Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 69 of 171
Found at i:25238821 original size:22 final size:22
Alignment explanation
Indices: 25238791--25238833 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
25238781 TCAACAATCT
* *
25238791 CCACGTCAGCGCCATGTCAGCA
1 CCACATCAGCGCCACGTCAGCA
*
25238813 CCACATCAGCGCTACGTCAGC
1 CCACATCAGCGCCACGTCAGC
25238834 CACGTGACCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.42, G:0.21, T:0.14
Consensus pattern (22 bp):
CCACATCAGCGCCACGTCAGCA
Found at i:25238832 original size:11 final size:11
Alignment explanation
Indices: 25238791--25238833 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
25238781 TCAACAATCT
25238791 CCACGTCAGCG
1 CCACGTCAGCG
* *
25238802 CCATGTCAGCA
1 CCACGTCAGCG
*
25238813 CCACATCAGCG
1 CCACGTCAGCG
*
25238824 CTACGTCAGC
1 CCACGTCAGC
25238834 CACGTGACCC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.23, C:0.42, G:0.21, T:0.14
Consensus pattern (11 bp):
CCACGTCAGCG
Found at i:25252416 original size:49 final size:49
Alignment explanation
Indices: 25252354--25252721 Score: 220
Period size: 49 Copynumber: 7.6 Consensus size: 49
25252344 AAGATAATGG
* * *
25252354 AGGGAAAGGTTTAAGTCGCAACGACGAACCTCGTACCTCAGAAGCATTA
1 AGGGAAAGATTTAAGCCGCAACGACGAACCTTGTACCTCAGAAGCATTA
* * * * *
25252403 AGGGAAAGATTTAAGCCGCAACGAAGAAACTAGTACCAC-GAA-TA-TA
1 AGGGAAAGATTTAAGCCGCAACGACGAACCTTGTACCTCAGAAGCATTA
* * *
25252449 CGGAGGGAAAGGTTTAAG-C-CAAC-AGCGAACCTTGTACCTCAGAA-AATGA
1 ---AGGGAAAGATTTAAGCCGCAACGA-CGAACCTTGTACCTCAGAAGCATTA
* * * * * * * * *
25252498 AGGGGAGGATTTAAACCGCAACGACAAATCTAGAACCACA-AAG-ATGCAA
1 AGGGAAAGATTTAAGCCGCAACGACGAACCTTGTACCTCAGAAGCAT--TA
* * * * * ** * *
25252547 AGGGGACGGTTTAAACCGCCACGGTGAACCTTGTACCTCAGAACCATAA
1 AGGGAAAGATTTAAGCCGCAACGACGAACCTTGTACCTCAGAAGCATTA
* * * *
25252596 AGGGAGAGATTTAAGCCACAACGACGAATCC-GGTACCACA-AAG-ATATAA
1 AGGGAAAGATTTAAGCCGCAACGACGAA-CCTTGTACCTCAGAAGCAT-T-A
** * * *
25252645 AGCAAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
1 AGGGAAAGATTTAAGCCGCAACGACGAACCTTGTACCTCAGAAGCATTA
*
25252694 AGGGAAAGATTTAAGCCGCAATGACGAA
1 AGGGAAAGATTTAAGCCGCAACGACGAA
25252722 TCCAGTACCA
Statistics
Matches: 237, Mismatches: 62, Indels: 40
0.70 0.18 0.12
Matches are distributed among these distances:
46 14 0.06
47 23 0.10
48 27 0.11
49 162 0.68
50 7 0.03
51 4 0.02
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (49 bp):
AGGGAAAGATTTAAGCCGCAACGACGAACCTTGTACCTCAGAAGCATTA
Found at i:25252656 original size:98 final size:97
Alignment explanation
Indices: 25252299--25252803 Score: 403
Period size: 98 Copynumber: 5.2 Consensus size: 97
25252289 ACCATAAAGA
* * * * * *
25252299 CATGAGGGGAAGGATTTAAGTCGCAAC-AGCGAATCCAATACCACGAAGATA-ATGGAGGGAAAG
1 CATGAAGGGAAAGATTTAAGCCGCAACGA-CGAATCCAGTACCACAAAGATACA--AAGGGAAAG
* * * *
25252362 GTTTAAGTCGCAACGACGAACCTCGTACCTCAGAAG
63 GTTTAA-ACGCCACGGCGAACCTTGTACCTCAGAAG
* * * * * * **
25252398 CATTAAGGGAAAGATTTAAGCCGCAACGAAGAAACTAGTACCACGAATATACGGAGGGAAAGGTT
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACAAAGATACAAAGGGAAAGGTT
*
25252463 T-AA-GCCAACAGCGAACCTTGTACCTCAGAA-
66 TAAACGCC-ACGGCGAACCTTGTACCTCAGAAG
* * * * * * * * * *
25252493 AATGAAGGGGAGGATTTAAACCGCAACGACAAATCTAGAACCACAAAGATGCAAAGGGGACGGTT
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACAAAGATACAAAGGGAAAGGTT
* *
25252558 TAAACCGCCACGGTGAACCTTGTACCTCAGAAC
66 TAAA-CGCCACGGCGAACCTTGTACCTCAGAAG
* * * * * **
25252591 CATAAAGGGAGAGATTTAAGCCACAACGACGAATCCGGTACCACAAAGATATAAAGCAAAAGGTT
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACAAAGATACAAAGGGAAAGGTT
* * *
25252656 TAAGTCGCAACGACGAACCTTGTACCTCAGAAG
66 TAA-ACGCCACGGCGAACCTTGTACCTCAGAAG
* ** * * *
25252689 CATGAAGGGAAAGATTTAAGCCGCAATGACGAATCCAGTACCAGGACGACAACGAAGGGAAAAGG
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACAAAGA-TACAAAGGG-AAAGG
* * *
25252754 TTTAAGCCGTCACGACGAACCATT-TACCTC-GAAAG
64 TTTAA-ACGCCACGGCGAACC-TTGTACCTCAG-AAG
25252789 CATGAAGGGAAAGAT
1 CATGAAGGGAAAGAT
25252804 CTAAATTGTA
Statistics
Matches: 323, Mismatches: 71, Indels: 23
0.77 0.17 0.06
Matches are distributed among these distances:
95 52 0.16
96 22 0.07
97 22 0.07
98 132 0.41
99 45 0.14
100 48 0.15
101 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.16
Consensus pattern (97 bp):
CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACAAAGATACAAAGGGAAAGGTT
TAAACGCCACGGCGAACCTTGTACCTCAGAAG
Found at i:25252730 original size:49 final size:48
Alignment explanation
Indices: 25252354--25252803 Score: 215
Period size: 49 Copynumber: 9.2 Consensus size: 48
25252344 AAGATAATGG
* * * *
25252354 AGGGAAAGGTTTAAGTCGCAACGACGAACCTCGTACCTCAGAAGCATTA
1 AGGGAAAGATTTAAGCCGCAACGACGAACC-AGTACCTCAGAAGCATGA
* * * * *
25252403 AGGGAAAGATTTAAGCCGCAACGAAGAAACTAGTACCAC-GAA-TATACGG
1 AGGGAAAGATTTAAGCCGCAACGACG-AACCAGTACCTCAGAAGCAT--GA
* * *
25252452 AGGGAAAGGTTTAAG-C-CAAC-AGCGAACCTTGTACCTCAGAA-AATGA
1 AGGGAAAGATTTAAGCCGCAACGA-CGAACC-AGTACCTCAGAAGCATGA
* * * * * * *
25252498 AGGGGAGGATTTAAACCGCAACGACAAATCTAGAACCACA-AAG-ATGCAA
1 AGGGAAAGATTTAAGCCGCAACGACGAA-CCAGTACCTCAGAAGCATG--A
* * * * * ** * * *
25252547 AGGGGACGGTTTAAACCGCCACGGTGAACCTTGTACCTCAGAACCATAA
1 AGGGAAAGATTTAAGCCGCAACGACGAACC-AGTACCTCAGAAGCATGA
* * * * * *
25252596 AGGGAGAGATTTAAGCCACAACGACGAATCCGGTACCACA-AAGATATAA
1 AGGGAAAGATTTAAGCCGCAACGACGAA-CCAGTACCTCAGAAG-CATGA
** * * *
25252645 AGCAAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
1 AGGGAAAGATTTAAGCCGCAACGACGAACC-AGTACCTCAGAAGCATGA
* * *
25252694 AGGGAAAGATTTAAGCCGCAATGACGAATCCAGTA-C-CAGGACGACAACGA
1 AGGGAAAGATTTAAGCCGCAACGACGAA-CCAGTACCTCA-GAAG-C-ATGA
* *
25252744 AGGGAAAAGGTTTAAGCCGTC-ACGACGAACCATTTACCTC-GAAAGCATGA
1 AGGG-AAAGATTTAAGCCG-CAACGACGAACCA-GTACCTCAG-AAGCATGA
25252794 AGGGAAAGAT
1 AGGGAAAGAT
25252804 CTAAATTGTA
Statistics
Matches: 297, Mismatches: 74, Indels: 60
0.69 0.17 0.14
Matches are distributed among these distances:
46 16 0.05
47 21 0.07
48 31 0.10
49 169 0.57
50 29 0.10
51 26 0.09
52 4 0.01
53 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (48 bp):
AGGGAAAGATTTAAGCCGCAACGACGAACCAGTACCTCAGAAGCATGA
Found at i:25253277 original size:23 final size:23
Alignment explanation
Indices: 25253247--25253292 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
25253237 AAAATAAATG
25253247 AATTTAAATTAAAA-TCCAAATTT
1 AATTTAAA-TAAAAGTCCAAATTT
25253270 AATTTAAATAAAATGTCCAAATT
1 AATTTAAATAAAA-GTCCAAATT
25253293 ACAGGCCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 8 0.38
24 8 0.38
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (23 bp):
AATTTAAATAAAAGTCCAAATTT
Found at i:25253399 original size:16 final size:16
Alignment explanation
Indices: 25253378--25253420 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
25253368 ACCATCACTG
*
25253378 CCACGTCAGCACGTGT
1 CCACGTCAGCACATGT
*
25253394 CCACGTTAGCACATGT
1 CCACGTCAGCACATGT
*
25253410 TCACGTCAGCA
1 CCACGTCAGCA
25253421 AGCGCCACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.21
Consensus pattern (16 bp):
CCACGTCAGCACATGT
Found at i:25257553 original size:17 final size:17
Alignment explanation
Indices: 25257531--25257582 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
25257521 CTTAAACCCA
*
25257531 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
25257548 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
25257565 ATTATAAATTTAAATTT
1 ATTTTAAATTTAAATTT
25257582 A
1 A
25257583 ATTAAAAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:25257559 original size:6 final size:6
Alignment explanation
Indices: 25257533--25257583 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
25257523 TAAACCCAAT
* *
25257533 TTTAAA TTTTAA TTT-AT TTTAAA TTTAAA TTT--A TTATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA
25257579 TTTAA
1 TTTAA
25257584 TTAAAAAGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 3 0.08
5 5 0.13
6 27 0.71
7 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:25259182 original size:29 final size:29
Alignment explanation
Indices: 25259150--25259568 Score: 220
Period size: 29 Copynumber: 14.3 Consensus size: 29
25259140 AACAATCTAG
* *
25259150 AAATAACATTTTGACCCTGAACTTTTCAA
1 AAATTACATTTTGACCCTAAACTTTTCAA
* * * *
25259179 AAATTACATTTTGATCGTCGAAC-TTTCTAG
1 AAATTACATTTTGACCCT-AAACTTTTC-AA
* * *
25259209 AAATTACCTTTTGACCCCAAACTTTCCAA
1 AAATTACATTTTGACCCTAAACTTTTCAA
* **
25259238 AAATTACATTTTTAACCCTAAACTTCCCAA
1 AAATTACA-TTTTGACCCTAAACTTTTCAA
* *
25259268 AAATTACACTTTGACCCCTGAAC-TTTCAAA
1 AAATTACATTTTGA-CCCTAAACTTTTC-AA
* * **
25259298 AAAATAAATTTTGA-CCTCAAACTACTCAAAAA
