Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007916.1 Hibiscus syriacus cultivar Beakdansim tig00110319_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: 3725575
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 16
Found at i:2659237 original size:21 final size:21
Alignment explanation
Indices: 2659211--2659250 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2659201 AGAATGGGGG
*
2659211 GAATCGGTACCCCTTCATAGA
1 GAATCGATACCCCTTCATAGA
2659232 GAATCGATACCCCTTCATA
1 GAATCGATACCCCTTCATA
2659251 ATATTCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (21 bp):
GAATCGATACCCCTTCATAGA
Found at i:2659366 original size:19 final size:19
Alignment explanation
Indices: 2659342--2659412 Score: 80
Period size: 19 Copynumber: 3.9 Consensus size: 19
2659332 AAACCATGCA
2659342 GGGGGAATCTGTACCCCTG
1 GGGGGAATCTGTACCCCTG
*
2659361 GGGGGAATCTGT-TCCC--
1 GGGGGAATCTGTACCCCTG
2659377 -GGGGAATC-GATACCCCCTG
1 GGGGGAATCTG-TA-CCCCTG
2659396 GGGGGAATCTGTACCCC
1 GGGGGAATCTGTACCCC
2659413 CTGGACAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
14 1 0.02
15 9 0.21
17 3 0.07
18 3 0.07
19 16 0.37
20 10 0.23
21 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.35, T:0.20
Consensus pattern (19 bp):
GGGGGAATCTGTACCCCTG
Found at i:2659402 original size:20 final size:20
Alignment explanation
Indices: 2659377--2659416 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2659367 ATCTGTTCCC
2659377 GGGGAATC-GATACCCCCTGG
1 GGGGAATCTG-TACCCCCTGG
2659397 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
2659417 ACAATATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.17, C:0.30, G:0.35, T:0.17
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTGG
Found at i:2664268 original size:53 final size:52
Alignment explanation
Indices: 2664200--2664326 Score: 175
Period size: 53 Copynumber: 2.4 Consensus size: 52
2664190 TTCATATAAG
*
2664200 GTCGAATGCAGGTCGGGTTCATTTTGACATTATTATGTTCAATTCAGATTCAA
1 GTCGAATGCAGGTCGGGTTCA-TTTGACATTATCATGTTCAATTCAGATTCAA
* *
2664253 GTCGAATGCAGGTCGGGTTCGATTTGATATTATCATGTTCAATTCAGATTTAA
1 GTCGAATGCAGGTCGGGTTC-ATTTGACATTATCATGTTCAATTCAGATTCAA
* *
2664306 GTCG-TTCACAGGTCGGGTTCA
1 GTCGAAT-GCAGGTCGGGTTCA
2664327 AATCCAAAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
52 2 0.03
53 64 0.96
54 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (52 bp):
GTCGAATGCAGGTCGGGTTCATTTGACATTATCATGTTCAATTCAGATTCAA
Found at i:2667276 original size:7 final size:6
Alignment explanation
Indices: 2667249--2667302 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
2667239 AAGAAAAATA
* * *
2667249 AAATTT AAATACT AAAATA AAATTT AAATTT AAATTT AAATATT AAATATT
1 AAATTT AAAT-TT AAATTT AAATTT AAATTT AAATTT AAAT-TT AAAT-TT
2667300 AAA
1 AAA
2667303 CGTATAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
6 24 0.60
7 16 0.40
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (6 bp):
AAATTT
Found at i:2667288 original size:19 final size:19
Alignment explanation
Indices: 2667243--2667302 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
2667233 ATTTTGAAGA
*
2667243 AAAATAAAATTTAAATACT
1 AAAATAAAATTTAAATATT
2667262 AAAATAAAATTTAAAT-TT
1 AAAATAAAATTTAAATATT
* *
2667280 AAATTTAAATATTAAATATT
1 AAAATAAAAT-TTAAATATT
2667300 AAA
1 AAA
2667303 CGTATAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.25
19 22 0.61
20 5 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATAAAATTTAAATATT
Found at i:2675125 original size:50 final size:51
Alignment explanation
Indices: 2674999--2675125 Score: 116
Period size: 50 Copynumber: 2.5 Consensus size: 51
2674989 GTTGATGAGT
* * * *
2674999 TTTTTAAAAATTATTTATTACAAATATTAAATACAATAAATAATATTATTTA
1 TTTTTAAATATTATTT-TTATAATTTTTAAATACAATAAATAATATTATTTA
** * * * * *
2675051 TCATAAAAT-TTAATATTATTATTTTTAAA-ATAATAAAATAAT-TTATTTA
1 TTTTTAAATATTATTTTTATAATTTTTAAATACAAT-AAATAATATTATTTA
2675100 TTTTTAAATATTATTTTTATAATTTT
1 TTTTTAAATATTATTTTTATAATTTT
2675126 ATTAATAAAA
Statistics
Matches: 56, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
49 17 0.30
50 30 0.54
51 4 0.07
52 5 0.09
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (51 bp):
TTTTTAAATATTATTTTTATAATTTTTAAATACAATAAATAATATTATTTA
Found at i:2675184 original size:31 final size:29
Alignment explanation
Indices: 2675116--2675185 Score: 70
Period size: 31 Copynumber: 2.2 Consensus size: 29
2675106 AATATTATTT
*
2675116 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
2675146 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
2675179 TTATATT
1 TTATATT
2675186 AATTATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 14 0.41
32 5 0.15
33 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:2675272 original size:24 final size:24
Alignment explanation
Indices: 2675240--2675292 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2675230 ATTAATTAGT
*
2675240 ATATT-TTAAA-TATCTTTATTAAA
1 ATATTATTAAATTAT-TATATTAAA
*
2675263 ATATTATTAAATTATTATATTAAT
1 ATATTATTAAATTATTATATTAAA
2675287 ATATTA
1 ATATTA
2675293 ATATTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 5 0.19
24 18 0.69
25 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATTATTAAATTATTATATTAAA
Found at i:2675285 original size:13 final size:15
Alignment explanation
Indices: 2675267--2675310 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2675257 ATTAAAATAT
2675267 TATTAAAT-TATT-A
1 TATTAAATATATTAA
2675280 TATT-AATATATTAA
1 TATTAAATATATTAA
*
2675294 TATTAAATATATAAA
1 TATTAAATATATTAA
2675309 TA
1 TA
2675311 ATATTATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 3 0.11
13 8 0.30
14 5 0.19
15 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTAAATATATTAA
Found at i:2675289 original size:8 final size:8
Alignment explanation
Indices: 2675256--2675343 Score: 54
Period size: 8 Copynumber: 10.6 Consensus size: 8
2675246 TAAATATCTT
*
2675256 TATTAAAA
1 TATTAATA
*
2675264 TATTATTA
1 TATTAATA
* *
2675272 AATTATTA
1 TATTAATA
2675280 TATTAATA
1 TATTAATA
2675288 TATTAATA
1 TATTAATA
*
2675296 T-TAAATA
1 TATTAATA
*
2675303 TATAAATAA
1 TATTAAT-A
*
2675312 TATTATTCA
1 TATTAAT-A
2675321 CTATTAATA
1 -TATTAATA
2675330 -ATTTAATAA
1 TA-TTAAT-A
2675339 TATTA
1 TATTA
2675344 TTTCTATGAA
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
7 7 0.11
8 38 0.59
9 12 0.19
10 7 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (8 bp):
TATTAATA
Found at i:2675318 original size:27 final size:27
Alignment explanation
Indices: 2675283--2675368 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
2675273 ATTATTATAT
*
2675283 TAATA-TATTAATATTAAATATATAAA
1 TAATATTATTACTATTAAATATATAAA
*
2675309 TAATATTATTCACTATT-AATA-ATTTAA
1 TAATATTATT-ACTATTAAATATA-TAAA
* *
2675336 TAATATTATTTCTATGAAAT-TAATAAA
1 TAATATTATTACTATTAAATAT-ATAAA
2675363 TAATAT
1 TAATAT
2675369 AAATTTTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
26 10 0.20
27 33 0.67
28 6 0.12
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.45
Consensus pattern (27 bp):
TAATATTATTACTATTAAATATATAAA
Found at i:2675398 original size:21 final size:22
Alignment explanation
Indices: 2675354--2675412 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
2675344 TTTCTATGAA
*
2675354 ATTAATAAATAATATAAATTTT
1 ATTAATAAATAATATAAATATT
* *
2675376 ATTAATAATTTAT-TAAATATT
1 ATTAATAAATAATATAAATATT
*
2675397 ATTAAAAAAATAATAT
1 ATT-AATAAATAATAT
2675413 CTTATATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 10 0.34
22 18 0.62
23 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTAATAAATAATATAAATATT
Found at i:2675495 original size:29 final size:29
Alignment explanation
Indices: 2675443--2675499 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2675433 TTGATTATTG
2675443 TATTATAATATTAAAATATAATATTTTAT
1 TATTATAATATTAAAATATAATATTTTAT
2675472 TATTATAAATATTAATAA-AT-ATATTTTA
1 TATTAT-AATATTAA-AATATAATATTTTA
2675500 AATATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 14 0.54
30 10 0.38
31 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TATTATAATATTAAAATATAATATTTTAT
Found at i:2676004 original size:15 final size:15
Alignment explanation
Indices: 2675984--2676013 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2675974 TATTTTAATG
2675984 TCGTACATGAACTAT
1 TCGTACATGAACTAT
2675999 TCGTACATGAACTAT
1 TCGTACATGAACTAT
2676014 AATGACTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (15 bp):
TCGTACATGAACTAT
Found at i:2679379 original size:43 final size:42
Alignment explanation
Indices: 2679242--2679457 Score: 175
Period size: 43 Copynumber: 5.1 Consensus size: 42
2679232 TTTGTTGATG
* * * *
2679242 TTCA-ACAAACGCCGCAAAAGGTATTGATATTTAGCGGCGTT
1 TTCACACAAACGCCACAATAGGTGTTGATATTTAGCGGCATT
* * *
2679283 TTGCAGAAAAACTCCACAATAGGTGTTGATATTTAGCGGCATT
1 TT-CACACAAACGCCACAATAGGTGTTGATATTTAGCGGCATT
* * * *
2679326 TGGCAGACAAACGCCACAATAGGTGTTGATGTTTAGCGACATT
1 T-TCACACAAACGCCACAATAGGTGTTGATATTTAGCGGCATT
* * * * * *
2679369 TTCTTCACAAACGCCGCAGTAGGTGTTGATTTTTATCGGCGTT
1 TTC-ACACAAACGCCACAATAGGTGTTGATATTTAGCGGCATT
* * * * *
