACTAAGAGTGCATTTCACGGAATTCATCAT
127 GAATTCATCCTAAGTGGATGAATAACCGTTTCGACACTAAGAGTGCATTTCACGGAATTCATCAT
* * *
2833140 ATGTGGATGAATAACCGTTTCGGCACTTAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAA
192 ATGTGGATGAATAACCGTTTCGGCACTAAATATGCATTTCACAGAATTCATCCTATGTGGATGAA
* *
2833205 TAATCATTTT
257 TAACCATTTC
*
2833215 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACAGTTTCAGCACTAAGTG
1 GGCACTAAATGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACAGTTTCAGCACTAAGTG
2833280 TGCATTTCACGGAATCCTATGTGGATGAATTATCGTTTCGTCACTAAGTGTCCATTTCACGGAAT
66 TGCATTTCACGGAATCCTATGTGGATGAATTATCGTTTCGTCACTAAGTGTCCATTTCACGGAAT
* * *
2833345 TCATCCTATGTGGATTAATAACCGTTTCGACACTAAGTGTGCATTTCACGGAATTCATCATATGT
131 TCATCCTAAGTGGATGAATAACCGTTTCGACACTAAGAGTGCATTTCACGGAATTCATCATATGT
* *
2833410 GGATGAATAACCGTTTCGGCACTAAATATGCATTTCACGGAATTCATCCTCTGTGGATGAATAAC
196 GGATGAATAACCGTTTCGGCACTAAATATGCATTTCACAGAATTCATCCTATGTGGATGAATAAC
*
2833475 CGTTTC
261 CATTTC
*
2833481 GGCACTAAATGTGCATTTCATGGAATTCATCCTATGTGGATGAATAAC
1 GGCACTAAATGTGCATTTCACGGAATTCATCCTATGTGGATGAATAAC
2833529 CATTTTGGCA
Statistics
Matches: 278, Mismatches: 27, Indels: 13
0.87 0.08 0.04
Matches are distributed among these distances:
257 22 0.08
259 2 0.01
260 1 0.00
261 73 0.26
266 180 0.65
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (266 bp):
GGCACTAAATGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACAGTTTCAGCACTAAGTG
TGCATTTCACGGAATCCTATGTGGATGAATTATCGTTTCGTCACTAAGTGTCCATTTCACGGAAT
TCATCCTAAGTGGATGAATAACCGTTTCGACACTAAGAGTGCATTTCACGGAATTCATCATATGT
GGATGAATAACCGTTTCGGCACTAAATATGCATTTCACAGAATTCATCCTATGTGGATGAATAAC
CATTTC
Found at i:2836493 original size:26 final size:26
Alignment explanation
Indices: 2836456--2836509 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
2836446 ACCAAAGTTC
* *
2836456 TAATACATATAAGATTGTGCCCACCA
1 TAATACACATAAGATCGTGCCCACCA
*
2836482 TAATACACATAAGGTCGTGCCCACCA
1 TAATACACATAAGATCGTGCCCACCA
2836508 TA
1 TA
2836510 TGCACTTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (26 bp):
TAATACACATAAGATCGTGCCCACCA
Found at i:2840346 original size:3 final size:3
Alignment explanation
Indices: 2840333--2840406 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
2840323 CAATATTAGC
*
2840333 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2840381 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2840407 TTAGACATCA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2841480 original size:26 final size:26
Alignment explanation
Indices: 2841444--2841493 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
2841434 ACCAAAGGGT
*
2841444 TAATACGCATAAGGTCGTGCCCACCA
1 TAATACACATAAGGTCGTGCCCACCA
*
2841470 TAATACACATAAGGTTGTGCCCAC
1 TAATACACATAAGGTCGTGCCCAC
2841494 TATATGCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (26 bp):
TAATACACATAAGGTCGTGCCCACCA
Found at i:2845009 original size:19 final size:19
Alignment explanation
Indices: 2844982--2845018 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2844972 TGGGTTCGAG
*
2844982 TATCGATACTAGATGAATA
1 TATCAATACTAGATGAATA
2845001 TATCAATACTAGATGAAT
1 TATCAATACTAGATGAAT