1 AAATTACATTTTGACCCT-AAACTTTTC---AA
25259330 AAATTACATTTTTG-CCCTCAAAC-TTTCAA
1 AAATTACA-TTTTGACCCT-AAACTTTTCAA
* * * * *
25259359 AAATCATATTTTTGTCCC-GAAC-TTCCAA
1 AAATTACA-TTTTGACCCTAAACTTTTCAA
* * * *
25259387 AAATTCCATTTTTGCCCCTGAACTTCT-AA
1 AAATTACA-TTTTGACCCTAAACTTTTCAA
* * * *
25259416 AAATCACATTTTTG-CCTTGAA-TTTCCAA
1 AAATTACA-TTTTGACCCTAAACTTTTCAA
*
25259444 AAATTACATTTTGACCCTAAACTTCTCAA
1 AAATTACATTTTGACCCTAAACTTTTCAA
25259473 AAATTACATTTTG-CCCTCAAAC-TTTCAA
1 AAATTACATTTTGACCCT-AAACTTTTCAA
* * * * *
25259501 AAATCACATTTTTACCCTAGAGC-TTCCAG
1 AAATTACATTTTGACCCTA-AACTTTTCAA
* *
25259530 AAATTCCATTCTTG-CTCCTAAAC-TTCCAA
1 AAATTACATT-TTGAC-CCTAAACTTTTCAA
25259559 AAATTACATT
1 AAATTACATT
25259569 CCTATAATCA
Statistics
Matches: 305, Mismatches: 62, Indels: 46
0.74 0.15 0.11
Matches are distributed among these distances:
27 7 0.02
28 66 0.22
29 128 0.42
30 80 0.26
32 11 0.04
33 13 0.04
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (29 bp):
AAATTACATTTTGACCCTAAACTTTTCAA
Found at i:25259262 original size:59 final size:60
Alignment explanation
Indices: 25259145--25259309 Score: 156
Period size: 59 Copynumber: 2.8 Consensus size: 60
25259135 CCCTGAACAA
* * * * * * * *
25259145 TCTAGAAATAACATTTTGACCCTGAACTTTTCAAAAATTACA-TTTTGATCGTCGAACTT
1 TCTAGAAATTACCTTTTGACCCCGAACTTTCCAAAAATTACATTTTTAACCCTCAAACTT
*
25259204 TCTAGAAATTACCTTTTGACCCCAAACTTTCCAAAAATTACATTTTTAACCCT-AAACTT
1 TCTAGAAATTACCTTTTGACCCCGAACTTTCCAAAAATTACATTTTTAACCCTCAAACTT
* * * * * *
25259263 CCCAAAAATTACAC-TTTGACCCCTGAACTTTCAAAAAAATAAATTTT
1 TCTAGAAATTAC-CTTTTGACCCC-GAACTTTCCAAAAATTACATTTT
25259310 GACCTCAAAC
Statistics
Matches: 87, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
59 60 0.69
60 27 0.31
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (60 bp):
TCTAGAAATTACCTTTTGACCCCGAACTTTCCAAAAATTACATTTTTAACCCTCAAACTT
Found at i:25259341 original size:32 final size:31
Alignment explanation
Indices: 25259295--25259361 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 31
25259285 CTGAACTTTC
25259295 AAAAAAATAAA-TTTTGACCTCAAACTACTCA
1 AAAAAAATAAATTTTTGACCTCAAACT-CTCA
* * *
25259326 AAAAAAATTACATTTTTGCCCTCAAACTTTCA
1 AAAAAAA-TAAATTTTTGACCTCAAACTCTCA
25259358 AAAA
1 AAAA
25259362 TCATATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 7 0.23
32 10 0.32
33 14 0.45
ACGTcount: A:0.49, C:0.19, G:0.03, T:0.28
Consensus pattern (31 bp):
AAAAAAATAAATTTTTGACCTCAAACTCTCA
Found at i:25259519 original size:57 final size:56
Alignment explanation
Indices: 25259150--25259568 Score: 267
Period size: 57 Copynumber: 7.2 Consensus size: 56
25259140 AACAATCTAG
* * * * * *
25259150 AAATAACATTTTGACCCTGAACTTTTCAAAAATTACATTTTGATCGTCGAACTTTCTAG
1 AAATTACATTTTGACCCTAAAC-TTTCAAAAATTACATTTTG-CCCTCAAACTTTC-AA
* * * *
25259209 AAATTACCTTTTGACCCCAAACTTTCCAAAAATTACATTTTTAACCCT-AAACTTCCCAA
1 AAATTACATTTTGACCCTAAACTTT-CAAAAATTACA-TTTT-GCCCTCAAACTT-TCAA
* * * * * *
25259268 AAATTACACTTTGACCCCTGAACTTTCAAAAAAATAAATTTTGACCTCAAACTACTCAAAAA
1 AAATTACATTTTGA-CCCTAAACTTTC-AAAAATTACATTTTGCCCTCAAACT-TTC---AA
* * * * *
25259330 AAATTACATTTTTG-CCCTCAAACTTTCAAAAATCATATTTTTGTCC-CGAACTTCCAA
1 AAATTACA-TTTTGACCCT-AAACTTTCAAAAATTACA-TTTTGCCCTCAAACTTTCAA
* * * * **
25259387 AAATTCCATTTTTGCCCCTGAAC-TTCTAAAAATCACATTTTTG-CCTTGAA-TTTCCAA
1 AAATTACA-TTTTGACCCTAAACTTTC-AAAAATTACA-TTTTGCCCTCAAACTTT-CAA
25259444 AAATTACATTTTGACCCTAAACTTCTCAAAAATTACATTTTGCCCTCAAACTTTCAA
1 AAATTACATTTTGACCCTAAACTT-TCAAAAATTACATTTTGCCCTCAAACTTTCAA
* * * * * * *
25259501 AAATCACATTTTTACCCTAGAGCTTCCAGAAATTCCATTCTTGCTCCT-AAACTTCCAA
1 AAATTACATTTTGACCCTA-AACTTTCAAAAATTACATT-TTGC-CCTCAAACTTTCAA
25259559 AAATTACATT
1 AAATTACATT
25259569 CCTATAATCA
Statistics
Matches: 287, Mismatches: 48, Indels: 51
0.74 0.12 0.13
Matches are distributed among these distances:
56 24 0.08
57 92 0.32
58 41 0.14
59 61 0.21
60 25 0.09
61 16 0.06
62 24 0.08
63 4 0.01
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (56 bp):
AAATTACATTTTGACCCTAAACTTTCAAAAATTACATTTTGCCCTCAAACTTTCAA
Found at i:25259569 original size:29 final size:28
Alignment explanation
Indices: 25259209--25259568 Score: 246
Period size: 29 Copynumber: 12.4 Consensus size: 28
25259199 AACTTTCTAG
* *
25259209 AAATTAC-CTTTTGACCCCAAACTTTCCAA
1 AAATTACATTTTTG-CCCTAAAC-TTCCAA
*
25259238 AAATTACATTTTTAACCCTAAACTTCCCAA
1 AAATTACATTTTT-GCCCTAAACTT-CCAA
* * *
25259268 AAATTACA-CTTTGACCCCTGAACTTTCAAA
1 AAATTACATTTTTG--CCCTAAAC-TTCCAA
* * * *
25259298 AAAATA-AATTTTGACCTCAAACTACTCAAAAA
1 AAATTACATTTTTGCCCT-AAACT--TC--CAA
*
25259330 AAATTACATTTTTGCCCTCAAACTTTCAA
1 AAATTACATTTTTGCCCT-AAACTTCCAA
* * *
25259359 AAATCATATTTTTGTCCC-GAACTTCCAA
1 AAATTACATTTTTG-CCCTAAACTTCCAA
* * *
25259387 AAATTCCATTTTTGCCCCTGAACTTCTAA
1 AAATTACATTTTTG-CCCTAAACTTCCAA
* * * *
25259416 AAATCACATTTTTGCCTTGAATTTCCAA
1 AAATTACATTTTTGCCCTAAACTTCCAA
25259444 AAATTACA-TTTTGACCCTAAACTTCTCAA
1 AAATTACATTTTTG-CCCTAAACTTC-CAA
*
25259473 AAATTACA-TTTTGCCCTCAAACTTTCAA
1 AAATTACATTTTTGCCCT-AAACTTCCAA
* * * *
25259501 AAATCACATTTTTACCCTAGAGCTTCCAG
1 AAATTACATTTTTGCCCTA-AACTTCCAA
* *
25259530 AAATTCCATTCTTGCTCCTAAACTTCCAA
1 AAATTACATTTTTGC-CCTAAACTTCCAA
25259559 AAATTACATT
1 AAATTACATT
25259569 CCTATAATCA
Statistics
Matches: 263, Mismatches: 47, Indels: 42
0.75 0.13 0.12
Matches are distributed among these distances:
27 5 0.02
28 67 0.25
29 114 0.43
30 51 0.19
31 3 0.01
32 8 0.03
33 15 0.06
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (28 bp):
AAATTACATTTTTGCCCTAAACTTCCAA
Found at i:25260054 original size:15 final size:14
Alignment explanation
Indices: 25260036--25260070 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
25260026 TTTTTTCAAA
25260036 TTAAATATTAATTTT
1 TTAAATATTAA-TTT
*
25260051 TTAAAAATTAATTT
1 TTAAATATTAATTT
25260065 TTAAAT
1 TTAAAT
25260071 TTTTTCCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTAAATATTAATTT
Found at i:25260058 original size:22 final size:22
Alignment explanation
Indices: 25260012--25260075 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
25260002 TATTATAATT
*
25260012 TTAAAGTATTAAAATTTTTTCAAA
1 TTAAA-TATT-AAATTTTTTAAAA
25260036 TTAAATATT-AATTTTTTAAAAA
1 TTAAATATTAAATTTTTT-AAAA
* *
25260058 TTAATTTTTAAATTTTTT
1 TTAAATATTAAATTTTTT
25260076 CCTAAAAACC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 8 0.23
22 10 0.29
23 12 0.34
24 5 0.14
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TTAAATATTAAATTTTTTAAAA
Found at i:25260069 original size:14 final size:15
Alignment explanation
Indices: 25260036--25260066 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25260026 TTTTTTCAAA
*
25260036 TTAAATATTAATTTT
1 TTAAAAATTAATTTT
25260051 TTAAAAATTAATTTT
1 TTAAAAATTAATTTT
25260066 T
1 T
25260067 AAATTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAAAAATTAATTTT
Found at i:25266034 original size:15 final size:15
Alignment explanation
Indices: 25266014--25266058 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 15
25266004 TTATTATTAT
25266014 GAAAAGGCAATGAAA
1 GAAAAGGCAATGAAA
25266029 GAAAAGGC-A--AAA
1 GAAAAGGCAATGAAA
*
25266041 TAAAAGGCAATG-AA
1 GAAAAGGCAATGAAA
25266055 GAAA
1 GAAA
25266059 TTTGAGTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
12 10 0.40
13 1 0.04
14 6 0.24
15 8 0.32
ACGTcount: A:0.62, C:0.07, G:0.24, T:0.07
Consensus pattern (15 bp):
GAAAAGGCAATGAAA
Found at i:25266705 original size:15 final size:14
Alignment explanation
Indices: 25266687--25266721 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
25266677 TTTTTTCAAA
25266687 TTAAATATTAATTTT
1 TTAAATATTAA-TTT
*
25266702 TTAAAAATTAATTT
1 TTAAATATTAATTT
25266716 TTAAAT
1 TTAAAT
25266722 TTTTTCCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTAAATATTAATTT
Found at i:25266709 original size:22 final size:22
Alignment explanation
Indices: 25266663--25266726 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
25266653 TATTATAATT
*
25266663 TTAAAGTATTAAAATTTTTTCAAA
1 TTAAA-TATT-AAATTTTTTAAAA
25266687 TTAAATATT-AATTTTTTAAAAA
1 TTAAATATTAAATTTTTT-AAAA
* *
25266709 TTAATTTTTAAATTTTTT
1 TTAAATATTAAATTTTTT
25266727 CCTAAAAACC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 8 0.23
22 10 0.29
23 12 0.34
24 5 0.14
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TTAAATATTAAATTTTTTAAAA
Found at i:25266720 original size:14 final size:15
Alignment explanation
Indices: 25266687--25266717 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25266677 TTTTTTCAAA
*
25266687 TTAAATATTAATTTT
1 TTAAAAATTAATTTT
25266702 TTAAAAATTAATTTT
1 TTAAAAATTAATTTT
25266717 T
1 T