2679412 TTCCCCACAAACGCCACAGA-AGATGTTGAGATTTGGCGGCGTT
1 TT-CACACAAACGCCACA-ATAGGTGTTGATATTTAGCGGCATT
2679455 TTC
1 TTC
2679458 GTTGCAAACA
Statistics
Matches: 141, Mismatches: 28, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
41 2 0.01
42 4 0.03
43 134 0.95
44 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (42 bp):
TTCACACAAACGCCACAATAGGTGTTGATATTTAGCGGCATT
Found at i:2679912 original size:21 final size:21
Alignment explanation
Indices: 2679887--2679950 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
2679877 ATTGCGCATT
2679887 TATGTGCTGCCGCTGCTTCTC
1 TATGTGCTGCCGCTGCTTCTC
* *
2679908 TATGTGCTACCGCTGCCTCTC
1 TATGTGCTGCCGCTGCTTCTC
* *
2679929 TCTGTGCTGCCACTGCTTCTC
1 TATGTGCTGCCGCTGCTTCTC
2679950 T
1 T
2679951 CTCTGCTTCC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.06, C:0.36, G:0.20, T:0.38
Consensus pattern (21 bp):
TATGTGCTGCCGCTGCTTCTC
Found at i:2679951 original size:21 final size:21
Alignment explanation
Indices: 2679889--2679963 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
2679879 TGCGCATTTA
* *
2679889 TGTGCTGCCGCTGCTTCTCTA
1 TGTGCTGCCACTGCTTCTCTC
* * *
2679910 TGTGCTACCGCTGCCTCTCTC
1 TGTGCTGCCACTGCTTCTCTC
2679931 TGTGCTGCCACTGCTTCTCTC
1 TGTGCTGCCACTGCTTCTCTC
* *
2679952 TCTGCTTCCACT
1 TGTGCTGCCACT
2679964 ACTGCTCTAG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.05, C:0.39, G:0.19, T:0.37
Consensus pattern (21 bp):
TGTGCTGCCACTGCTTCTCTC
Found at i:2679971 original size:21 final size:21
Alignment explanation
Indices: 2679926--2680023 Score: 88
Period size: 21 Copynumber: 4.7 Consensus size: 21
2679916 ACCGCTGCCT
* * * *
2679926 CTCTCTGTGCTGCCACTGCTT
1 CTCTCTCTGCTTCCACTACTG
2679947 CTCTCTCTGCTTCCACTACTG
1 CTCTCTCTGCTTCCACTACTG
** *
2679968 CTCTAGCTGCTTCCGCTACTG
1 CTCTCTCTGCTTCCACTACTG
** * * *
2679989 CTCTAGCTACTTCCGCTGCTG
1 CTCTCTCTGCTTCCACTACTG
2680010 CTCTCTCTGCTTCC
1 CTCTCTCTGCTTCC
2680024 CTTGCTTCAT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.07, C:0.41, G:0.15, T:0.37
Consensus pattern (21 bp):
CTCTCTCTGCTTCCACTACTG
Found at i:2688546 original size:42 final size:41
Alignment explanation
Indices: 2688513--2688840 Score: 422
Period size: 42 Copynumber: 7.8 Consensus size: 41
2688503 ATGTTAACCA
* *
2688513 TATTGCGACGTTTGAGCTATAAAAGCCGCTATATTACAACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTAC-ACTC
* *
2688555 TATTGCGGCGCTTGATCTATAAACGCCGCTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTAC-ACTC
* *
2688597 TATTACGGCGTTTGAGCTATAAATGCCGCTATATTACAACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTAC-ACTC
* *
2688639 TATTACGGCGTTTGATCTATAAACGCCGCTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTAC-ACTC
* * * *
2688681 TATTGCGACGTTTGAGCTACAAACGTCACTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTAC-ACTC
* *
2688723 TATTGCGGCATTTTAGCTATAAACGCCGCTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTAC-ACTC
* * *
2688765 TATTACGGCGTTTTAGCTACAAACGCCGCTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTAC-ACTC
* *
2688807 TATTGCGACGTTTGAGCTACAAACGCCGCTATAT
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATAT
2688841 GCTTAAAGTT
Statistics
Matches: 255, Mismatches: 31, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 255 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (41 bp):
TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACACTC
Found at i:2688673 original size:126 final size:126
Alignment explanation
Indices: 2688521--2688840 Score: 496
Period size: 126 Copynumber: 2.5 Consensus size: 126
2688511 CATATTGCGA
* * * * * *
2688521 CGTTTGAGCTATAAAAGCCGCTATATTACAACTCTATTGCGGCGCTTGATCTATAAACGCCGCTA
1 CGTTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCGACGTTTGAGCTACAAACGCCGCTA
* *
2688586 TATTACTACTCTATTACGGCGTTTGAGCTATAAATGCCGCTATATTACAACTCTATTACGG
66 TATTACTACTCTATTACGGCATTTGAGCTATAAACGCCGCTATATTACAACTCTATTACGG
* * *
2688647 CGTTTGATCTATAAACGCCGCTATATTACTACTCTATTGCGACGTTTGAGCTACAAACGTCACTA
1 CGTTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCGACGTTTGAGCTACAAACGCCGCTA
* * *
2688712 TATTACTACTCTATTGCGGCATTTTAGCTATAAACGCCGCTATATTACTACTCTATTACGG
66 TATTACTACTCTATTACGGCATTTGAGCTATAAACGCCGCTATATTACAACTCTATTACGG
* *
2688773 CGTTTTAGCTACAAACGCCGCTATATTACTACTCTATTGCGACGTTTGAGCTACAAACGCCGCTA
1 CGTTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCGACGTTTGAGCTACAAACGCCGCTA
2688838 TAT
66 TAT
2688841 GCTTAAAGTT
Statistics
Matches: 175, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
126 175 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (126 bp):
CGTTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCGACGTTTGAGCTACAAACGCCGCTA
TATTACTACTCTATTACGGCATTTGAGCTATAAACGCCGCTATATTACAACTCTATTACGG
Found at i:2689227 original size:83 final size:81
Alignment explanation
Indices: 2689110--2689350 Score: 236
Period size: 82 Copynumber: 2.9 Consensus size: 81
2689100 TTTTGTGACG
* * *
2689110 TTTTTATAAAAGCGCCACTATAGACAAAC-ATATTGCGGCGTTTGTAGGAAAATCGCCGCTAAAT
1 TTTTTAGAAAA-CGCCACTATAAAC-AACTATATTGCGGCGTTTGTA-GAAAAACGCCGCTAAAT
* *
2689174 TATTACTCTTTTACGGCG-
63 TACTACTCTATTACGGCGT
* * * *
2689192 TTTTTAGCACAAATGCCACTATAAACAACTCTATTGCGGCGTTTATATAAAAACGCCGCTAAATT
1 TTTTTAG-A-AAACGCCACTATAAACAACTATATTGCGGCGTTTGTAGAAAAACGCCGCTAAATT
* *
2689257 ACTACTCTATTGCGGTGTT
64 ACTACTCTATTACGGCG-T
* * * *
2689276 TTTTTAGAAAACGCCACTATAAACAATTATATTCCGGCGTTTG-AGCTATAAACGCCGCTAACTT
1 TTTTTAGAAAACGCCACTATAAACAACTATATTGCGGCGTTTGTAG--AAAAACGCCGCTAAATT
* *
2689340 ACCACCCTATT
64 ACTACTCTATT
2689351 GCAGCATTTG
Statistics
Matches: 131, Mismatches: 21, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
81 1 0.01
82 68 0.52
83 52 0.40
84 10 0.08
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (81 bp):
TTTTTAGAAAACGCCACTATAAACAACTATATTGCGGCGTTTGTAGAAAAACGCCGCTAAATTAC
TACTCTATTACGGCGT
Found at i:2689232 original size:41 final size:39
Alignment explanation
Indices: 2689108--2689317 Score: 122
Period size: 41 Copynumber: 5.1 Consensus size: 39
2689098 GTTTTTGTGA
* * *
2689108 CGTTTTTATAAAAGCGCCACTATAGACAAAC-ATATTGCGG
1 CGTTTTTAGAAAA-CGCCACTATAAAC-AACTCTATTGCGG
* * ** * *
2689148 CGTTTGTAGGAAAATCGCCGCTA-AATTATTACTCTTTTACGG
1 CGTTTTTA-GAAAA-CGCCACTATAA--ACAACTCTATTGCGG
*
2689190 CGTTTTTAGCACAAATGCCACTATAAACAACTCTATTGCGG
1 CGTTTTTAG-A-AAACGCCACTATAAACAACTCTATTGCGG
* *
2689231 CGTTTATATA-AAAACGCCGCTA-AATTACTACTCTATTGCGG
1 CGTTT-T-TAGAAAACGCCACTATAA--ACAACTCTATTGCGG
* * * *
2689272 TGTTTTTTTAGAAAACGCCACTATAAACAATTATATTCCGG
1 CG--TTTTTAGAAAACGCCACTATAAACAACTCTATTGCGG
2689313 CGTTT
1 CGTTT
2689318 GAGCTATAAA
Statistics
Matches: 128, Mismatches: 27, Indels: 31
0.69 0.15 0.17
Matches are distributed among these distances:
39 5 0.04
40 17 0.13
41 60 0.47
42 34 0.27
43 12 0.09
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (39 bp):
CGTTTTTAGAAAACGCCACTATAAACAACTCTATTGCGG
Found at i:2689370 original size:83 final size:82
Alignment explanation
Indices: 2689206--2689372 Score: 190
Period size: 83 Copynumber: 2.0 Consensus size: 82
2689196 TAGCACAAAT
* * * * * *
2689206 GCCACTATAAACAACTCTATTGCGGCGTTTATATAAAAACGCCGCTAAATTACTACTCTATTGCG
1 GCCACTATAAACAACTATATTCCGGCGTTTAGATAAAAACGCCGCTAAATTACCACCCTATTGCA
** * * *
2689271 GTGTTTTTTTAGAAAAC
66 GCATTTGTTGAAAAAAC
* * * *
2689288 GCCACTATAAACAATTATATTCCGGCGTTTGAGCTATAAACGCCGCTAACTTACCACCCTATTGC
1 GCCACTATAAACAACTATATTCCGGCGTTT-AGATAAAAACGCCGCTAAATTACCACCCTATTGC
2689353 AGCATTTGTTGAAAAAAC
65 AGCATTTGTTGAAAAAAC
2689371 GC
1 GC
2689373 TGCTAAAGTT
Statistics
Matches: 69, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
82 27 0.39
83 42 0.61
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (82 bp):
GCCACTATAAACAACTATATTCCGGCGTTTAGATAAAAACGCCGCTAAATTACCACCCTATTGCA
GCATTTGTTGAAAAAAC
Found at i:2689460 original size:12 final size:12
Alignment explanation
Indices: 2689443--2689468 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2689433 GGCGTTTTCC
2689443 CTAAAAACGCCG
1 CTAAAAACGCCG
2689455 CTAAAAACGCCG
1 CTAAAAACGCCG
2689467 CT
1 CT
2689469 GCATAACACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.35, G:0.15, T:0.12
Consensus pattern (12 bp):
CTAAAAACGCCG
Found at i:2690256 original size:60 final size:60
Alignment explanation
Indices: 2690184--2690299 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
2690174 AGTTTTTAAT
* * * *
2690184 GTTCTAATTTCATCTCCAAATTATGACTTTAATTCTAAATTAATCAT-CAAACTTTTAAAG
1 GTTCCAATTTCATCTCAAAACTATGACCTTAATTCTAAATTAATC-TCCAAACTTTTAAAG
* *
2690244 GTTCCAATTTCATCTCAAAACTATGACCTTCATTCTAAATTGATCTCCAAACTTTT
1 GTTCCAATTTCATCTCAAAACTATGACCTTAATTCTAAATTAATCTCCAAACTTTT
2690300 GAACATACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 1 0.02
60 48 0.98
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.41
Consensus pattern (60 bp):
GTTCCAATTTCATCTCAAAACTATGACCTTAATTCTAAATTAATCTCCAAACTTTTAAAG
Found at i:2690313 original size:60 final size:60
Alignment explanation
Indices: 2690189--2690326 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 60
2690179 TTAATGTTCT
* * ** * *