2845019 TAGGATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (19 bp):
TATCAATACTAGATGAATA
Found at i:2867271 original size:23 final size:24
Alignment explanation
Indices: 2867240--2867285 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2867230 GATGGCTCGA
*
2867240 TCGGCTCGGTTCCGTTCAGATGGC
1 TCGGCTCGGCTCCGTTCAGATGGC
*
2867264 TCGG-TCGGCTCGGTTCAGATGG
1 TCGGCTCGGCTCCGTTCAGATGG
2867286 TCCAGTCGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.09, C:0.26, G:0.37, T:0.28
Consensus pattern (24 bp):
TCGGCTCGGCTCCGTTCAGATGGC
Found at i:2869295 original size:36 final size:36
Alignment explanation
Indices: 2869255--2869325 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
2869245 TGGTCAACTC
* * *
2869255 GGCTCGGTCAGACGGCTTGGTCGGCTCGGTTCAGAT
1 GGCTCAGTCAGACGGCTCGGTCGGCTCGATTCAGAT
2869291 GGCTCAGTCAGACGGCTCGGTCGGCTCGATTCAGA
1 GGCTCAGTCAGACGGCTCGGTCGGCTCGATTCAGA
2869326 CAGTCTAGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.14, C:0.27, G:0.37, T:0.23
Consensus pattern (36 bp):
GGCTCAGTCAGACGGCTCGGTCGGCTCGATTCAGAT
Found at i:2870830 original size:22 final size:22
Alignment explanation
Indices: 2870780--2870830 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2870770 ACTGTTCAAC
* *
2870780 TCAGCTTGGTCAGATGGCTCAG
1 TCAGCTCGGTCAGACGGCTCAG
*
2870802 TCGGCTCGGTCAGACGGCT-AGG
1 TCAGCTCGGTCAGACGGCTCA-G
2870824 TCAGCTC
1 TCAGCTC
2870831 AGTTTAGACG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.16, C:0.27, G:0.33, T:0.24
Consensus pattern (22 bp):
TCAGCTCGGTCAGACGGCTCAG
Found at i:2872334 original size:20 final size:18
Alignment explanation
Indices: 2872309--2872357 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
2872299 TAGTTCATTA
2872309 TCTTAATTTTATCTTTATTT
1 TCTTAATTTTA-CTTT-TTT
*
2872329 TCTTAATGTTACTTTTTT
1 TCTTAATTTTACTTTTTT
*
2872347 TGTTCAATTTT
1 TCTT-AATTTT
2872358 CTAGTAAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 9 0.36
20 10 0.40
ACGTcount: A:0.18, C:0.10, G:0.04, T:0.67
Consensus pattern (18 bp):
TCTTAATTTTACTTTTTT
Found at i:2878979 original size:13 final size:13
Alignment explanation
Indices: 2878961--2878987 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2878951 CCATCAAAAT
2878961 TTAAGCCTCCCTA
1 TTAAGCCTCCCTA
2878974 TTAAGCCTCCCTA
1 TTAAGCCTCCCTA
2878987 T
1 T
2878988 GAAATAGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.37, G:0.07, T:0.33
Consensus pattern (13 bp):
TTAAGCCTCCCTA
Found at i:2890081 original size:52 final size:52
Alignment explanation
Indices: 2890003--2890129 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
2889993 AGAAAAAAGG
*
2890003 CTATCTCTTGATGCTCTTACAGTGCCAAGACATATTTTACCAAAACCCAAGA
1 CTATCTCTCGATGCTCTTACAGTGCCAAGACATATTTTACCAAAACCCAAGA
* *
2890055 CTATCTCTCGATGCTCTTACAGTGCCAAGACATGTTTTACCAAAACCCAAGG
1 CTATCTCTCGATGCTCTTACAGTGCCAAGACATATTTTACCAAAACCCAAGA
*
2890107 CTATCTCTCGA--CGCTTACAGTGC
1 CTATCTCTCGATGCTCTTACAGTGC
2890130 TAAGGTAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 11 0.15
52 60 0.85
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.28
Consensus pattern (52 bp):
CTATCTCTCGATGCTCTTACAGTGCCAAGACATATTTTACCAAAACCCAAGA
Done.