25266718 AAATTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAAAAATTAATTTT
Found at i:25269645 original size:17 final size:17
Alignment explanation
Indices: 25269623--25269674 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
25269613 CTTAAACCCA
*
25269623 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
25269640 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
25269657 ATTATAAATTTAAATTT
1 ATTTTAAATTTAAATTT
25269674 A
1 A
25269675 ATTAAAAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:25269651 original size:6 final size:6
Alignment explanation
Indices: 25269625--25269675 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
25269615 TAAACCCAAT
* *
25269625 TTTAAA TTTTAA TTT-AT TTTAAA TTTAAA TTT--A TTATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA
25269671 TTTAA
1 TTTAA
25269676 TTAAAAAGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 3 0.08
5 5 0.13
6 27 0.71
7 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:25271281 original size:29 final size:29
Alignment explanation
Indices: 25271249--25271385 Score: 114
Period size: 30 Copynumber: 4.7 Consensus size: 29
25271239 TGAACAATCT
* *
25271249 AGAAATCACATTTTGACCCTGAACTTTTC
1 AGAAATTACATTTTGACCCTAAACTTTTC
* * *
25271278 AGAAATTAAATTTTGATCGTCAAAC-TTTC
1 AGAAATTACATTTTGACCCT-AAACTTTTC
* * *
25271307 TAGAAATTACCTTTTGACCCCAAACTTTCC
1 -AGAAATTACATTTTGACCCTAAACTTTTC
* * **
25271337 AAAAATTACATTTTTACCCCTAAACTTCCC
1 AGAAATTACATTTTGA-CCCTAAACTTTTC
* *
25271367 AAAAATTACACTTTGACCC
1 AGAAATTACATTTTGACCC
25271386 CCGAACTTTC
Statistics
Matches: 86, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
29 40 0.47
30 46 0.53
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.34
Consensus pattern (29 bp):
AGAAATTACATTTTGACCCTAAACTTTTC
Found at i:25271312 original size:30 final size:28
Alignment explanation
Indices: 25271249--25271825 Score: 133
Period size: 29 Copynumber: 19.9 Consensus size: 28
25271239 TGAACAATCT
* **
25271249 AGAAATCACATTTTGACCCTGAACTTTTC
1 AGAAATTACATTTTGACCCCAAAC-TTTC
* **
25271278 AGAAATTAAATTTTGATCGTCAAACTTTC
1 AGAAATTACATTTTGA-CCCCAAACTTTC
*
25271307 TAGAAATTACCTTTTGACCCCAAACTTTCC
1 -AGAAATTACATTTTGACCCCAAACTTT-C
* * *
25271337 AAAAATTACATTTTTACCCCTAAACTTCCC
1 AGAAATTACATTTTGACCCC-AAACTT-TC
* * *
25271367 AAAAATTACACTTTGACCCCCGAACTTTC
1 AGAAATTACATTTTGA-CCCCAAACTTTC
* * * * * *
25271396 AAAAAAATAAATTTTGACCTCGAACTACTC
1 -AGAAATTACATTTTGACCCCAAACT-TTC
* *
25271426 AAAAAAATTACATTTTTG-CCTTCAAACTTTC
1 --AGAAATTACA-TTTTGACC-CCAAACTTTC
* * * * * *
25271457 AAAAATCATATTTTTG-TCCCGAACTTCC
1 AGAAATTACA-TTTTGACCCCAAACTTTC
* * * * *
25271485 AAAAATTCCATTTTTGCCCCCGAACTTCC
1 AGAAATTACA-TTTTGACCCCAAACTTTC
* * * *
25271514 AAAAATTCCATTTTTGCCCCCGAAC-TTC
1 AGAAATTACA-TTTTGACCCCAAACTTTC
* * ***
25271542 TAAAAATCACATTTTTG-CCTTGAA-TTTCC
1 -AGAAATTACA-TTTTGACCCCAAACTTT-C
* * * *
25271571 AAAAATCACATTTTTACCCCAGAACTTCC
1 AGAAATTACATTTTGACCCCA-AACTTTC
* * * *
25271600 AAAAAATCCATTCTTG-CCCCTAAACTTCC
1 AGAAATTACATT-TTGACCCC-AAACTTTC
*
25271629 AAAAATTACATTTTG-CCCTCAAA-TTTCC
1 AGAAATTACATTTTGACCC-CAAACTTT-C
* * *
25271657 AAAAAATACATTTTTACCCCTAAACTTTC
1 AGAAATTACATTTTGACCCC-AAACTTTC
* * *
25271686 AAAAATCACATTTTTG-CCCTCAAACTTCC
1 AGAAATTACA-TTTTGACCC-CAAACTTTC
* * *
25271715 A-AAATTTCTATTTTTGCCCCCGAAC-TTC
1 AGAAATTAC-A-TTTTGACCCCAAACTTTC
* *
25271743 TA-AAAATACATTTCT-ACCCCAAATTTTCCC
1 -AGAAATTACATTT-TGACCCCAAACTTT--C
* *
25271773 A-AAATAACATTTTTACCCCTAAAACTTTCC
1 AGAAATTACATTTTGACCCC--AAACTTT-C
* *
25271803 A-AAATTGCATTTT-ACCCTAAACT
1 AGAAATTACATTTTGACCCCAAACT
25271826 CTCCGAAACT
Statistics
Matches: 436, Mismatches: 75, Indels: 76
0.74 0.13 0.13
Matches are distributed among these distances:
27 20 0.05
28 77 0.18
29 215 0.49
30 90 0.21
31 23 0.05
32 11 0.03
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (28 bp):
AGAAATTACATTTTGACCCCAAACTTTC
Found at i:25271343 original size:59 final size:59
Alignment explanation
Indices: 25271246--25271414 Score: 162
Period size: 59 Copynumber: 2.8 Consensus size: 59
25271236 CCCTGAACAA
* * * * * * *
25271246 TCTAGAAATCACATTTTGACCCTGAACTTTTCAGAAATTAAATTTTGA-TCGTCAAACTT
1 TCTAGAAATTACCTTTTGACCCCGAACTTTCCAAAAATTAAATTTTGACCCCT-AAACTT
* * *
25271305 TCTAGAAATTACCTTTTGACCCCAAACTTTCCAAAAATTACATTTTTACCCCTAAACTT
1 TCTAGAAATTACCTTTTGACCCCGAACTTTCCAAAAATTAAATTTTGACCCCTAAACTT
* * * * *
25271364 CCCAAAAATTACAC-TTTGACCCCCGAACTTTCAAAAAAATAAATTTTGACC
1 TCTAGAAATTAC-CTTTTGA-CCCCGAACTTTCCAAAAATTAAATTTTGACC
25271415 TCGAACTACT
Statistics
Matches: 89, Mismatches: 18, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
59 60 0.67
60 29 0.33
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (59 bp):
TCTAGAAATTACCTTTTGACCCCGAACTTTCCAAAAATTAAATTTTGACCCCTAAACTT
Found at i:25271470 original size:29 final size:28
Alignment explanation
Indices: 25271428--25271806 Score: 286
Period size: 29 Copynumber: 13.1 Consensus size: 28
25271418 AACTACTCAA
* * *
25271428 AAAAATTACATTTTTGCCTTCAAACTTTC
1 AAAAATCACATTTTTGCC-CCAAACTTCC
* * *
25271457 AAAAATCATATTTTTGTCCCGAACTTCC
1 AAAAATCACATTTTTGCCCCAAACTTCC
*
25271485 AAAAATTC-CATTTTTGCCCCCGAACTTCC
1 AAAAA-TCACATTTTTG-CCCCAAACTTCC
* *
25271514 AAAAATTC-CATTTTTGCCCCCGAACTTCT
1 AAAAA-TCACATTTTTG-CCCCAAACTTCC
*** *
25271543 AAAAATCACATTTTTGCCTTGAATTTCC
1 AAAAATCACATTTTTGCCCCAAACTTCC
*
25271571 AAAAATCACATTTTTACCCCAGAACTTCC
1 AAAAATCACATTTTTGCCCCA-AACTTCC
*
25271600 AAAAAATC-CATTCTTGCCCCTAAACTTCC
1 -AAAAATCACATTTTTGCCCC-AAACTTCC
* *
25271629 AAAAATTACA-TTTTGCCCTCAAATTTCC
1 AAAAATCACATTTTTGCCC-CAAACTTCC
* *
25271657 AAAAAAT-ACATTTTTACCCCTAAACTTTC
1 -AAAAATCACATTTTTGCCCC-AAACTTCC
25271686 AAAAATCACATTTTTGCCCTCAAACTTCC
1 AAAAATCACATTTTTGCCC-CAAACTTCC
* * * *
25271715 AAAATTTC-TATTTTTGCCCCCGAACTTCT
1 AAAA-ATCACATTTTTG-CCCCAAACTTCC
* * *
25271744 AAAAAT-ACATTTCTACCCCAAATTTTCC
1 AAAAATCACATTTTTGCCCCAAA-CTTCC
* * *
25271772 CAAAATAACATTTTTACCCCTAAAACTTTCC
1 AAAAATCACATTTTTGCCCC--AAAC-TTCC
25271803 AAAA
1 AAAA
25271807 TTGCATTTTA
Statistics
Matches: 286, Mismatches: 43, Indels: 40
0.78 0.12 0.11
Matches are distributed among these distances:
27 6 0.02
28 90 0.31
29 166 0.58
30 14 0.05
31 10 0.03
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.34
Consensus pattern (28 bp):
AAAAATCACATTTTTGCCCCAAACTTCC
Found at i:25271481 original size:28 final size:28
Alignment explanation
Indices: 25271318--25271791 Score: 275
Period size: 29 Copynumber: 16.3 Consensus size: 28
25271308 AGAAATTACC
* *
25271318 TTTTGACCCCAAACTTTCCAAAAATTACAT
1 TTTTG-CCCCGAAC-TTCCAAAAATCACAT
* * *
25271348 TTTTACCCCTAAACTTCCCAAAAATTACA-
1 TTTTGCCCC-GAACTT-CCAAAAATCACAT
* * *
25271377 CTTTGACCCCCGAACTTTCAAAAAAAT-A-AA
1 TTTTG--CCCCGAAC-TTC-CAAAAATCACAT
* * *
25271407 TTTTGACCTCGAACTACTCAAAAAAATTACAT
1 TTTTG-CCCCGAACT--TC-CAAAAATCACAT
* * * *
25271439 TTTTGCCTTCAAACTTTCAAAAATCATAT
1 TTTTGCC-CCGAACTTCCAAAAATCACAT
*
25271468 TTTTGTCCCGAACTTCCAAAAATTC-CAT
1 TTTTGCCCCGAACTTCCAAAAA-TCACAT
25271496 TTTTGCCCCCGAACTTCCAAAAATTC-CAT
1 TTTTG-CCCCGAACTTCCAAAAA-TCACAT
*
25271525 TTTTGCCCCCGAACTTCTAAAAATCACAT
1 TTTTG-CCCCGAACTTCCAAAAATCACAT
** *
25271554 TTTTGCCTTGAATTTCCAAAAATCACAT
1 TTTTGCCCCGAACTTCCAAAAATCACAT
*
25271582 TTTTACCCCAGAACTTCCAAAAAATC-CAT
1 TTTTGCCCC-GAACTTCC-AAAAATCACAT
* * *
25271611 TCTTGCCCCTAAACTTCCAAAAATTACA-
1 TTTTGCCCC-GAACTTCCAAAAATCACAT
* *
25271639 TTTTGCCCTCAAATTTCCAAAAAAT-ACAT
1 TTTTGCCC-CGAACTTCC-AAAAATCACAT
* * *
25271668 TTTTACCCCTAAACTTTCAAAAATCACAT
1 TTTTGCCCC-GAACTTCCAAAAATCACAT
* * *
25271697 TTTTGCCCTCAAACTTCCAAAATTTC-TAT
1 TTTTGCCC-CGAACTTCCAAAA-ATCACAT
*
25271726 TTTTGCCCCCGAACTTCTAAAAAT-ACAT
1 TTTTG-CCCCGAACTTCCAAAAATCACAT
* * * * * *
25271754 TTCTACCCCAAATTTTCCCAAAATAACAT
1 TTTTGCCCCGAA-CTTCCAAAAATCACAT
*
25271783 TTTTACCCC
1 TTTTGCCCC
25271792 TAAAACTTTC
Statistics
Matches: 361, Mismatches: 54, Indels: 59
0.76 0.11 0.12
Matches are distributed among these distances:
27 6 0.02
28 91 0.25
29 184 0.51
30 53 0.15
31 15 0.04
32 12 0.03
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (28 bp):
TTTTGCCCCGAACTTCCAAAAATCACAT
Found at i:25271502 original size:57 final size:56
Alignment explanation
Indices: 25271318--25271755 Score: 291
Period size: 57 Copynumber: 7.5 Consensus size: 56
25271308 AGAAATTACC
* * * *
25271318 TTTTGACCCCAAACTTTCCAAAAATTACATTTTTACCCCTAAACTTCCCAAAAATTACA-
1 TTTTG-CCCCAAACTTT-CAAAAATCACATTTTTGCCCC-GAACTT-CCAAAAATTCCAT
* * * * * *
25271377 CTTTGACCCCCGAACTTTCAAAAAAAT-A-AATTTTGACCTCGAACTACTCAAAAAAATTACAT
1 TTTTG--CCCCAAACTTTC--AAAAATCACATTTTTG-CCCCGAACT--TC-CAAAAATTCCAT
* * *