2690189 AATTTCATCTCCAAATTATGACTTTAATTCTAAATTAATCATCAAACTTTTAAAGGTTCC
1 AATTTCATCTCCAAACTATGACCTTAATTCTAAATTAATCATCAAACTTTTAAACATACA
* * * *
2690249 AATTTCATCTCAAAACTATGACCTTCATTCTAAATTGATC-TCCAAACTTTTGAACATACA
1 AATTTCATCTCCAAACTATGACCTTAATTCTAAATTAATCAT-CAAACTTTTAAACATACA
*
2690309 AATTTTATC-CCAAACTAT
1 AATTTCATCTCCAAACTAT
2690327 CAGTATATAA
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 9 0.14
60 56 0.86
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.38
Consensus pattern (60 bp):
AATTTCATCTCCAAACTATGACCTTAATTCTAAATTAATCATCAAACTTTTAAACATACA
Found at i:2690530 original size:57 final size:58
Alignment explanation
Indices: 2690441--2690585 Score: 141
Period size: 57 Copynumber: 2.5 Consensus size: 58
2690431 TTTGGATGCT
** * * * *
2690441 TTTGGGAATGAAATGGGAAGATTCATAAGTTTG-GGAATCAATTTAAAATG-AGTCATAA
1 TTTGGG-ATGAAATTAGAATATTCAAAAGTTTGAGG-ATCAATTTAAAATGAAGTAACAA
* *
2690499 TTTGGGATGAAATTAGAATATTCAAAAGTTTGAGGATTAATTTAGAATGAAAGTAACAA
1 TTTGGGATGAAATTAGAATATTCAAAAGTTTGAGGATCAATTTAAAATG-AAGTAACAA
* * *
2690558 TTTAGGGATTAAGTTAGAATATTTAAAA
1 TTT-GGGATGAAATTAGAATATTCAAAA
2690586 AATGTAAGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
57 34 0.47
58 8 0.11
59 9 0.12
60 21 0.29
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.33
Consensus pattern (58 bp):
TTTGGGATGAAATTAGAATATTCAAAAGTTTGAGGATCAATTTAAAATGAAGTAACAA
Found at i:2696392 original size:12 final size:13
Alignment explanation
Indices: 2696361--2696394 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2696351 AAATTAGATG
*
2696361 CACTTAATTAAAT
1 CACTTAAATAAAT
2696374 CACTTAAATAAAT
1 CACTTAAATAAAT
2696387 -ACTTAAAT
1 CACTTAAAT
2696395 TACATATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (13 bp):
CACTTAAATAAAT
Found at i:2696643 original size:20 final size:20
Alignment explanation
Indices: 2696615--2696656 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2696605 AGTCAATGGG
*
2696615 TCAGACCAGTTCAGGTTGAC
1 TCAGACCAGGTCAGGTTGAC
* *
2696635 TCAGGCCAGGTCGGGTTGAC
1 TCAGACCAGGTCAGGTTGAC
2696655 TC
1 TC
2696657 GAACCGGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.26, G:0.31, T:0.24
Consensus pattern (20 bp):
TCAGACCAGGTCAGGTTGAC
Found at i:2700995 original size:13 final size:13
Alignment explanation
Indices: 2700977--2701003 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2700967 ACTCATCACC
2700977 ACCAAACCAACAA
1 ACCAAACCAACAA
2700990 ACCAAACCAACAA
1 ACCAAACCAACAA
2701003 A
1 A
2701004 GACGCATTTG
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:0.63, C:0.37, G:0.00, T:0.00
Consensus pattern (13 bp):
ACCAAACCAACAA
Found at i:2715323 original size:167 final size:167
Alignment explanation
Indices: 2715047--2715379 Score: 666
Period size: 167 Copynumber: 2.0 Consensus size: 167
2715037 TATATATCTT
2715047 ATATGATTAGAGAAAGTCAAAAAAATTAGAATCAATCATTATCATAATACTATAAATAATTATAA
1 ATATGATTAGAGAAAGTCAAAAAAATTAGAATCAATCATTATCATAATACTATAAATAATTATAA
2715112 GAAAATTAATATAGAAATTCGAATAACTCGACTCAAATTTCTTAAACTCGACTCAACTTGAAAAT
66 GAAAATTAATATAGAAATTCGAATAACTCGACTCAAATTTCTTAAACTCGACTCAACTTGAAAAT
2715177 ATTTCAAGTTAAGTTCAAATTATAAAATATGAATCAA
131 ATTTCAAGTTAAGTTCAAATTATAAAATATGAATCAA
2715214 ATATGATTAGAGAAAGTCAAAAAAATTAGAATCAATCATTATCATAATACTATAAATAATTATAA
1 ATATGATTAGAGAAAGTCAAAAAAATTAGAATCAATCATTATCATAATACTATAAATAATTATAA
2715279 GAAAATTAATATAGAAATTCGAATAACTCGACTCAAATTTCTTAAACTCGACTCAACTTGAAAAT
66 GAAAATTAATATAGAAATTCGAATAACTCGACTCAAATTTCTTAAACTCGACTCAACTTGAAAAT
2715344 ATTTCAAGTTAAGTTCAAATTATAAAATATGAATCA
131 ATTTCAAGTTAAGTTCAAATTATAAAATATGAATCA
2715380 TCAACTCGAA
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 166 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.31
Consensus pattern (167 bp):
ATATGATTAGAGAAAGTCAAAAAAATTAGAATCAATCATTATCATAATACTATAAATAATTATAA
GAAAATTAATATAGAAATTCGAATAACTCGACTCAAATTTCTTAAACTCGACTCAACTTGAAAAT
ATTTCAAGTTAAGTTCAAATTATAAAATATGAATCAA
Found at i:2716118 original size:84 final size:87
Alignment explanation
Indices: 2716007--2716179 Score: 316
Period size: 84 Copynumber: 2.0 Consensus size: 87
2715997 AGTTAGAGTG
2716007 ACTTAATATGAATTTTACTCTAAAATTAATGACTAAACTGAAAATATTAAATATTTATTATGAAA
1 ACTTAATATGAA-TTTACTCTAAAATTAATGACTAAACTGAAAATATTAAATATTTATTATGAAA
2716072 TAAACTTTT-AA-AAGTCAGACC
65 TAAACTTTTAAACAAGTCAGACC
2716093 ACTTAATATGAA-TTACTCTAAAATTAATGACTAAACTGAAAATATTAAATATTTATTATGAAAT
1 ACTTAATATGAATTTACTCTAAAATTAATGACTAAACTGAAAATATTAAATATTTATTATGAAAT
2716157 AAACTTTTAAACAAGTCAGACC
66 AAACTTTTAAACAAGTCAGACC
2716179 A
1 A
2716180 AACCCAAATA
Statistics
Matches: 85, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
84 60 0.71
85 2 0.02
86 23 0.27
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (87 bp):
ACTTAATATGAATTTACTCTAAAATTAATGACTAAACTGAAAATATTAAATATTTATTATGAAAT
AAACTTTTAAACAAGTCAGACC
Found at i:2723450 original size:18 final size:18
Alignment explanation
Indices: 2723427--2723463 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2723417 AGAATAAATA
* *
2723427 AATGAAAAATACTTTAAT
1 AATGAAAAAGACCTTAAT
2723445 AATGAAAAAGACCTTAAT
1 AATGAAAAAGACCTTAAT
2723463 A
1 A
2723464 GAAAATTTTA
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:0.57, C:0.08, G:0.08, T:0.27
Consensus pattern (18 bp):
AATGAAAAAGACCTTAAT
Found at i:2728853 original size:30 final size:30
Alignment explanation
Indices: 2728810--2728868 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
2728800 TTCAATTTAT
* * *
2728810 AATTTTATGTTTATTCAATTTAATCCTTAG
1 AATTATATGTTTATTCAAATTAACCCTTAG
*
2728840 AATTATATTTTTATTCAAATTAACCCTTA
1 AATTATATGTTTATTCAAATTAACCCTTA
2728869 TTTATTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.51
Consensus pattern (30 bp):
AATTATATGTTTATTCAAATTAACCCTTAG
Found at i:2732093 original size:15 final size:15
Alignment explanation
Indices: 2732069--2732118 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
2732059 ATGGTAAAAT
*
2732069 GAATTAAGAAATTAA
1 GAATTTAGAAATTAA
2732084 GAATTTAGAATATTAA
1 GAATTTAGAA-ATTAA
2732100 GATAATTT--AAATTAA
1 G--AATTTAGAAATTAA
2732115 GAAT
1 GAAT
2732119 GAATTTATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
13 3 0.10
15 15 0.48
16 8 0.26
18 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.34
Consensus pattern (15 bp):
GAATTTAGAAATTAA
Found at i:2732112 original size:24 final size:24
Alignment explanation
Indices: 2732071--2732118 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2732061 GGTAAAATGA
*
2732071 ATTAAGAAATTAAGAATTTAGAAT
1 ATTAAGAAATTAAGAATTAAGAAT
*
2732095 ATTAAGATAATTTA-AATTAAGAAT
1 ATTAAGA-AATTAAGAATTAAGAAT
2732119 GAATTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.35
Consensus pattern (24 bp):
ATTAAGAAATTAAGAATTAAGAAT
Found at i:2739416 original size:15 final size:14
Alignment explanation
Indices: 2739375--2739412 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
2739365 AACTCTATTT
2739375 TTTTATAATATTTAA
1 TTTTATAATA-TTAA
2739390 TTATTATAATATTAA
1 TT-TTATAATATTAA
2739405 TTTTATAA
1 TTTTATAA
2739413 ATATAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.27
15 8 0.36
16 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTATAATATTAA
Found at i:2739442 original size:19 final size:21
Alignment explanation
Indices: 2739417--2739464 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2739407 TTATAAATAT
*
2739417 AAAAAAAT-C-AAAAATTTCA
1 AAAAAAATCCGAAAAATTACA
*
2739436 GAAAAAATCCGAAAAATTACA
1 AAAAAAATCCGAAAAATTACA
2739457 AAAAAAAT
1 AAAAAAAT
2739465 AGTTTGATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 7 0.29
20 1 0.04
21 16 0.67
ACGTcount: A:0.69, C:0.10, G:0.04, T:0.17
Consensus pattern (21 bp):
AAAAAAATCCGAAAAATTACA
Found at i:2743863 original size:40 final size:39
Alignment explanation
Indices: 2743819--2743897 Score: 90
Period size: 39 Copynumber: 2.0 Consensus size: 39
2743809 TTAGTGTTGA
2743819 TTTTTTAAGTT-TTTCC-TTAATTTGATTGTGTTTTAAATTG
1 TTTTTT-AGTTCTTTCCTTTAATTTG-TT-TGTTTTAAATTG
* * *
2743859 TTTTTTTGTTCTTTCCTTTATTTTGTTTTTTTTAAATTG
1 TTTTTTAGTTCTTTCCTTTAATTTGTTTGTTTTAAATTG
2743898 ATTTCTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
39 14 0.41
40 13 0.38
41 7 0.21
ACGTcount: A:0.15, C:0.06, G:0.10, T:0.68
Consensus pattern (39 bp):
TTTTTTAGTTCTTTCCTTTAATTTGTTTGTTTTAAATTG
Found at i:2743995 original size:40 final size:41
Alignment explanation
Indices: 2743946--2744027 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
2743936 ATAAAATTTT
2743946 ATTTTATTTTAATTTT-TTTCCTTTTTAATTTAATATTCTA
1 ATTTTATTTTAATTTTCTTTCCTTTTTAATTTAATATTCTA
2743986 ATTTTATTTTAATTTTCTTTCCTTTTTAATTTAATATTCTA
1 ATTTTATTTTAATTTTCTTTCCTTTTTAATTTAATATTCTA
2744027 A
1 A
2744028 AAGTTTCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 16 0.39
41 25 0.61
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (41 bp):
ATTTTATTTTAATTTTCTTTCCTTTTTAATTTAATATTCTA
Found at i:2746165 original size:23 final size:23
Alignment explanation
Indices: 2746139--2746182 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2746129 ATATTTAATG
2746139 TATTGAATATATT-AATAATTTTA