25271439 TTTTGCCTTCAAACTTTCAAAAATCATATTTTTGTCCCGAACTTCCAAAAATTCCAT
1 TTTTGCC-CCAAACTTTCAAAAATCACATTTTTGCCCCGAACTTCCAAAAATTCCAT
* * *
25271496 TTTTGCCCCCGAACTTCCAAAAATTC-CATTTTTGCCCCCGAACTTCTAAAAA-TCACAT
1 TTTTG-CCCCAAACTTTCAAAAA-TCACATTTTTG-CCCCGAACTTCCAAAAATTC-CAT
*** * *
25271554 TTTTGCCTTGAA-TTTCCAAAAATCACATTTTTACCCCAGAACTTCCAAAAAATCCAT
1 TTTTGCCCCAAACTTT-CAAAAATCACATTTTTGCCCC-GAACTTCCAAAAATTCCAT
* * * * * * *
25271611 TCTTGCCCCTAAACTTCCAAAAATTACA-TTTTGCCCTCAAATTTCCAAAAAATACAT
1 TTTTGCCCC-AAACTTTCAAAAATCACATTTTTGCCC-CGAACTTCCAAAAATTCCAT
* * * *
25271668 TTTTACCCCTAAACTTTCAAAAATCACATTTTTGCCCTCAAACTTCCAAAATTTCTAT
1 TTTTGCCCC-AAACTTTCAAAAATCACATTTTTGCCC-CGAACTTCCAAAAATTCCAT
*
25271726 TTTTGCCCCCGAAC-TTCTAAAAAT-ACATTT
1 TTTTG-CCCCAAACTTTC-AAAAATCACATTT
25271756 CTACCCCAAA
Statistics
Matches: 306, Mismatches: 48, Indels: 52
0.75 0.12 0.13
Matches are distributed among these distances:
56 8 0.03
57 131 0.43
58 81 0.26
59 26 0.08
60 25 0.08
61 31 0.10
62 4 0.01
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (56 bp):
TTTTGCCCCAAACTTTCAAAAATCACATTTTTGCCCCGAACTTCCAAAAATTCCAT
Found at i:25271547 original size:86 final size:87
Alignment explanation
Indices: 25271310--25271763 Score: 338
Period size: 86 Copynumber: 5.2 Consensus size: 87
25271300 AACTTTCTAG
* * * *
25271310 AAATTACC-TTTTGACCCCA-AACTTTCCAAAAATTACATTTTTACCCCTAAACTTCCCAAAAAT
1 AAATT-CCATTTTTACCCCAGAAC-TTCCAAAAATTCCATTTTTGCCCCCAAACTT-CCAAAAAT
* * * *
25271373 TACA-CTTTGACCCCCGAACTTTCAAA
63 CACATTTTTG-CCCTCGAAC-TTCCAA
* ** * * * * ** *
25271399 AAAATAAATTTTGACCTC-GAACTACTCAAAAAAATTACATTTTTGCCTTCAAACTTTCAAAAAT
1 AAATTCCATTTTTACCCCAGAACT--TC-CAAAAATTCCATTTTTGCCCCCAAACTTCCAAAAAT
* *
25271463 CATATTTTTGTCC-CGAACTTCCAA
63 CACATTTTTGCCCTCGAACTTCCAA
* * * *
25271487 AAATTCCATTTTTGCCCCCGAACTTCCAAAAATTCCATTTTTGCCCCCGAACTTCTAAAAATCAC
1 AAATTCCATTTTTACCCCAGAACTTCCAAAAATTCCATTTTTGCCCCCAAACTTCCAAAAATCAC
* *
25271552 ATTTTTG-CCTTGAATTTCCAA
66 ATTTTTGCCCTCGAACTTCCAA
* * * *
25271573 AAA-TCACATTTTTACCCCAGAACTTCCAAAAAATCCATTCTTGCCCCTAAACTTCCAAAAATTA
1 AAATTC-CATTTTTACCCCAGAACTTCCAAAAATTCCATTTTTGCCCCCAAACTTCCAAAAATCA
* *
25271637 CA-TTTTGCCCTCAAATTTCCAA
65 CATTTTTGCCCTCGAACTTCCAA
* * * * *
25271659 AAAATACATTTTTACCCCTA-AACTTTCAAAAA-TCACATTTTTGCCCTCAAACTTCCAAAATTT
1 AAATTCCATTTTTACCCC-AGAACTTCCAAAAATTC-CATTTTTGCCCCCAAACTTCCAAAA-AT
* * *
25271722 C-TATTTTTGCCCCCGAACTTCTAA
63 CACATTTTTGCCCTCGAACTTCCAA
* *
25271746 AAA-TACATTTCTACCCCA
1 AAATTCCATTTTTACCCCA
25271764 AATTTTCCCA
Statistics
Matches: 296, Mismatches: 54, Indels: 34
0.77 0.14 0.09
Matches are distributed among these distances:
85 12 0.04
86 176 0.59
87 24 0.08
88 18 0.06
89 26 0.09
90 13 0.04
91 27 0.09
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (87 bp):
AAATTCCATTTTTACCCCAGAACTTCCAAAAATTCCATTTTTGCCCCCAAACTTCCAAAAATCAC
ATTTTTGCCCTCGAACTTCCAA
Found at i:25272277 original size:97 final size:97
Alignment explanation
Indices: 25272098--25272291 Score: 268
Period size: 97 Copynumber: 2.0 Consensus size: 97
25272088 AAAATATTTA
* * * * *
25272098 AAATCGATGTAATATTCCTTTATTTCGGGTTTTGAAAATTCATTCCTTAACTTACTAGGCGCGAT
1 AAATCGAGGCAATATTCCATTACTTCGGGTTTTGAAAATTCATGCCTTAACTTACTAGGCGCGAT
25272163 TTTCCATTAAATCGGGATAATCGAATACCCTT
66 TTTCCATTAAATCGGGATAATCGAATACCCTT
* **
25272195 AAATCGAGGCAATATTCCATTACTTCGGGTTTTGGAAATTTGTGCCTTAACTTACTAGGCGCGAC
1 AAATCGAGGCAATATTCCATTACTTCGGGTTTTGAAAATTCATGCCTTAACTTACTAGGCGCGA-
25272260 TTTT-C-TTCAAA-CTGGGATAATCGAATACCCTT
65 TTTTCCATT-AAATC-GGGATAATCGAATACCCTT
25272292 TTTCAAGGTT
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
96 3 0.03
97 79 0.92
98 4 0.05
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (97 bp):
AAATCGAGGCAATATTCCATTACTTCGGGTTTTGAAAATTCATGCCTTAACTTACTAGGCGCGAT
TTTCCATTAAATCGGGATAATCGAATACCCTT
Found at i:25272832 original size:16 final size:16
Alignment explanation
Indices: 25272813--25272844 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25272803 TAAATGTGAA
25272813 AAATAATAAATTAAAT
1 AAATAATAAATTAAAT
25272829 AAATAATAAATTAAAT
1 AAATAATAAATTAAAT
25272845 TTAAAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATAATAAATTAAAT
Found at i:25276677 original size:17 final size:16
Alignment explanation
Indices: 25276648--25276695 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
25276638 ATAATTAACC
*
25276648 TTTTTTT-TCAATATCA
1 TTTTTTTATAAATAT-A
25276664 TTTTTTTATAAATATA
1 TTTTTTTATAAATATA
*
25276680 TTTGTTATATAAATAT
1 TTT-TTTTATAAATAT
25276696 TTCATTCACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTTTTATAAATATA
Found at i:25276810 original size:3 final size:3
Alignment explanation
Indices: 25276802--25276827 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25276792 AATTACTTAA
25276802 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
25276828 ACCGAATATA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:25277669 original size:14 final size:14
Alignment explanation
Indices: 25277650--25277685 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
25277640 ACAAAGTAAG
25277650 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
*
25277664 TCATTTTCCGGAAA
1 TCATTTTCCAGAAA
*
25277678 CCATTTTC
1 TCATTTTC
25277686 AATGAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.39
Consensus pattern (14 bp):
TCATTTTCCAGAAA
Found at i:25284304 original size:20 final size:20
Alignment explanation
Indices: 25284270--25284308 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
25284260 TATCTTTTTC
25284270 GATCTATAATATTTTCTCTTT
1 GATCTATAATATTTT-TCTTT
*
25284291 GATCT-TAATTTTTTTCTT
1 GATCTATAATATTTTTCTT
25284309 AAATTTGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.62
Consensus pattern (20 bp):
GATCTATAATATTTTTCTTT
Found at i:25284596 original size:18 final size:17
Alignment explanation
Indices: 25284552--25284596 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
25284542 TTTATATTCA
25284552 ATTCTTATTTTTTTTAT
1 ATTCTTATTTTTTTTAT
*
25284569 ATT-TTGATTTTTTTTCT
1 ATTCTT-ATTTTTTTTAT
25284586 AGTTCTTATTT
1 A-TTCTTATTT
25284597 ACCTTGTGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 2 0.08
17 14 0.58
18 6 0.25
19 2 0.08
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.73
Consensus pattern (17 bp):
ATTCTTATTTTTTTTAT
Found at i:25286545 original size:81 final size:81
Alignment explanation
Indices: 25286410--25286564 Score: 265
Period size: 81 Copynumber: 1.9 Consensus size: 81
25286400 TCTCCCTTGT
** *
25286410 TTTTCACTTTCACCATCTAATCCTTCTTTTCTTTCATAACGAAGATTAACATGGCAGCCCCTCTA
1 TTTTCACTTTCACCATCTAATCCTTCTTCCCTTTCATAACGAAGATTAACATGGCAACCCCTCTA
*
25286475 AACGCTCGAGTCAGCC
66 AACACTCGAGTCAGCC
*
25286491 TTTTCACTTTCACCATCTAATCCTTCTTCCCTTTCATAACGGAGATTAACATGGCAACCCCTCTA
1 TTTTCACTTTCACCATCTAATCCTTCTTCCCTTTCATAACGAAGATTAACATGGCAACCCCTCTA
25286556 AACACTCGA
66 AACACTCGA
25286565 TTCAACCCCA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 69 1.00
ACGTcount: A:0.26, C:0.32, G:0.10, T:0.33
Consensus pattern (81 bp):
TTTTCACTTTCACCATCTAATCCTTCTTCCCTTTCATAACGAAGATTAACATGGCAACCCCTCTA
AACACTCGAGTCAGCC
Found at i:25287890 original size:6 final size:6
Alignment explanation
Indices: 25287870--25287915 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
25287860 TTAAATTGAT
* * *
25287870 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AC TTTAAG TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
25287916 ATAGTATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
5 8 0.24
6 25 0.76
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:25287890 original size:17 final size:17
Alignment explanation
Indices: 25287870--25287913 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
25287860 TTAAATTGAT
*
25287870 TTTAAATTTATTTTAAA
1 TTTAAATTTACTTTAAA
*
25287887 TTTAAATTTACTTTAAG
1 TTTAAATTTACTTTAAA
25287904 TTTAAATTTA
1 TTTAAATTTA
25287914 AAATAGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:25287902 original size:11 final size:11
Alignment explanation
Indices: 25287859--25287890 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
25287849 TTGATTGAGG
*
25287859 TTTAAATTGAT
1 TTTAAATTTAT
25287870 TTTAAATTTAT
1 TTTAAATTTAT
25287881 TTTAAATTTA
1 TTTAAATTTA
25287891 AATTTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:25288812 original size:22 final size:22
Alignment explanation
Indices: 25288787--25288832 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
25288777 AGTTTTAAAA
25288787 AATTAATA-AACATAATATTAAT
1 AATTAATATAA-ATAATATTAAT
*
25288809 AATTAATATTAATAATATTAAT
1 AATTAATATAAATAATATTAAT
25288831 AA
1 AA