1 TATTGAATAT-TTAAATAATTTTA
**
2746162 TATTTTATATTTAAATAATTT
1 TATTGAATATTTAAATAATTT
2746183 CTTATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TATTGAATATTTAAATAATTTTA
Found at i:2747662 original size:3 final size:3
Alignment explanation
Indices: 2747654--2747679 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2747644 ACCACCTTGA
2747654 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
2747680 GTCTTGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:2752195 original size:23 final size:23
Alignment explanation
Indices: 2752169--2752214 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2752159 TTTATAGTTA
* *
2752169 ATATTATTTTAAAATTAAAATTT
1 ATATAATTATAAAATTAAAATTT
* *
2752192 ATATAATTATATAATTACAATTT
1 ATATAATTATAAAATTAAAATTT
2752215 GTACTACTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATAATTATAAAATTAAAATTT
Found at i:2753368 original size:15 final size:16
Alignment explanation
Indices: 2753344--2753376 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2753334 GACTCGACTC
*
2753344 AAAATATTTCGAGCTT
1 AAAATATTTCAAGCTT
2753360 AAAAT-TTTCAAGCTT
1 AAAATATTTCAAGCTT
2753375 AA
1 AA
2753377 CTCAAGTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (16 bp):
AAAATATTTCAAGCTT
Found at i:2755382 original size:21 final size:21
Alignment explanation
Indices: 2755356--2755395 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2755346 AAACTAGGGG
2755356 TGATATTCGCTATATTTCGAC
1 TGATATTCGCTATATTTCGAC
* *
2755377 TGATATTTGGTATATTTCG
1 TGATATTCGCTATATTTCG
2755396 TAAAGGTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.47
Consensus pattern (21 bp):
TGATATTCGCTATATTTCGAC
Found at i:2771995 original size:2 final size:2
Alignment explanation
Indices: 2771988--2772012 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2771978 TGTGTTAGAC
2771988 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2772013 AGATTATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2777323 original size:28 final size:28
Alignment explanation
Indices: 2777286--2777348 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
2777276 TAAATCTCAG
2777286 ATGACGCGCAATTGTGTGTCATAAATCT
1 ATGACGCGCAATTGTGTGTCATAAATCT
2777314 ATGACGCGCAATTGTGTGTCATAAATCT
1 ATGACGCGCAATTGTGTGTCATAAATCT
2777342 ATGACGC
1 ATGACGC
2777349 ACATTTATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (28 bp):
ATGACGCGCAATTGTGTGTCATAAATCT
Found at i:2777359 original size:13 final size:13
Alignment explanation
Indices: 2777341--2777405 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
2777331 GTCATAAATC
*
2777341 TATGACGCACATT
1 TATGACGCGCATT
* *
2777354 TATGACACGTATT
1 TATGACGCGCATT
*
2777367 TATGACGTGCATT
1 TATGACGCGCATT
* *
2777380 TATGATGCTCATT
1 TATGACGCGCATT
*
2777393 TATGACACGCATT
1 TATGACGCGCATT
2777406 GCACGTCATT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:2777570 original size:2 final size:2
Alignment explanation
Indices: 2777563--2777593 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2777553 GTTGTAAATT
2777563 TA TA TA 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 TA TA TA T
2777594 TGTAGATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2778367 original size:16 final size:16
Alignment explanation
Indices: 2778346--2778378 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2778336 AAACGATAGT
2778346 AAAGTGTGAACTGATG
1 AAAGTGTGAACTGATG
2778362 AAAGTGTGAACTGATG
1 AAAGTGTGAACTGATG
2778378 A
1 A
2778379 CACACAAGCA
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:0.39, C:0.06, G:0.30, T:0.24
Consensus pattern (16 bp):
AAAGTGTGAACTGATG
Found at i:2787701 original size:19 final size:18
Alignment explanation
Indices: 2787632--2787699 Score: 86
Period size: 17 Copynumber: 3.8 Consensus size: 18
2787622 TTAACAGTTT
2787632 TGAACCGGTTTGACGGT-
1 TGAACCGGTTTGACGGTC
2787649 TCGAA-CGGTTTGACGGTC
1 T-GAACCGGTTTGACGGTC
*
2787667 TGAACCGATTTGACCGGTC
1 TGAACCGGTTTGA-CGGTC
*
2787686 TGAACCGGGTTGAC
1 TGAACCGGTTTGAC
2787700 CGACCCGCTG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
17 16 0.36
18 12 0.27
19 16 0.36
ACGTcount: A:0.19, C:0.22, G:0.32, T:0.26
Consensus pattern (18 bp):
TGAACCGGTTTGACGGTC
Found at i:2793727 original size:10 final size:10
Alignment explanation
Indices: 2793698--2793785 Score: 94
Period size: 10 Copynumber: 9.1 Consensus size: 10
2793688 GCTGCTGGAA
2793698 AACCGGTTTG
1 AACCGGTTTG
*
2793708 -ACCAGTTTTG
1 AACC-GGTTTG
2793718 AACCGGTTTG
1 AACCGGTTTG
*
2793728 -ACCGGTTCG
1 AACCGGTTTG
2793737 AACCGGTTTG
1 AACCGGTTTG
*
2793747 -ACCGGTCTG
1 AACCGGTTTG
2793756 AACCGGTTTG
1 AACCGGTTTG
*
2793766 -ACCGGTCTG
1 AACCGGTTTG
*
2793775 AACCGGGTTG
1 AACCGGTTTG
2793785 A
1 A
2793786 CCCGACCCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
9 27 0.42
10 34 0.53
11 3 0.05
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:2793741 original size:19 final size:19
Alignment explanation
Indices: 2793698--2793787 Score: 128
Period size: 19 Copynumber: 4.7 Consensus size: 19
2793688 GCTGCTGGAA
* *
2793698 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
2793718 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
2793737 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
2793756 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
2793775 AACCGGGTTGACC
1 AACCGGTTTGACC
2793788 CGACCCGACT
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
18 1 0.02
19 51 0.77
20 14 0.21
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:2793803 original size:17 final size:17
Alignment explanation
Indices: 2793781--2793826 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
2793771 TCTGAACCGG
2793781 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
2793798 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
2793815 GTTGACCCGACC
1 GTTGACCCGACC
2793827 GTTGACCGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:2793835 original size:7 final size:7
Alignment explanation
Indices: 2793823--2793859 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
2793813 CTGTTGACCC
2793823 GACCGTT
1 GACCGTT
2793830 GACCGTT
1 GACCGTT
2793837 GACCG-T
1 GACCGTT
2793843 GACCGTT
1 GACCGTT
2793850 GACCGTT
1 GACCGTT
2793857 GAC
1 GAC
2793860 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:2793847 original size:13 final size:13
Alignment explanation
Indices: 2793823--2793855 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2793813 CTGTTGACCC
2793823 GACCGTTGACCGTT
1 GACCG-TGACCGTT
2793837 GACCGTGACCGTT
1 GACCGTGACCGTT
2793850 GACCGT
1 GACCGT
2793856 TGACTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:2798789 original size:20 final size:21
Alignment explanation
Indices: 2798764--2798993 Score: 235
Period size: 20 Copynumber: 11.3 Consensus size: 21
2798754 TATTGCAAAT
*
2798764 AATCGCAATGCGA-TTACGTA
1 AATCGCATTGCGATTTACGTA
* * * *
2798784 AATCGCAATGCGAATTAGGAA
1 AATCGCATTGCGATTTACGTA
* * * * *
2798805 AATCACAATGCGAATTAGGAA
1 AATCGCATTGCGATTTACGTA
2798826 AATCGCATTGCGA-TTACGTA
1 AATCGCATTGCGATTTACGTA
2798846 AATCGCATTGCGA-TTACGT-
1 AATCGCATTGCGATTTACGTA
*
2798865 ATTCGCATTGCGATTTACGT-
1 AATCGCATTGCGATTTACGTA
* *
2798885 AATCGCATTGCGATTTTCCTA
1 AATCGCATTGCGATTTACGTA
*
2798906 ATTCGCATTGCGATTTACGT-
1 AATCGCATTGCGATTTACGTA
* *
2798926 AATCGCATTGCGATTTTCCTA
1 AATCGCATTGCGATTTACGTA
*
2798947 ATTCGCACTT-CGATTTACGT-
1 AATCGCA-TTGCGATTTACGTA
2798967 AATCGCATTGCGATTTA-GTA
1 AATCGCATTGCGATTTACGTA
2798987 AATCGCA
1 AATCGCA
2798994 ACGAGATTCT
Statistics
Matches: 182, Mismatches: 21, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
19 16 0.09
20 97 0.53
21 67 0.37
22 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (21 bp):
AATCGCATTGCGATTTACGTA
Found at i:2798920 original size:41 final size:41
Alignment explanation
Indices: 2798828--2798982 Score: 246
Period size: 41 Copynumber: 3.8 Consensus size: 41
2798818 ATTAGGAAAA
* *
2798828 TCGCATTGCGA-TTACGTAAATCGCATTGCGA-TTACGT-AT
1 TCGCATTGCGATTTACGT-AATCGCATTGCGATTTTCCTAAT
2798867 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
2798908 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
2798949 TCGCACTT-CGATTTACGTAATCGCATTGCGATTT
1 TCGCA-TTGCGATTTACGTAATCGCATTGCGATTT
2798983 AGTAAATCGC
Statistics
Matches: 110, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
39 24 0.22
40 10 0.09
41 74 0.67
42 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
Found at i:2798937 original size:61 final size:60
Alignment explanation
Indices: 2798826--2798993 Score: 218
Period size: 61 Copynumber: 2.8 Consensus size: 60
2798816 GAATTAGGAA
* *
2798826 AATCGCATTGCGA-TTACGTAAATCGCATTGCGA-TTACGTATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT-AATCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
2798885 AATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCT
1 AATCGCATTGCGATTTACGTAA-TCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
2798946 AATTCGCACTT-CGATTTACGTAATCGCATTGCGATTTA-GTAAATCGCA
1 AA-TCGCA-TTGCGATTTACGTAATCGCATTGCGATTTACGT-AATCGCA
2798994 ACGAGATTCT
Statistics
Matches: 96, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
59 15 0.16
60 17 0.18
61 47 0.49
62 15 0.16
63 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (60 bp):
AATCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:2799883 original size:24 final size:24
Alignment explanation
Indices: 2799856--2799909 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
2799846 GTATTCGAAA
2799856 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
2799880 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
2799904 TTTGAT
1 TTTGAT
2799910 GATTTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:2800118 original size:15 final size:14
Alignment explanation
Indices: 2800100--2800135 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
2800090 GAAAAAGAAG
2800100 AAGAAGAAATCCCCA
1 AAGAA-AAATCCCCA
*
2800115 AAGAAAAGTCCCCA
1 AAGAAAAATCCCCA
2800129 AAGAAAA
1 AAGAAAA
2800136 TGCCACGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.58, C:0.22, G:0.14, T:0.06
Consensus pattern (14 bp):
AAGAAAAATCCCCA
Found at i:2802445 original size:20 final size:19
Alignment explanation
Indices: 2802417--2802471 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
2802407 CAATCATCTT
*
2802417 AATATCTATCGCAACGCGGA
1 AATAACTATCGCAACGC-GA
*
2802437 AATAACTATCGCAATGCGA
1 AATAACTATCGCAACGCGA
*
2802456 AATGAA-AATCGCAACG
1 AAT-AACTATCGCAACG
2802472 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (19 bp):
AATAACTATCGCAACGCGA
Found at i:2802466 original size:19 final size:19
Alignment explanation
Indices: 2802444--2802541 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
2802434 GGAAATAACT
2802444 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2802463 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2802477 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
2802496 ATCGCAA--C--CA-GAGA
1 ATCGCAATGCGAAATGAAA
*
2802510 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2802529 ATCGCAACGCGAA
1 ATCGCAATGCGAA
2802542 TTATGTTCAC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 20 0.33
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 31 0.51
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2802486 original size:33 final size:33
Alignment explanation
Indices: 2802444--2802537 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
2802434 GGAAATAACT
2802444 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2802477 ATCGCAATGCGAAATGAAAATCGCAACCAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2802510 ATCGCAATGCAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2802538 CGAATTATGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2802580 original size:14 final size:14
Alignment explanation
Indices: 2802561--2802597 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2802551 CATCAATTAA
2802561 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2802575 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2802589 ACAAATCAA
1 ACAAATCAA
2802598 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2804012 original size:21 final size:21
Alignment explanation
Indices: 2803946--2804012 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2803936 GTGAATCGGG
*
2803946 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2803966 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2803988 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2804009 CTCT
1 CTCT
2804013 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2804031 original size:42 final size:41
Alignment explanation
Indices: 2803946--2804068 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
2803936 GTGAATCGGG
* * * *
2803946 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
2803988 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
2804030 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
2804069 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:2804584 original size:20 final size:20
Alignment explanation
Indices: 2804559--2804648 Score: 79
Period size: 19 Copynumber: 4.9 Consensus size: 20
2804549 CGCGATTATA
*
2804559 GTTTCGTGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTG
2804579 GTTTCGCGTTGCGA-TTTT-
1 GTTTCGCGTTGCGATTTTTG
*
2804597 G--T--CGTTGCGA-TTTTC
1 GTTTCGCGTTGCGATTTTTG
* * *
2804612 ATTTCACGTTGCGA-TTTTC
1 GTTTCGCGTTGCGATTTTTG
2804631 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
2804649 CATTCTCTCG
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
14 12 0.20
16 1 0.02
17 1 0.02
18 1 0.02
19 29 0.48
20 16 0.27
ACGTcount: A:0.08, C:0.17, G:0.26, T:0.50
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTTG
Found at i:2804623 original size:19 final size:19
Alignment explanation
Indices: 2804599--2804675 Score: 109
Period size: 19 Copynumber: 4.0 Consensus size: 19
2804589 GCGATTTTGT
2804599 CGTTGCGATTTTCATTTCA
1 CGTTGCGATTTTCATTTCA
* *
2804618 CGTTGCGATTTTCGTTTCG
1 CGTTGCGATTTTCATTTCA
*
2804637 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATT-TCA
*
2804657 CGTTACGATTTTCATTTCA
1 CGTTGCGATTTTCATTTCA
2804676 ACCAAAAGAC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
19 34 0.67
20 17 0.33
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.48
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCA
Found at i:2804873 original size:94 final size:89
Alignment explanation
Indices: 2804763--2805031 Score: 384
Period size: 94 Copynumber: 3.0 Consensus size: 89
2804753 ATGGATTGCA
* *
2804763 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
2804828 TAGCAGAATTGGCAGCAAACGAACAAAT
66 TAGCAGAATTGGCAGC-AAC---CAAAT
2804856 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
2804921 TTAGCAGAATTGGCAGCAACCGAAT
65 TTAGCAGAATTGGCAGCAACCAAAT
* *
2804946 ATACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* **
2805007 TTAGAAGTTTTGGCAGCAACCAAAT
65 TTAGCAGAATTGGCAGCAACCAAAT
2805032 AAATTTACTA
Statistics
Matches: 165, Mismatches: 9, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
86 30 0.18
89 19 0.12
90 34 0.21
93 7 0.04
94 75 0.45
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.21
Consensus pattern (89 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCAAAT
Found at i:2806727 original size:20 final size:20
Alignment explanation
Indices: 2806702--2806764 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
2806692 TTTTGGTTGA
2806702 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
2806722 AATGAAAATCGCAACGCAGA-
1 AATGAAAATCGCAACG-AGAG
**
2806742 AATGACTATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
2806762 AAT
1 AAT
2806765 CGCAACACGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.08
20 33 0.85
21 3 0.08
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:2806768 original size:14 final size:14
Alignment explanation
Indices: 2806749--2806837 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
2806739 AGAAATGACT
2806749 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
2806763 ATCGCAACACGAAATGAAA
1 ATCGC-A-ACG--A-GAGA
*
2806782 ATCGCAATGAGAGA
1 ATCGCAACGAGAGA
* *
2806796 ATCGCAACGCGAAATAAAA
1 ATCGCAA--CG--A-GAGA
2806815 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
2806829 ATCGCAACG
1 ATCGCAACG
2806838 CGAAAAGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
14 26 0.46
15 3 0.05
16 4 0.07
17 4 0.07
18 3 0.05
19 17 0.30
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:2806786 original size:33 final size:33
Alignment explanation
Indices: 2806700--2806854 Score: 193
Period size: 33 Copynumber: 4.5 Consensus size: 33
2806690 TCTTTTGGTT
2806700 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
** *
2806739 AGAAATGACTATCGCAACGAGAGAATCGCAACAC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2806773 GAAATGAAAATCGCAATGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2806806 GAAATAAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2806839 GAAAAGAAAATCGCAA
1 GAAATGAAAATCGCAA
2806855 TGCGATTTTG
Statistics
Matches: 104, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
33 74 0.71
34 10 0.10
36 1 0.01
37 1 0.01
38 3 0.03
40 15 0.14
ACGTcount: A:0.48, C:0.19, G:0.22, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2806852 original size:19 final size:19
Alignment explanation
Indices: 2806700--2806859 Score: 64
Period size: 19 Copynumber: 9.1 Consensus size: 19
2806690 TCTTTTGGTT
* *
2806700 GAAATGAAAATCGCAACGA
1 GAAAAGAAAATCGCAACGC
*
2806719 GAGAATGAAAATCGCAACGC
1 GA-AAAGAAAATCGCAACGC
* **
2806739 AGAAATGACTATCGCAA--C
1 -GAAAAGAAAATCGCAACGC
* *
2806757 G---AGAGAATCGCAACAC
1 GAAAAGAAAATCGCAACGC
* *
2806773 GAAATGAAAATCGCAA--T
1 GAAAAGAAAATCGCAACGC
*
2806790 G---AGAGAATCGCAACGC
1 GAAAAGAAAATCGCAACGC
2806806 GAAATA-AAAATCGCAA--C
1 GAAA-AGAAAATCGCAACGC
*
2806823 G---AGAGAATCGCAACGC
1 GAAAAGAAAATCGCAACGC
*
2806839 GAAAAGAAAATCGCAATGC
1 GAAAAGAAAATCGCAACGC
2806858 GA
1 GA
2806860 TTTTGGTTTC
Statistics
Matches: 106, Mismatches: 16, Indels: 38
0.66 0.10 0.24
Matches are distributed among these distances:
13 1 0.01
14 28 0.26
16 5 0.05
17 4 0.04