25288833 AAAAAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAATATAAATAATATTAAT
Found at i:25288817 original size:13 final size:13
Alignment explanation
Indices: 25288799--25288824 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25288789 TTAATAAACA
25288799 TAATATTAATAAT
1 TAATATTAATAAT
25288812 TAATATTAATAAT
1 TAATATTAATAAT
25288825 ATTAATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATATTAATAAT
Found at i:25289881 original size:29 final size:28
Alignment explanation
Indices: 25289834--25290009 Score: 83
Period size: 29 Copynumber: 6.0 Consensus size: 28
25289824 GCTTATAGGT
* *
25289834 CCCTAAACTGTTCTAAAATTACATTTTTA
1 CCCTGAACT-TTCCAAAATTACATTTTTA
**
25289863 CCCTTGAACTTTCCAAAATCCCATTTTTAA
1 CCC-TGAACTTTCCAAAATTACATTTTT-A
* *
25289893 CACT-AATTTTACCAAAAATTACCA-TTTTA
1 CCCTGAACTTT-CC-AAAATTA-CATTTTTA
* *
25289922 CCCCTGAATTTTCTAAAATCT-CATTTTTAA
1 -CCCTGAACTTTCCAAAAT-TACATTTTT-A
* *
25289952 CCCCG-ATTTTACCAAAAATTACCA-TTTTA
1 CCCTGAACTTT-CC-AAAATTA-CATTTTTA
* **
25289981 CCCTCAAACTTTCCAAAATCCCATTTTTA
1 CCCT-GAACTTTCCAAAATTACATTTTTA
25290010 ACTCCGGTTT
Statistics
Matches: 113, Mismatches: 17, Indels: 34
0.69 0.10 0.21
Matches are distributed among these distances:
28 14 0.12
29 51 0.45
30 34 0.30
31 14 0.12
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (28 bp):
CCCTGAACTTTCCAAAATTACATTTTTA
Found at i:25289921 original size:30 final size:30
Alignment explanation
Indices: 25289887--25289984 Score: 89
Period size: 29 Copynumber: 3.3 Consensus size: 30
25289877 AAAATCCCAT
*
25289887 TTTTAACACTAATTTTACCAAAAATTACCA
1 TTTTAACCCTAATTTTACCAAAAATTACCA
* *
25289917 TTTTACCCCTGAATTTT--CTAAAA-T-CTCA
1 TTTTAACCCT-AATTTTACCAAAAATTAC-CA
**
25289945 TTTTTAACCCCGATTTTACCAAAAATTACCA
1 -TTTTAACCCTAATTTTACCAAAAATTACCA
25289976 TTTT-ACCCT
1 TTTTAACCCT
25289985 CAAACTTTCC
Statistics
Matches: 53, Mismatches: 8, Indels: 15
0.70 0.11 0.20
Matches are distributed among these distances:
27 1 0.02
28 8 0.15
29 17 0.32
30 17 0.32
31 9 0.17
32 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (30 bp):
TTTTAACCCTAATTTTACCAAAAATTACCA
Found at i:25289940 original size:59 final size:59
Alignment explanation
Indices: 25289848--25290089 Score: 292
Period size: 59 Copynumber: 4.1 Consensus size: 59
25289838 AAACTGTTCT
* * * *
25289848 AAAATTA-CATTTTTACCCTTGAACTTTCCAAAATCCCATTTTTAACACTAATTTTACCA
1 AAAATTACCA-TTTTACCCCTGAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACCA
* * * * *
25289907 AAAATTACCATTTTACCCCTGAATTTTCTAAAATCTCATTTTTAACCCCGATTTTACCA
1 AAAATTACCATTTTACCCCTGAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACCA
* * **
25289966 AAAATTACCATTTTA-CCCTCAAACTTTCCAAAATCCCATTTTTAACTCCGGTTTCACCA
1 AAAATTACCATTTTACCCCT-GAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACCA
* * * *
25290025 AAAATTACTATTTTACCCCCGAACTTTTCAAAA-CCCATTTTTAGCCCCAATTTCACCA
1 AAAATTACCATTTTACCCCTGAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACCA
25290083 AAAATTA
1 AAAATTA
25290090 TATTTTTACC
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
58 32 0.20
59 121 0.77
60 5 0.03
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTGAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACCA
Found at i:25292343 original size:29 final size:29
Alignment explanation
Indices: 25292306--25292371 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
25292296 ATACGATAAT
*
25292306 AATTATAA-TCTTCAATAGTTGAATAATTA
1 AATTATAATTCTTC-ATAATTGAATAATTA
* *
25292335 AATTGTAATTTTTCATAATTGAATAATTA
1 AATTATAATTCTTCATAATTGAATAATTA
*
25292364 AAATATAA
1 AATTATAA
25292372 ATTTACGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (29 bp):
AATTATAATTCTTCATAATTGAATAATTA
Found at i:25292953 original size:23 final size:22
Alignment explanation
Indices: 25292922--25292968 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
25292912 CATAAAAACT
*
25292922 AAAAAAAAATCAAAATATAAAA
1 AAAAAAAAAACAAAATATAAAA
**
25292944 AAAAATAAAAACTGAATATAAAA
1 AAAAA-AAAAACAAAATATAAAA
25292967 AA
1 AA
25292969 TTAAAGGGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (22 bp):
AAAAAAAAAACAAAATATAAAA
Found at i:25309442 original size:4 final size:4
Alignment explanation
Indices: 25309433--25309494 Score: 54
Period size: 4 Copynumber: 15.2 Consensus size: 4
25309423 AAAAAAAGGG
* * *
25309433 GAAA GAAA GAGAG GAAA GAAA GAAA GAAA GAAG GAGAG GAAA GAAA G-AA
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA
* *
25309482 GAAG GAAA AAAA G
1 GAAA GAAA GAAA G
25309495 GTAATGTGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
3 3 0.06
4 37 0.79
5 7 0.15
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:25309469 original size:25 final size:25
Alignment explanation
Indices: 25309433--25309489 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
25309423 AAAAAAAGGG
25309433 GAAAGAAAGAGAGGAAAGAAAGAAA
1 GAAAGAAAGAGAGGAAAGAAAGAAA
*
25309458 GAAAGAAGGAGAGGAAAGAAAG-AA
1 GAAAGAAAGAGAGGAAAGAAAGAAA
*
25309482 GAAGGAAA
1 GAAAGAAA
25309490 AAAAGGTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (25 bp):
GAAAGAAAGAGAGGAAAGAAAGAAA
Found at i:25309474 original size:17 final size:15
Alignment explanation
Indices: 25309432--25309494 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 15
25309422 CAAAAAAAGG
25309432 GGAAAGAAAG-AG-A
1 GGAAAGAAAGAAGAA
25309445 GGAAAGAAAG-A-AA
1 GGAAAGAAAGAAGAA
*
25309458 -GAAAG-AAGGAG-A
1 GGAAAGAAAGAAGAA
25309470 GGAAAGAAAGAAGAA
1 GGAAAGAAAGAAGAA
*
25309485 GGAAAAAAAG
1 GGAAAGAAAG
25309495 GTAATGTGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
11 3 0.07
12 7 0.17
13 17 0.40
14 5 0.12
15 10 0.24
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
GGAAAGAAAGAAGAA
Found at i:25312885 original size:12 final size:12
Alignment explanation
Indices: 25312870--25312903 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
25312860 CAATGCCTCT
*
25312870 TCCTCCTCTTCC
1 TCCTCTTCTTCC
25312882 TCCTCTTCTTCC
1 TCCTCTTCTTCC
25312894 TCCTCTTCTT
1 TCCTCTTCTT
25312904 GTTGTTCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (12 bp):
TCCTCTTCTTCC
Found at i:25312901 original size:9 final size:9
Alignment explanation
Indices: 25312865--25312895 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
25312855 TCATCCAATG
25312865 CCTCTTCCT
1 CCTCTTCCT
25312874 CCTCTTCCT
1 CCTCTTCCT
*
25312883 CCTCTTCTT
1 CCTCTTCCT
25312892 CCTC
1 CCTC
25312896 CTCTTCTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (9 bp):
CCTCTTCCT
Found at i:25315978 original size:23 final size:23
Alignment explanation
Indices: 25315952--25316072 Score: 147
Period size: 23 Copynumber: 5.2 Consensus size: 23
25315942 ACACTAGCGC
*
25315952 GCTCTTTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
25315975 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
25315998 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
25316023 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
25316046 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
25316069 GCTC
1 GCTC
25316073 AGTACTTTGT
Statistics
Matches: 85, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
22 4 0.05
23 61 0.72
24 1 0.01
25 16 0.19
26 3 0.04
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:25316004 original size:25 final size:24
Alignment explanation
Indices: 25315976--25316061 Score: 74
Period size: 25 Copynumber: 3.6 Consensus size: 24
25315966 ACTGTGTGTG
*
25315976 CTCTCTGTTTAGCACGTCTCGTGCT
1 CTCTCTGATTAGCACGT-TCGTGCT
* *
25316001 CTCTGTTATTAGCACTGTGT-GTGCT
1 CTCTCTGATTAGCAC-GT-TCGTGCT
25316026 CTC-C-GATTAGCAC-TTCGTG-T
1 CTCTCTGATTAGCACGTTCGTGCT
25316046 GCTCTCTGATTAGCAC
1 -CTCTCTGATTAGCAC
25316062 TTTGTGTGCT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
20 2 0.04
21 7 0.14
22 1 0.02
23 17 0.34
25 20 0.40
26 3 0.06
ACGTcount: A:0.13, C:0.28, G:0.21, T:0.38
Consensus pattern (24 bp):
CTCTCTGATTAGCACGTTCGTGCT
Found at i:25316021 original size:48 final size:46
Alignment explanation
Indices: 25315952--25316072 Score: 163
Period size: 48 Copynumber: 2.6 Consensus size: 46
25315942 ACACTAGCGC
* * *
25315952 GCTCTTTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGT-GT
*
25315998 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
*
25316046 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
25316073 AGTACTTTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
46 25 0.37
48 41 0.61
49 1 0.01
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
Found at i:25316101 original size:39 final size:39
Alignment explanation
Indices: 25316037--25316111 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