18 1 0.01
19 36 0.34
20 29 0.27
21 2 0.02
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (19 bp):
GAAAAGAAAATCGCAACGC
Found at i:2806903 original size:33 final size:33
Alignment explanation
Indices: 2806855--2806947 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
2806845 AAAATCGCAA
**
2806855 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
* *
2806888 TTCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
**
2806921 TGCGATAGTCATTTCCGCGTTGCGATT
1 TGCGATTTTCATTT-CGCGTTGCGATT
2806948 TTCATTCTCG
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 40 0.77
34 12 0.23
ACGTcount: A:0.11, C:0.22, G:0.24, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:2807543 original size:21 final size:21
Alignment explanation
Indices: 2807497--2807611 Score: 155
Period size: 20 Copynumber: 5.6 Consensus size: 21
2807487 CGATAGTCAG
*
2807497 ATTCGCATTGCGATTTACGT-
1 ATTCGCATTGCGATTTACCTA
*
2807517 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACCTA
*
2807538 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACCTA
*
2807559 ATTCGCATTGCGATTTACTTA
1 ATTCGCATTGCGATTTACCTA
* *
2807580 A-TCGCGTTGCGATTTACGT-
1 ATTCGCATTGCGATTTACCTA
2807599 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2807612 ATTATGAAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
19 1 0.01
20 44 0.51
21 41 0.48
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (21 bp):
ATTCGCATTGCGATTTACCTA
Found at i:2807632 original size:21 final size:21
Alignment explanation
Indices: 2807608--2807648 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2807598 TATTCGCATT
2807608 GCGAA-TTATGAAAATCGCAAC
1 GCGAATTTA-GAAAATCGCAAC
*
2807629 GCGAATTTAGGAAATCGCAA
1 GCGAATTTAGAAAATCGCAA
2807649 TACGATAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (21 bp):
GCGAATTTAGAAAATCGCAAC
Found at i:2810087 original size:21 final size:21
Alignment explanation
Indices: 2810061--2810137 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
2810051 ATTCTGACTA
* *
2810061 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTACCTAAT
*
2810082 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACCTAAT
*
2810103 TCGCACTT-CGATTTACGTAA-
1 TCGCA-TTGCGATTTACCTAAT
2810123 TCGCATTGCGATTTA
1 TCGCATTGCGATTTA
2810138 GTAAATCGCA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
19 2 0.04
20 12 0.24
21 34 0.68
22 2 0.04
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTACCTAAT
Found at i:2810144 original size:20 final size:20
Alignment explanation
Indices: 2810060--2810147 Score: 81
Period size: 20 Copynumber: 4.3 Consensus size: 20
2810050 GATTCTGACT
* *
2810060 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTACTAA
*
2810080 ATTCGCATTGCGATTTTCCTAA
1 A-TCGCATTGCGA-TTTACTAA
*
2810102 TTCGCACTT-CGATTTACGT-A
1 ATCGCA-TTGCGATTTAC-TAA
*
2810122 ATCGCATTGCGATTTAGTAA
1 ATCGCATTGCGATTTACTAA
2810142 ATCGCA
1 ATCGCA
2810148 ACGAGATTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
19 3 0.05
20 25 0.44
21 20 0.35
22 9 0.16
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATTTACTAA
Found at i:2811370 original size:14 final size:14
Alignment explanation
Indices: 2811342--2811382 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
2811332 TAATGAACCT
*
2811342 TAAACCTTAAA-CC
1 TAAACCCTAAATCC
2811355 TAAACCCTAAATCC
1 TAAACCCTAAATCC
2811369 TAAACCCTAAATCC
1 TAAACCCTAAATCC
2811383 GATTATGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAATCC
Found at i:2812721 original size:11 final size:11
Alignment explanation
Indices: 2812705--2812865 Score: 106
Period size: 11 Copynumber: 13.7 Consensus size: 11
2812695 TAACCCGTTT
2812705 TCGAGCTTGAA
1 TCGAGCTTGAA
2812716 TCGAGCTTGAA
1 TCGAGCTTGAA
*
2812727 ACGAGCTTGAA
1 TCGAGCTTGAA
* *
2812738 ACGAGTTTGAA
1 TCGAGCTTGAA
*
2812749 TCGAGCTTAAAA
1 TCGAGCTT-GAA
* *
2812761 TTGAGCTATTTAA
1 TCGAGC--TTGAA
*
2812774 TCGAGCTTCTCAA
1 TCGAGC-T-TGAA
*
2812787 TCGAGCTTGCA
1 TCGAGCTTGAA
* *
2812798 TCGAGTTTTTCAA
1 TCGAG--CTTGAA
**
2812811 TCGAGCTCAAAA
1 TCGAGCT-TGAA
*
2812823 TCGAGCTTTAA
1 TCGAGCTTGAA
*
2812834 TCGAGCTTGAG
1 TCGAGCTTGAA
2812845 TCTAGAGCTTGAA
1 TC--GAGCTTGAA
2812858 TCGAGCTT
1 TCGAGCTT
2812866 TTAAAATTTT
Statistics
Matches: 118, Mismatches: 23, Indels: 18
0.74 0.14 0.11
Matches are distributed among these distances:
11 64 0.54
12 18 0.15
13 34 0.29
14 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:2812951 original size:31 final size:31
Alignment explanation
Indices: 2812891--2812951 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
2812881 GTTCGAGCCT
** *
2812891 TTTCGAGTTCGAGTCGAGTTTCAATATTTTC
1 TTTCGAGTTCGAGTCGAGCCTCAAAATTTTC
*
2812922 TTTCGAGTTCGAGTCGAGCCTGAAAATTTT
1 TTTCGAGTTCGAGTCGAGCCTCAAAATTTT
2812952 AGGCTCGCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.41
Consensus pattern (31 bp):
TTTCGAGTTCGAGTCGAGCCTCAAAATTTTC
Found at i:2813282 original size:24 final size:24
Alignment explanation
Indices: 2813250--2813303 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2813240 GTATTCGAAA
2813250 TTTGATCTTGGCCAATACCCGGAC
1 TTTGATCTTGGCCAATACCCGGAC
* * *
2813274 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGCCAATACCCGGAC
2813298 TTTGAT
1 TTTGAT
2813304 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGCCAATACCCGGAC
Found at i:2815838 original size:20 final size:19
Alignment explanation
Indices: 2815810--2815864 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
2815800 CAATCATCTT
* *
2815810 AATGTCTATCGTAACGCGGA
1 AATGACTATCGCAACGC-GA
*
2815830 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
2815849 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
2815865 AGAGAATCGC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:2815852 original size:19 final size:17
Alignment explanation
Indices: 2815837--2815967 Score: 82
Period size: 19 Copynumber: 7.8 Consensus size: 17
2815827 GGAAATGACT
2815837 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
2815856 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
2815870 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
2815889 ATCGCAA--CGAAA-GA
1 ATCGCAATGCGAAATGA
2815903 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
**
2815922 ATCGCAA--CG-AGGGA
1 ATCGCAATGCGAAATGA
*
2815936 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
2815955 ATCGCAACGCGAA
1 ATCGCAATGCGAA
2815968 TTTAGTTTCG
Statistics
Matches: 90, Mismatches: 7, Indels: 30
0.71 0.06 0.24
Matches are distributed among these distances:
14 24 0.27
16 15 0.17
17 15 0.17
19 36 0.40
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:2815874 original size:14 final size:14
Alignment explanation
Indices: 2815855--2815942 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
2815845 GCGAAATGAA
2815855 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2815869 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
2815888 AATCGCAACGAAAG
1 AATCGCAACGAGAG
*
2815902 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
2815921 AATCGCAACGAGGG
1 AATCGCAACGAGAG
2815935 AATCGCAA
1 AATCGCAA
2815943 AGCGAAATGA
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 26 0.46
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 19 0.33
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2815879 original size:33 final size:33
Alignment explanation
Indices: 2815837--2815963 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
2815827 GGAAATGACT
2815837 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2815870 ATCGCAATGCGAAATGAAAATCGCAACGAAAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2815903 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2815936 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2815964 CGAATTTAGT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2816015 original size:33 final size:33
Alignment explanation
Indices: 2815973--2816052 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
2815963 GCGAATTTAG
* *
2815973 TTTCGCGTTGCGATTTTGTCGGTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGGTGCGATTTTCA
*
2816006 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGGTGCGATTTTCA
*
2816039 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
2816053 AGTCATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.10, C:0.21, G:0.24, T:0.45
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGGTGCGATTTTCA
Found at i:2816019 original size:19 final size:19
Alignment explanation
Indices: 2815995--2816052 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
2815985 ATTTTGTCGG
2815995 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
2816014 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
2816028 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCGT
2816047 TGCGAT
1 TGCGAT
2816053 AGTCATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
14 10 0.32
16 3 0.10
17 3 0.10
19 15 0.48
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:2816178 original size:14 final size:14
Alignment explanation
Indices: 2816159--2816195 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2816149 CATCAATTAA
2816159 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2816173 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2816187 ACAAATCAA
1 ACAAATCAA
2816196 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2817611 original size:21 final size:21
Alignment explanation
Indices: 2817545--2817611 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2817535 GTGAATTGGG
*
2817545 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2817565 TCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2817587 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2817608 CTCT
1 CTCT
2817612 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2817630 original size:42 final size:41
Alignment explanation
Indices: 2817545--2817667 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 41
2817535 GTGAATTGGG
* * * *
2817545 CTCTTGAATGGTGGGA-GGGATCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
2817587 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * * *
2817629 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGGCAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
2817668 CGAGTCGGGC
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 4 0.06
42 56 0.85
43 6 0.09
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:2818110 original size:19 final size:19
Alignment explanation
Indices: 2818088--2818171 Score: 79
Period size: 19 Copynumber: 4.6 Consensus size: 19
2818078 AAAAATGACT
2818088 ATCGCAACGCGAAATAAAA
1 ATCGCAACGCGAAATAAAA
* *
2818107 ATCGCAA--CG--A-CAGA
1 ATCGCAACGCGAAATAAAA
*
2818121 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATAAAA
* *
2818140 ATCGCAATGCGAAACCAAAA
1 ATCGCAACGCGAAA-TAAAA
2818160 ATCGCAACGCGA
1 ATCGCAACGCGA
2818172 TTATAGTTCC
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
14 9 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 22 0.43
20 14 0.27
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (19 bp):
ATCGCAACGCGAAATAAAA
Found at i:2818223 original size:33 final size:33
Alignment explanation
Indices: 2818181--2818261 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
2818171 ATTATAGTTC
*
2818181 CGCGTTGCGATTTTGTCGTTGTGATTTTCATTT
1 CGCGTTGCGATTTTCTCGTTGTGATTTTCATTT
* * *
2818214 CGCGTTGCGATTCTCTTGTTGTGATTTTCGTTT
1 CGCGTTGCGATTTTCTCGTTGTGATTTTCATTT
2818247 CGCGTTGCGATTTTC
1 CGCGTTGCGATTTTC
2818262 ATTCTCTCGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.07, C:0.19, G:0.25, T:0.49
Consensus pattern (33 bp):
CGCGTTGCGATTTTCTCGTTGTGATTTTCATTT
Found at i:2818225 original size:19 final size:19
Alignment explanation
Indices: 2818197--2818286 Score: 91
Period size: 19 Copynumber: 4.9 Consensus size: 19
2818187 GCGATTTTGT
*
2818197 CGTTGTGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2818216 CGTTGCGATTCTC--TT--
1 CGTTGCGATTTTCATTTCG
* *
2818231 -GTTGTGATTTTCGTTTCG
1 CGTTGCGATTTTCATTTCG
*
2818249 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
2818269 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
2818287 AACCAAAAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.17
16 2 0.03
17 2 0.03
19 26 0.45
20 18 0.31
ACGTcount: A:0.09, C:0.20, G:0.20, T:0.51
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2818274 original size:20 final size:20
Alignment explanation
Indices: 2818223--2818284 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
2818213 TCGCGTTGCG
* *
2818223 ATTCTCTTGTTGTGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* *
2818243 GTT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
2818262 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
2818282 ATT
1 ATT
2818285 TCAACCAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 15 0.43
20 20 0.57
ACGTcount: A:0.10, C:0.19, G:0.18, T:0.53
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:2818279 original size:39 final size:34
Alignment explanation
Indices: 2818181--2818286 Score: 119
Period size: 33 Copynumber: 3.0 Consensus size: 34
2818171 ATTATAGTTC
2818181 CGCGTTGCGATT-T-TGTCGTTGTGATTTTCATTT
1 CGCGTTGCGATTCTCT-TCGTTGTGATTTTCATTT
*
2818214 CGCGTTGCGATTCTCTT-GTTGTGATTTTCGTTT
1 CGCGTTGCGATTCTCTTCGTTGTGATTTTCATTT
*
2818247 CGCGTTGCGATTTTCATTCTCTCGTTGCGATTTTCATTT
1 CGCGTTGCGA--TTC--TCT-TCGTTGTGATTTTCATTT
2818286 C
1 C
2818287 AACCAAAAGA
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
33 37 0.60
34 2 0.03
35 4 0.06
37 3 0.05
38 1 0.02
39 15 0.24
ACGTcount: A:0.08, C:0.20, G:0.22, T:0.50
Consensus pattern (34 bp):
CGCGTTGCGATTCTCTTCGTTGTGATTTTCATTT
Found at i:2818549 original size:86 final size:86
Alignment explanation
Indices: 2818376--2818550 Score: 289
Period size: 86 Copynumber: 2.0 Consensus size: 86
2818366 TGGATTGCAT
*
2818376 TACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTT
1 TACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTT
2818441 AGCAGAATTGGCAGCAACCGAATA
63 AGCAGAATTGGCAGCAACCGAATA
2818465 TACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 TACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAG
*
2818529 CAGTATTGGCAGCAACCGAATA
65 CAGAATTGGCAGCAACCGAATA
2818551 AATTTACTAA
Statistics
Matches: 83, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
86 34 0.41
89 22 0.27
90 27 0.33
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (86 bp):
TACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGC
AGAATTGGCAGCAACCGAATA
Found at i:2820271 original size:20 final size:20
Alignment explanation
Indices: 2820246--2820308 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
2820236 TTTTGGTTGA
2820246 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
2820266 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
2820285 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
2820306 AAT
1 AAT
2820309 CGCAACACGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:2820382 original size:14 final size:14
Alignment explanation
Indices: 2820363--2820399 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2820353 TTTGGTTTCG
2820363 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
2820377 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
2820391 CGTTGCGAT
1 CGTTGCGAT
2820400 AGTCATTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:2820993 original size:20 final size:20
Alignment explanation
Indices: 2820970--2821084 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
2820960 CGATAGTCAG
2820970 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
2820990 ATTCACATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
* * *
2821010 AATTCGCATTGGGATTTTCCT
1 -ATTCGCATTGCGATTTACGT
* *
2821031 AATTTGCATTGGGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* * *
2821052 AATCTCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2821072 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2821085 ATTAGGAAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
20 42 0.54
21 36 0.46
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2821019 original size:21 final size:21
Alignment explanation
Indices: 2820970--2821084 Score: 121
Period size: 21 Copynumber: 5.6 Consensus size: 21
2820960 CGATAGTCAG
2820970 ATTCGCATTGCGATTTACGT-
1 ATTCGCATTGCGATTTACGTA
* * *
2820990 ATTCACATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTA
* * *
2821011 ATTCGCATTGGGATTTTCCTA
1 ATTCGCATTGCGATTTACGTA
* *
2821032 ATTTGCATTGGGATTTACGTA
1 ATTCGCATTGCGATTTACGTA
2821053 ATCTCG--TTGCGATTTACGT-
1 AT-TCGCATTGCGATTTACGTA
2821072 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2821085 ATTAGGAAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
18 3 0.04
19 2 0.02
20 35 0.43
21 39 0.48
22 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (21 bp):
ATTCGCATTGCGATTTACGTA
Found at i:2821105 original size:21 final size:21
Alignment explanation
Indices: 2821081--2821121 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2821071 TATTCGCATT
2821081 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
2821102 GCGAATTTGGGAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
2821122 TGTGATAGTC
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:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:2834614 original size:2 final size:2
Alignment explanation
Indices: 2834607--2834645 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2834597 AGTTACATGG
2834607 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
2834646 CCCTAGGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2835581 original size:20 final size:20
Alignment explanation
Indices: 2835543--2835581 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2835533 TGGAGAAGAA
*
2835543 AAAGCATGACAATTATAATC
1 AAAGCATGACAAATATAATC
2835563 AAAGCATGTACAAAT-TAAT
1 AAAGCATG-ACAAATATAAT
2835582 ATATGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.26
Consensus pattern (20 bp):
AAAGCATGACAAATATAATC
Found at i:2836406 original size:60 final size:60
Alignment explanation
Indices: 2836270--2836383 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