25316027 TCCGATTAGC
*
25316037 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
25316076 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
25316112 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:25316106 original size:23 final size:23
Alignment explanation
Indices: 25316071--25316164 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
25316061 CTTTGTGTGC
*
25316071 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
25316094 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
25316117 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
25316142 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
25316164 T
1 T
25316165 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:25320761 original size:14 final size:14
Alignment explanation
Indices: 25320742--25320771 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
25320732 AAATTTTAGG
25320742 CCCTGTGCACGACC
1 CCCTGTGCACGACC
25320756 CCCTGTGCACGACC
1 CCCTGTGCACGACC
25320770 CC
1 CC
25320772 TCAATGAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.53, G:0.20, T:0.13
Consensus pattern (14 bp):
CCCTGTGCACGACC
Found at i:25321544 original size:95 final size:94
Alignment explanation
Indices: 25321443--25321993 Score: 742
Period size: 99 Copynumber: 5.8 Consensus size: 94
25321433 TTATATTATT
25321443 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTTACTAACAACAAAATAAAAT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTTACTAACAACAAAATAAAAT
*
25321508 TACAAACTAATTTTTTTAAACATTATTAAA
66 TACTAACTAA-TTTTTTAAACATTATTAAA
* *
25321538 TTTTAAATAAAAAAATATGAACAATATTTTTTACTTACTACTA-TTACTACTACTAACAAAAAAT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTTACTA--AC-AAC--AAAAT
25321602 AAAATTACTAACTAATTTTTTAAACATTATTAAA
61 AAAATTACTAACTAATTTTTTAAACATTATTAAA
* *
25321636 TTTTAAATCAAAAAATATGAACAATGTTTTTTACTTACTACTACTAATACTAACAACAACAAAAT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACT--TACT---AACAACAAAAT
* *
25321701 AAAATTATTAACTAATTTTTTAAAAATTATTAAA
61 AAAATTACTAACTAATTTTTTAAACATTATTAAA
* * *
25321735 TTTTAAATCAATAAATATAAATAATGTTTTTTACTTACTACTA-TTACTAACAACAAAATAAAAT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTTACTAACAACAAAATAAAAT
*
25321799 TACTAATTAAATTTTTTTAAA-ATTATTAAA
66 TACTAACT-AA-TTTTTTAAACATTATTAAA
* *
25321829 TTTTAAATCAATAAATATAAACAAT-GTTTTTACTTACTACTAC-TACTAACAACAAAATAAAAT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTTACTAACAACAAAATAAAAT
***
25321892 TACTAACTAGCAAAATTTAAACATTATTAAA
66 TACTAACTA--ATTTTTTAAACATTATTAAA
* *
25321923 TTTTAAATCAATAAATATGAACAATATTTTTTACTTA-T--TAC-CACTAATAACAAAATAAAAT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTTACTAACAACAAAATAAAAT
25321984 TACTAACTAA
66 TACTAACTAA
25321994 CAAAATTAAA
Statistics
Matches: 416, Mismatches: 22, Indels: 41
0.87 0.05 0.09
Matches are distributed among these distances:
90 1 0.00
92 31 0.07
93 71 0.17
94 76 0.18
95 60 0.14
96 6 0.01
97 3 0.01
98 61 0.15
99 97 0.23
101 7 0.02
102 2 0.00
104 1 0.00
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.38
Consensus pattern (94 bp):
TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTTACTAACAACAAAATAAAAT
TACTAACTAATTTTTTAAACATTATTAAA
Found at i:25321654 original size:193 final size:187
Alignment explanation
Indices: 25321443--25321993 Score: 754
Period size: 193 Copynumber: 2.9 Consensus size: 187
25321433 TTATATTATT
25321443 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTTACTAACAACAAAATAAAAT
1 TTTTAAATCAATAAATATGAACAAT-TTTTTTACTTACTACTACTTACTAACAACAAAATAAAAT
* * *
25321508 TACAAACTAATTTTTTTAAACATTATTAAATTTTAAATAAAAAAATATGAACAATATTTTTTACT
65 TACTAACTAA-TTTTTTAAACATTATTAAATTTTAAATCAATAAATATGAACAATATTTTTTACT
25321573 TACTACTATTACTACTACTAACAAAAAATAAAATTACTAACT-AA-TTTTTTAAACATTATTAAA
129 TACTACTATTACTA--AC-AAC--AAAATAAAATTACTAACTAAATTTTTTTAAA-ATTATTAAA
*
25321636 TTTTAAATCAAAAAATATGAACAATGTTTTTTACTTACTACTACTAATACTAACAACAACAAAAT
1 TTTTAAATCAATAAATATGAACAAT-TTTTTTACTTACTACTACT--TACT---AACAACAAAAT
* * * * *
25321701 AAAATTATTAACTAATTTTTTAAAAATTATTAAATTTTAAATCAATAAATATAAATAATGTTTTT
60 AAAATTACTAACTAATTTTTTAAACATTATTAAATTTTAAATCAATAAATATGAACAATATTTTT
*
25321766 TACTTACTACTATTACTAACAACAAAATAAAATTACTAATTAAATTTTTTTAAAATTATTAAA
125 TACTTACTACTATTACTAACAACAAAATAAAATTACTAACTAAATTTTTTTAAAATTATTAAA
* *
25321829 TTTTAAATCAATAAATATAAACAATGTTTTTACTTACTACTAC-TACTAACAACAAAATAAAATT
1 TTTTAAATCAATAAATATGAACAATTTTTTTACTTACTACTACTTACTAACAACAAAATAAAATT
***
25321893 ACTAACTAGCAAAATTTAAACATTATTAAATTTTAAATCAATAAATATGAACAATATTTTTTACT
66 ACTAACTA--ATTTTTTAAACATTATTAAATTTTAAATCAATAAATATGAACAATATTTTTTACT
** *
25321958 TA-T--TACCACTAATAACAAAATAAAATTACTAACTAA
129 TACTACTATTACTAACAACAAAATAAAATTACTAACTAA
25321994 CAAAATTAAA
Statistics
Matches: 323, Mismatches: 26, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
185 29 0.09
186 24 0.07
187 1 0.00
188 50 0.15
189 4 0.01
192 34 0.11
193 77 0.24
194 12 0.04
195 6 0.02
197 62 0.19
198 24 0.07
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.38
Consensus pattern (187 bp):
TTTTAAATCAATAAATATGAACAATTTTTTTACTTACTACTACTTACTAACAACAAAATAAAATT
ACTAACTAATTTTTTAAACATTATTAAATTTTAAATCAATAAATATGAACAATATTTTTTACTTA
CTACTATTACTAACAACAAAATAAAATTACTAACTAAATTTTTTTAAAATTATTAAA
Found at i:25321995 original size:21 final size:20
Alignment explanation
Indices: 25321965--25322006 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
25321955 ACTTATTACC
25321965 ACTAATAACAAAATAAAATT
1 ACTAATAACAAAATAAAATT
*
25321985 ACTAACTAACAAAATTAAATT
1 ACTAA-TAACAAAATAAAATT
25322006 A
1 A
25322007 AAATAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (20 bp):
ACTAATAACAAAATAAAATT
Found at i:25322130 original size:22 final size:21
Alignment explanation
Indices: 25322095--25322141 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
25322085 AATAACAAAT
* *
25322095 AAATTAAAAATTAAATTAAAA
1 AAATAAAAAATTAAAATAAAA
*
25322116 AAATAAAAAACTTAAAATAAAC
1 AAATAAAAAA-TTAAAATAAAA
25322138 AAAT
1 AAAT
25322142 TAACTACCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATAAAAAATTAAAATAAAA
Found at i:25322366 original size:4 final size:4
Alignment explanation
Indices: 25322359--25322399 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
25322349 TCCTCCTTCC
*
25322359 TCTT TC-T TCTT TCTT TCTT TCTCT TTTT TCTT TCTT T-TT TC
1 TCTT TCTT TCTT TCTT TCTT TCT-T TCTT TCTT TCTT TCTT TC
25322400 ACTCAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 6 0.19
4 23 0.72
5 3 0.09
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:25322383 original size:17 final size:17
Alignment explanation
Indices: 25322363--25322395 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25322353 CCTTCCTCTT
25322363 TCTTCTTTCTTTCTTTC
1 TCTTCTTTCTTTCTTTC
*
25322380 TCTTTTTTCTTTCTTT
1 TCTTCTTTCTTTCTTT
25322396 TTTCACTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TCTTCTTTCTTTCTTTC
Found at i:25322384 original size:21 final size:20
Alignment explanation
Indices: 25322358--25322399 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
25322348 TTCCTCCTTC
25322358 CTCTTTCTTCTTTCTTTCTTT
1 CTCTTTCTTCTTTCTTT-TTT
*
25322379 CTCTTTTTTCTTTCTTTTTT
1 CTCTTTCTTCTTTCTTTTTT
25322399 C
1 C
25322400 ACTCAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (20 bp):
CTCTTTCTTCTTTCTTTTTT
Found at i:25322396 original size:11 final size:11
Alignment explanation
Indices: 25322359--25322399 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
25322349 TCCTCCTTCC
*
25322359 TCTTTCTTCTT
1 TCTTTTTTCTT
25322370 TCTTTCTTTC--
1 TCTTT-TTTCTT
25322380 TCTTTTTTCTT
1 TCTTTTTTCTT
25322391 TCTTTTTTC
1 TCTTTTTTC
25322400 ACTCAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 4 0.15
10 5 0.19
11 14 0.54
12 3 0.12
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TCTTTTTTCTT
Found at i:25327711 original size:3 final size:3
Alignment explanation
Indices: 25327703--25327731 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
25327693 TCTTACTTCT
25327703 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25327732 ATTAATAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:25329380 original size:22 final size:22
Alignment explanation
Indices: 25329338--25329380 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
25329328 TTGTAAAAGT
*
25329338 TAATTAATTAAAATATTTAAAA
1 TAATTAATTAAAATATATAAAA
25329360 TAATTAAGTTAAAAT-TATAAA
1 TAATTAA-TTAAAATATATAAA
25329381 TGCAATGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TAATTAATTAAAATATATAAAA
Found at i:25332085 original size:324 final size:323
Alignment explanation
Indices: 25331485--25332173 Score: 812