2836260 AATAGTTGGT
*** * * *
2836270 GACCATTTTGTAACTTTTAGTAGTTAGGGGACTCAACAAAACAATGTCTTGTAGCTAATG
1 GACCATTTTGTAACTTTTAGTAGTTAAAAGACTCAACAAAACAATGTCCTATAGCTAAGG
*
2836330 GACCATTTTGTAACTTTTAGTAGTTAAAAGACTCAACAAAGCAATGTCCTATAG
1 GACCATTTTGTAACTTTTAGTAGTTAAAAGACTCAACAAAACAATGTCCTATAG
2836384 TTGAGGGGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAGTAGTTAAAAGACTCAACAAAACAATGTCCTATAGCTAAGG
Found at i:2866115 original size:35 final size:34
Alignment explanation
Indices: 2866069--2866179 Score: 141
Period size: 35 Copynumber: 3.2 Consensus size: 34
2866059 TAAAATATCC
*
2866069 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAA-TTCCAAAATAAT
*
2866104 TCAATTTCATTCTAAACCCTAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAATTCCAAAATAAT
** * * *
2866138 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCC-AATTCCAAAATAAT
2866173 TCAATTT
1 TCAATTT
2866180 AAGGTTTAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
34 27 0.41
35 39 0.59
ACGTcount: A:0.41, C:0.23, G:0.01, T:0.36
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCCAATTCCAAAATAAT
Found at i:2866243 original size:35 final size:35
Alignment explanation
Indices: 2866175--2866249 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
2866165 AAAATACTTC
* * *
2866175 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
* *
2866210 AATTTAGGGTTTAGAATGAAATT-AAGGTGTTTTGA
1 AATTTAAGGTTTAGAATGAAATTGAA-GTATTTTGA
2866245 AATTT
1 AATTT
2866250 TGAACATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
Found at i:2869578 original size:29 final size:29
Alignment explanation
Indices: 2869515--2869584 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
2869505 AGCAACGAGT
2869515 CGAGTC-AAGCAACAAGTTTTTTTAACGAA
1 CGAGTCGAAGCAACAAG-TTTTTTAACGAA
*
2869544 CAAGTCGAA-CAACAA-TTTTTTAACGAGCA
1 CGAGTCGAAGCAACAAGTTTTTTAACGA--A
2869573 CGAGTCG-AGCAA
1 CGAGTCGAAGCAA
2869585 AGATTTGACG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
27 11 0.31
28 1 0.03
29 21 0.60
30 2 0.06
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.23
Consensus pattern (29 bp):
CGAGTCGAAGCAACAAGTTTTTTAACGAA
Found at i:2873428 original size:23 final size:23
Alignment explanation
Indices: 2873387--2873434 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
2873377 TTCACGTTTG
*
2873387 TTTATTTATTATTCACGAACATA
1 TTTATTTAATATTCACGAACATA
* * *
2873410 TTTATTTAATGTTCGCGAACGTA
1 TTTATTTAATATTCACGAACATA
2873433 TT
1 TT
2873435 CACTTATATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.48
Consensus pattern (23 bp):
TTTATTTAATATTCACGAACATA
Found at i:2888240 original size:12 final size:12
Alignment explanation
Indices: 2888225--2888250 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2888215 GTTATTTAAA
2888225 CGGGTATTGGGC
1 CGGGTATTGGGC
2888237 CGGGTATTGGGC
1 CGGGTATTGGGC
2888249 CG
1 CG
2888251 AGAATCGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.19, G:0.50, T:0.23
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:2891181 original size:35 final size:35
Alignment explanation
Indices: 2891125--2891202 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 35
2891115 GTATCAATGA
*
2891125 GTAAGGGACATGTACAACTATTGAAATGATACAAG
1 GTAAAGGACATGTACAACTATTGAAATGATACAAG
* *
2891160 GTAAAGGACATGTACAGCTATTGAAATGATGCAAG
1 GTAAAGGACATGTACAACTATTGAAATGATACAAG
2891195 GTAAAGGA
1 GTAAAGGA
2891203 ATAGTTCTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.22
Consensus pattern (35 bp):
GTAAAGGACATGTACAACTATTGAAATGATACAAG
Found at i:2891928 original size:27 final size:26
Alignment explanation
Indices: 2891890--2891966 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 26
2891880 TCATTTAAAT
2891890 TTATTATTATTATTAAA-T-TTATTA
1 TTATTATTATTATTAAATTATTATTA
2891914 TTATTATTATTATTAAA-TATTATTA
1 TTATTATTATTATTAAATTATTATTA
*
2891939 TTAGTATATTATTATTAAATAATTATTA
1 TTA-T-TATTATTATTAAATTATTATTA
2891967 CAAGCCCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
24 18 0.38
25 9 0.19
26 1 0.02
27 13 0.27
28 7 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTATTATTATTATTAAATTATTATTA
Found at i:2891966 original size:3 final size:3
Alignment explanation
Indices: 2891890--2891955 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
2891880 TCATTTAAAT
* *
2891890 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTAA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
2891936 TTA TTA GTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
2891956 AATAATTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
2 3 0.06
3 48 0.89
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2901387 original size:94 final size:93
Alignment explanation
Indices: 2901214--2901496 Score: 417
Period size: 94 Copynumber: 3.0 Consensus size: 93
2901204 AGAAGACCCA
* *
2901214 ATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAAAACCAA
2901279 TCATTGAATTTGGAAGATGAATGTGCTC
66 TCATTGAATTTGGAAGATGAATGTGCTC
* * * *
2901307 ATAGCATCTTTTGGGAAGTGTTCTTTGAGTTATCTGGTCTGGTTTGGTATGAAACCACATAATCA
1 ATAGCATCTTCT-GGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAAAACCA
**
2901372 ATCATTGAATTTGGAAGATGAATGCACTC
65 ATCATTGAATTTGGAAGATGAATGTGCTC
* *
2901401 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATG-AACTC-CAAAACCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAAC-CACAAAACCA
* * *
2901464 ATCATTGGATTTGAAAGATGAATTTGCTC
65 ATCATTGAATTTGGAAGATGAATGTGCTC
2901493 ATAG
1 ATAG
2901497 TAGAAATAAG
Statistics
Matches: 170, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
92 37 0.22
93 46 0.27
94 87 0.51
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (93 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAAAACCAA
TCATTGAATTTGGAAGATGAATGTGCTC
Found at i:2903810 original size:54 final size:54
Alignment explanation
Indices: 2903704--2903815 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 54
2903694 CAATGATTGA
* * ***
2903704 GAACATCTGAGCAGAAGCTACAAAAAAGGATGAATGTGTTGTCAAATATTTTAC
1 GAACATCTGAGCAAAAGCCACAAAAAAGGATGAATGCACTGTCAAATATTTTAC
** * *
2903758 GAACATCTGAGCAAAAGCCACAGGAAAGGATGAATGCACTGTTAAATGTTTTAC
1 GAACATCTGAGCAAAAGCCACAAAAAAGGATGAATGCACTGTCAAATATTTTAC
2903812 GAAC
1 GAAC
2903816 CTGCTATTCT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.23
Consensus pattern (54 bp):
GAACATCTGAGCAAAAGCCACAAAAAAGGATGAATGCACTGTCAAATATTTTAC
Found at i:2904987 original size:76 final size:76
Alignment explanation
Indices: 2904861--2905723 Score: 1607
Period size: 76 Copynumber: 11.5 Consensus size: 76
2904851 CTATTTCCCA
*
2904861 CATCTGTAAATCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2904926 AGCCTTCGGGT
66 AGCCTTCGGGT
2904937 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2905002 AGCCTTCGGGT
66 AGCCTTCGGGT
2905013 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2905078 AGCCTTCGGGT
66 AGCCTTCGGGT
2905089 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2905154 AGCCTTCGGGT
66 AGCCTTCGGGT
2905165 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2905230 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2905241 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2905306 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2905317 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2905382 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2905393 TATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2905458 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2905469 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2905534 AGCCTTCGGGT
66 AGCCTTCGGGT
2905545 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2905610 AGCCTTCGGGT
66 AGCCTTCGGGT
2905621 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTT---
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2905682 ----TTCGGGT
66 AGCCTTCGGGT
* *
2905689 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
2905724 CATTTCCATC
Statistics
Matches: 776, Mismatches: 11, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
68 40 0.05
75 3 0.00
76 733 0.94
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:2905866 original size:18 final size:18
Alignment explanation
Indices: 2905843--2905881 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2905833 TTTTTTTCAT
2905843 TTAAATTTATTATTATTA
1 TTAAATTTATTATTATTA
2905861 TTAAATTTATTATTATTA
1 TTAAATTTATTATTATTA
2905879 TTA
1 TTA
2905882 TTATTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAAATTTATTATTATTA
Found at i:2905876 original size:24 final size:24
Alignment explanation
Indices: 2905849--2905922 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
2905839 TCATTTAAAT
2905849 TTATTATTATTATTAAATTTATTA
1 TTATTATTATTATTAAATTTATTA
2905873 TTATTATTATTATTAAATATTATTA
1 TTATTATTATTATTAAAT-TTATTA
* *
2905898 GTA-TATTATTATTAAA-TAATTA
1 TTATTATTATTATTAAATTTATTA
2905920 TTA
1 TTA
2905923 CAAGCCCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
22 7 0.15
24 31 0.67
25 8 0.17
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (24 bp):
TTATTATTATTATTAAATTTATTA
Done.