Period size: 324 Copynumber: 2.1 Consensus size: 323
25331475 TTTTTCTCGT
* * *
25331485 GAAATCAATTTT-ATTTCTAATTTTAACTTTATTTATTGTTTCGACACTGTTTTTTCTCTTTTAT
1 GAAATCAATTTTAATTT-TAATTTTAACTTTATTTATTGTTTCAACACTGTTCTCTCTCTTTTAT
* * * * *
25331549 TTTTATTATTATTTTTGGCCATTTTTTACCATTAATTTTGCAAGTATAGCAGTTCCTTCTTTCTA
65 TTTTAATATTATTTTTGACCA-TTTTCACCATTAATTTTGCAAGTATAGCAGTTCCTTCTCTCCA
* * ** *
25331614 GGGTTACAAGTAAAGTAAGAAGGCAAACACATTGTAGGAACCTATAATGGTCGAGTAGACACAGA
129 AGGTTACAAGCAAAGTAAGAAGGCAAACACATAATAGGAACCTATAATGGTCGAGTAGACACAAA
* * ** *
25331679 AGAATGATGTGACATTAGTATTTATAGCCCATCTTGACCGCACAATATTCATAGTCGATGTTAGT
194 AGAATGATGTGACATTAGTATTGATAACCCATCTCCACCACACAATATTCATAGTCGATGTTAGT
* * * ** * *
25331744 ATATTCTATAGGCCTTACCTTCACAACTATTTTTTATTAGTATGTCGGTTCACAATTCTTCTACC
259 ATATTCTATAAGCCTTACCTTCACAACTATTTGTTATTAGCATGTCAATTCACAATCCTTCTACA
* * **
25331809 GAAATCAATTTTAATTTTAATTTTAACTTTTTTTACTGTTTCAACGTTGCTCTCTCTCTCTTTTA
1 GAAATCAATTTTAATTTTAATTTTAACTTTATTTATTGTTTCAACACTG-T-TCTCTCTCTTTTA
* * *
25331874 TTTTTAATATTATTTTTTGACCA-TTTCCCCCTTTATTTTGCAAGTATAGCAGTTCC-TC-CTCC
64 TTTTTAATATTA-TTTTTGACCATTTTCACCATTAATTTTGCAAGTATAGCAGTTCCTTCTCTCC
** * *
25331936 AATTTTACAAGCAAAGTAGGAAGGCAAACATTATAATAGGAACCTATAATGGTC-AGGTAGACAC
128 AAGGTTACAAGCAAAGTAAGAAGGCAAACA-CATAATAGGAACCTATAATGGTCGA-GTAGACAC
* * * **
25332000 AAAAGAATGATGTGACATTAGTATTGATAACCCATCTCCACCATATAATATTTATTTTCGATGTT
191 AAAAGAATGATGTGACATTAGTATTGATAACCCATCTCCACCACACAATATTCATAGTCGATGTT
* * * * * * *
25332065 GGTTTATTCTGTAAGCCTTACCTTCACAAGTATTTGTTATTGGCATGTTAATTTACAATCCTTCT
256 AGTATATTCTATAAGCCTTACCTTCACAACTATTTGTTATTAGCATGTCAATTCACAATCCTTCT
25332130 ACA
321 ACA
* * * *
25332133 AAAATCAAATTTATTTTTAATTTTAACTTTCTTTATTGTTT
1 GAAATCAATTTTAATTTTAATTTTAACTTTATTTATTGTTT
25332174 TGCATTTGTA
Statistics
Matches: 306, Mismatches: 53, Indels: 12
0.82 0.14 0.03
Matches are distributed among these distances:
323 28 0.09
324 213 0.70
325 34 0.11
326 22 0.07
327 9 0.03
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (323 bp):
GAAATCAATTTTAATTTTAATTTTAACTTTATTTATTGTTTCAACACTGTTCTCTCTCTTTTATT
TTTAATATTATTTTTGACCATTTTCACCATTAATTTTGCAAGTATAGCAGTTCCTTCTCTCCAAG
GTTACAAGCAAAGTAAGAAGGCAAACACATAATAGGAACCTATAATGGTCGAGTAGACACAAAAG
AATGATGTGACATTAGTATTGATAACCCATCTCCACCACACAATATTCATAGTCGATGTTAGTAT
ATTCTATAAGCCTTACCTTCACAACTATTTGTTATTAGCATGTCAATTCACAATCCTTCTACA
Found at i:25336923 original size:3 final size:3
Alignment explanation
Indices: 25336915--25336942 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
25336905 TCATCTTTAC
25336915 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
25336943 GGGGAAGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:25337144 original size:3 final size:3
Alignment explanation
Indices: 25337136--25337169 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
25337126 TCTTTACATT
25337136 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
25337170 AAAGAAGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25343899 original size:14 final size:15
Alignment explanation
Indices: 25343882--25343910 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
25343872 GCCTGATGGG
25343882 AAAAGAAAAA-AAGA
1 AAAAGAAAAACAAGA
25343896 AAAAGAAAAACAAGA
1 AAAAGAAAAACAAGA
25343911 GAACAGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAACAAGA
Found at i:25347119 original size:25 final size:25
Alignment explanation
Indices: 25347090--25347140 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
25347080 TGATTGACTA
*
25347090 AATAAATTGGCAGGATGTTGATCGC
1 AATAAATTGACAGGATGTTGATCGC
25347115 AATAAATTGACAGGATGTTGATCGC
1 AATAAATTGACAGGATGTTGATCGC
25347140 A
1 A
25347141 TCCGTCGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.27
Consensus pattern (25 bp):
AATAAATTGACAGGATGTTGATCGC
Found at i:25351573 original size:29 final size:30
Alignment explanation
Indices: 25351508--25351583 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
25351498 TCAAAATTGT
* * *
25351508 ACATGAACTTTAATTTAATGTGCAATTGTAT
1 ACATGAACTTTAATTT-AGGTGCAATTATAC
25351539 ACATGAACTTTAATTT-GGTGCAATTATAC
1 ACATGAACTTTAATTTAGGTGCAATTATAC
* *
25351568 ATATGAGACTCTAATT
1 ACATGA-ACTTTAATT
25351584 GTGATTCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 15 0.38
30 8 0.21
31 16 0.41
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (30 bp):
ACATGAACTTTAATTTAGGTGCAATTATAC
Found at i:25351827 original size:29 final size:30
Alignment explanation
Indices: 25351784--25351860 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
25351774 GAATTGGATC
*
25351784 AAATCAAAATTTCATGTATAAAATTGCACA-
1 AAATC-AAAGTTCATGTATAAAATTGCACAT
**
25351814 AAATCAAAGTTCATGTATACGATTGCACATT
1 AAATCAAAGTTCATGTATAAAATTGCACA-T
* *
25351845 AAACCATAGTTCATGT
1 AAATCAAAGTTCATGT
25351861 GTAGTTTTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 21 0.52
30 5 0.12
31 14 0.35
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTGCACAT
Found at i:25352276 original size:26 final size:24
Alignment explanation
Indices: 25352227--25352274 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
25352217 ACAAATACCC
25352227 CACTAAAGATATAATATATATATA
1 CACTAAAGATATAATATATATATA
25352251 CACTAAAGATATAATATATATATA
1 CACTAAAGATATAATATATATATA
25352275 TATATATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
CACTAAAGATATAATATATATATA
Found at i:25354522 original size:19 final size:19
Alignment explanation
Indices: 25354500--25354537 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
25354490 TTAAAAGAAA
25354500 GGTAATGTAATATTT-TATT
1 GGTAATGTAA-ATTTATATT
*
25354519 GGTAATTTAAATTTATATT
1 GGTAATGTAAATTTATATT
25354538 TTGTTTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (19 bp):
GGTAATGTAAATTTATATT
Found at i:25354567 original size:29 final size:29
Alignment explanation
Indices: 25354534--25354589 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
25354524 TTTAAATTTA
*
25354534 TATTT-TGTTTAGTATTTATTATTTTAAGT
1 TATTTATGTTTAGTATTTA-AATTTTAAGT
*
25354563 TATTTATTTTTAGTATTTAAATTTTAA
1 TATTTATGTTTAGTATTTAAATTTTAA
25354590 TTGATTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (29 bp):
TATTTATGTTTAGTATTTAAATTTTAAGT
Found at i:25354579 original size:13 final size:15
Alignment explanation
Indices: 25354541--25354581 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
25354531 TTATATTTTG
25354541 TTTAGTATTTATTAT
1 TTTAGTATTTATTAT
25354556 TTTAAGTTATTTA-T-T
1 TTT-AG-TATTTATTAT
25354571 TTTAGTATTTA
1 TTTAGTATTTA
25354582 AATTTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 6 0.25
14 2 0.08
15 7 0.29
16 3 0.12
17 6 0.25
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (15 bp):
TTTAGTATTTATTAT
Found at i:25354863 original size:47 final size:46
Alignment explanation
Indices: 25354813--25354995 Score: 143
Period size: 47 Copynumber: 3.9 Consensus size: 46
25354803 TATGGATACT
*
25354813 ATTTTGGTATATAAATATTTATTTTGTATCATTTTAGTAAATAATTT
1 ATTTTGGTATATAAATA-TTATTTTGTATCATTTTAGTAAATAATTC
* * * * * * * *
25354860 ATTTTGGTATTTAATTATTATTTTTGTATTA-TATCGATATATCCATCAC
1 ATTTTGGTATATAAATATTA-TTTTGTATCATTTTAG-TAAAT-AAT-TC
* * * *
25354909 ATTTTCGTATATAAATATTTATTTTATACCATTTTAGTAAATAACTC
1 ATTTTGGTATATAAATA-TTATTTTGTATCATTTTAGTAAATAATTC
* * * * *
25354956 ATTTTGATATTTAATTATTATTTTGTATCATATTGGTAAA
1 ATTTTGGTATATAAATATTATTTTGTATCATTTTAGTAAA
25354996 AAATAATAAA
Statistics
Matches: 101, Mismatches: 29, Indels: 13
0.71 0.20 0.09
Matches are distributed among these distances:
46 25 0.25
47 42 0.42
48 3 0.03
49 25 0.25
50 6 0.06
ACGTcount: A:0.33, C:0.07, G:0.08, T:0.53
Consensus pattern (46 bp):
ATTTTGGTATATAAATATTATTTTGTATCATTTTAGTAAATAATTC
Found at i:25354922 original size:96 final size:95
Alignment explanation
Indices: 25354813--25354988 Score: 280
Period size: 96 Copynumber: 1.8 Consensus size: 95
25354803 TATGGATACT
* * * * * *
25354813 ATTTTGGTATATAAATATTTATTTTGTATCATTTTAGTAAATAATTTATTTTGGTATTTAATTAT
1 ATTTTCGTATATAAATATTTATTTTATACCATTTTAGTAAATAACTCATTTTGATATTTAATTAT
*
25354878 TATTTTTGTATTATATCGATATATCCATCAC
66 TA-TTTTGTATCATATCGATATATCCATCAC
25354909 ATTTTCGTATATAAATATTTATTTTATACCATTTTAGTAAATAACTCATTTTGATATTTAATTAT
1 ATTTTCGTATATAAATATTTATTTTATACCATTTTAGTAAATAACTCATTTTGATATTTAATTAT
25354974 TATTTTGTATCATAT
66 TATTTTGTATCATAT
25354989 TGGTAAAAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
95 12 0.16
96 61 0.84
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (95 bp):
ATTTTCGTATATAAATATTTATTTTATACCATTTTAGTAAATAACTCATTTTGATATTTAATTAT
TATTTTGTATCATATCGATATATCCATCAC
Found at i:25357497 original size:12 final size:12
Alignment explanation
Indices: 25357453--25357493 Score: 57
Period size: 11 Copynumber: 3.4 Consensus size: 12
25357443 TTTACTCAAC
25357453 TAAATAAAAACAT
1 TAAATAAAAA-AT
25357466 TAAATAAAAAAT
1 TAAATAAAAAAT
*
25357478 T-AATTAAAAAT
1 TAAATAAAAAAT
25357489 TAAAT
1 TAAAT
25357494 TAAACAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 10 0.38
12 6 0.23
13 10 0.38
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (12 bp):
TAAATAAAAAAT
Found at i:25357735 original size:4 final size:4
Alignment explanation
Indices: 25357719--25357781 Score: 51
Period size: 4 Copynumber: 15.8 Consensus size: 4
25357709 AATTTACTGC
* * *
25357719 CTTT CTCT CTTT CTTT CTTT C-CT CTTT -TTT TTTT CCCTTT -TTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT --CTTT CTTT CTTT
25357766 CTCTT CTTT CTTT CTT
1 CT-TT CTTT CTTT CTT
25357782 CTCTGGTGCT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
3 8 0.17
4 33 0.69
5 4 0.08
6 3 0.06
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
CTTT
Found at i:25357760 original size:13 final size:14
Alignment explanation
Indices: 25357719--25357779 Score: 72
Period size: 13 Copynumber: 4.4 Consensus size: 14
25357709 AATTTACTGC
25357719 CTTTCTCTCTTTCTTT
1 CTTTC-CTCTTT-TTT
25357735 CTTTCCTCTTTTTT
1 CTTTCCTCTTTTTT
*
25357749 TTTTCC-CTTTTTT
1 CTTTCCTCTTTTTT
*
25357762 CTTT-CTCTTCTTT
1 CTTTCCTCTTTTTT
25357775 CTTTC
1 CTTTC
25357780 TTCTCTGGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
12 1 0.03
13 20 0.50
14 8 0.20
15 6 0.15
16 5 0.12
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
CTTTCCTCTTTTTT
Found at i:25358811 original size:45 final size:45
Alignment explanation
Indices: 25358747--25358847 Score: 157
Period size: 45 Copynumber: 2.2 Consensus size: 45
25358737 ATCCTGATTA
* * *
25358747 ATGAACTGCAGTCTTACATAAATGAAAATGTCTTAATTAGGGAGT
1 ATGAACTTCAGTCGTACATAAATGAAAATGTCTTAATTAGGAAGT
25358792 ATGAACTTCAGTCGTACATAAATGAAAATGTCTTAATTAGGAAGT
1 ATGAACTTCAGTCGTACATAAATGAAAATGTCTTAATTAGGAAGT
* *
25358837 AAGAAATTCAG
1 ATGAACTTCAG
25358848 CCATAATATA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.30
Consensus pattern (45 bp):
ATGAACTTCAGTCGTACATAAATGAAAATGTCTTAATTAGGAAGT
Found at i:25359882 original size:166 final size:170
Alignment explanation
Indices: 25359647--25360010 Score: 453
Period size: 171 Copynumber: 2.2 Consensus size: 170
25359637 TCAGACCAAA
* * * * * *
25359647 AAAACTTAAATGGAACGGTAATGAAAACAGAAGGAATGGAACAGGAAAT---AA-AGAGTATGAG
1 AAAACTTAAATAGAATGGTAATGAAAACAGAAGAAATGTAGCAAGAAATAAAAAGAGAGTATGAG
* * * *
25359708 AGTAATG-AATG-AGAA-AT-T-GGGTTGGGTTGTAATATTGTTCATGACCAAGAAATCCAACCG
66 AGTAATGAAAAGAAAAAGATATAGGGTTGGGTTGTAATAGTGTTCATGACCAAGAAAGCCAACCG
*
25359768 TTGATGTCCTCAGGCGGTAGAATTTCAAAAATGTTATTTTTG
131 TT-ATGTCCTCAGGCGGTAGAATTTCAAAAATGTT-TTTATG
*
25359810 AAAATTTAGAA-AGAATGGTAA-GAAAACAGAAGAAATGTAGCAAGAAATAAAAAGAGAGTATGA
1 AAAACTTA-AATAGAATGGTAATGAAAACAGAAGAAATGTAGCAAGAAATAAAAAGAGAGTATGA
* **
25359873 GAGTAATGAAAAAGAAAAAGATATAGGGTTGGGTTGTAATGGTGTTCATGACCAAGTCAGCCAAC
65 GAGTAATG-AAAAGAAAAAGATATAGGGTTGGGTTGTAATAGTGTTCATGACCAAGAAAGCCAAC
* *
25359938 CGTTATGTTCTCAGGCGGTATAATTTCAAAAATGTTTTTATG
129 CGTTATGTCCTCAGGCGGTAGAATTTCAAAAATGTTTTTATG
*
25359980 AAAACTTAAATGGAATGGTAATGAAAACAGA
1 AAAACTTAAATAGAATGGTAATGAAAACAGA
25360011 TTAAATGGAG
Statistics
Matches: 169, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
162 23 0.14
163 15 0.09
164 2 0.01
165 2 0.01
166 17 0.10
168 3 0.02
169 5 0.03
170 23 0.14
171 40 0.24
172 39 0.23
ACGTcount: A:0.42, C:0.09, G:0.24, T:0.25
Consensus pattern (170 bp):
AAAACTTAAATAGAATGGTAATGAAAACAGAAGAAATGTAGCAAGAAATAAAAAGAGAGTATGAG
AGTAATGAAAAGAAAAAGATATAGGGTTGGGTTGTAATAGTGTTCATGACCAAGAAAGCCAACCG
TTATGTCCTCAGGCGGTAGAATTTCAAAAATGTTTTTATG
Found at i:25361327 original size:26 final size:26
Alignment explanation
Indices: 25361298--25361358 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
25361288 TTTTAAACCC
*
25361298 TAAACATAATTAATGAAATACAAACA
1 TAAACATAATTAATAAAATACAAACA
* *
25361324 TAAACATGATTAATAAAATACAAATA
1 TAAACATAATTAATAAAATACAAACA
25361350 TAAACATAA
1 TAAACATAA
25361359 ACTGAGCTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.25
Consensus pattern (26 bp):
TAAACATAATTAATAAAATACAAACA
Found at i:25366117 original size:46 final size:47
Alignment explanation
Indices: 25366022--25366131 Score: 161
Period size: 48 Copynumber: 2.3 Consensus size: 47
25366012 CTTGCCGTTC
*
25366022 AGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATT
1 AGCACTGTGTGTGCTCTCTGATTAGCACGTCTCGTGCTCTCTG-TATT
*
25366070 AGCACTGTGTGTGCTCTCTGATTAGCACTTCGT-GTGCTCTCTG-ATT
1 AGCACTGTGTGTGCTCTCTGATTAGCACGTC-TCGTGCTCTCTGTATT
*
25366116 AGCACTTTGTGTGCTC
1 AGCACTGTGTGTGCTC
25366132 AGTACTTTGT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
46 18 0.31
48 39 0.67
49 1 0.02
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.40
Consensus pattern (47 bp):
AGCACTGTGTGTGCTCTCTGATTAGCACGTCTCGTGCTCTCTGTATT
Found at i:25366121 original size:23 final size:22
Alignment explanation
Indices: 25366022--25366131 Score: 130
Period size: 23 Copynumber: 4.7 Consensus size: 22
25366012 CTTGCCGTTC
*
25366022 AGCACTGTGTGTGCTCTCTGTTT
1 AGCACT-TGTGTGCTCTCTGATT
* *
25366045 AGCACGTCTCGTGCTCTCTGTTATT
1 AGCACTTGT-GTGCTCTCTG--ATT
25366070 AGCACTGTGTGTGCTCTCTGATT
1 AGCACT-TGTGTGCTCTCTGATT
25366093 AGCACTTCGTGTGCTCTCTGATT
1 AGCACTT-GTGTGCTCTCTGATT
25366116 AGCACTTTGTGTGCTC
1 AGCAC-TTGTGTGCTC
25366132 AGTACTTTGT
Statistics
Matches: 76, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
22 3 0.04
23 52 0.68
24 2 0.03
25 17 0.22
26 2 0.03
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.40
Consensus pattern (22 bp):
AGCACTTGTGTGCTCTCTGATT
Found at i:25366160 original size:39 final size:39
Alignment explanation
Indices: 25366096--25366170 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
25366086 TCTGATTAGC
*
25366096 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
25366135 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
25366171 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:25367237 original size:6 final size:6
Alignment explanation
Indices: 25367226--25367268 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
25367216 TGTATTTAAT
25367226 TGTTTA TGTTTA TGTTTA TGTTTTA T-TAATTA TGTTTA TGTTT
1 TGTTTA TGTTTA TGTTTA TG-TTTA TGT--TTA TGTTTA TGTTT
25367269 GTTTTTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 1 0.03
6 22 0.67
7 9 0.27
8 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.67
Consensus pattern (6 bp):
TGTTTA
Found at i:25370095 original size:27 final size:27
Alignment explanation
Indices: 25370057--25370124 Score: 136
Period size: 27 Copynumber: 2.5 Consensus size: 27
25370047 TGCTTAAATA
25370057 AACACTGGTGTCGCCTATTTGTTTGGC
1 AACACTGGTGTCGCCTATTTGTTTGGC
25370084 AACACTGGTGTCGCCTATTTGTTTGGC
1 AACACTGGTGTCGCCTATTTGTTTGGC
25370111 AACACTGGTGTCGC
1 AACACTGGTGTCGC
25370125 TTACCAGATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.16, C:0.24, G:0.26, T:0.34
Consensus pattern (27 bp):
AACACTGGTGTCGCCTATTTGTTTGGC
Found at i:25370147 original size:27 final size:27
Alignment explanation
Indices: 25370117--25370168 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
25370107 TGGCAACACT
* * *
25370117 GGTGTCGCTTACCAGATGGGTACCATA
1 GGTGCCGCCTACCAGATGGGCACCATA
*
25370144 GGTGCCGCCTATCAGATGGGCACCA
1 GGTGCCGCCTACCAGATGGGCACCA
25370169 GCCAATATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.21, C:0.27, G:0.31, T:0.21
Consensus pattern (27 bp):
GGTGCCGCCTACCAGATGGGCACCATA
Found at i:25373162 original size:16 final size:17
Alignment explanation
Indices: 25373143--25373175 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
25373133 TAGTGTATTA
*
25373143 TATTTTTAA-AAAAAAT
1 TATTTTAAATAAAAAAT
25373159 TATTTTAAATAAAAAAT
1 TATTTTAAATAAAAAAT
25373176 AATATGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATTTTAAATAAAAAAT
Found at i:25376116 original size:100 final size:99
Alignment explanation
Indices: 25375944--25376135 Score: 273
Period size: 100 Copynumber: 1.9 Consensus size: 99
25375934 AATGCACCTG
* * *
25375944 CATATTTCGTGTAAAAATTTGCGATTCCAGAAAGAGAAAAAAGATACGTTTTTACCCAAAAGAAT
1 CATATTTCGTGTAAAAATTTGCAATTCCAGAAAGAGAAAAAAGACACATTTTTACCCAAAAGAAT
*
25376009 AGGTTAGAGAAAGCATTGTCAAATATACATAGGT
66 AGGTTAGAGAAAGCAGTGTCAAATATACATAGGT
* *
25376043 CATATTTTC-TGTAAAAATTT-CAATTCCAGAAAGACCGGAAAAA-ACACATTTTTGTCCCAAAA
1 CATA-TTTCGTGTAAAAATTTGCAATTCCAGAAAGA--GAAAAAAGACACATTTTT-ACCCAAAA
25376105 GAATAGGTTAGAGAAAGCAGTGTCAAATATA
62 GAATAGGTTAGAGAAAGCAGTGTCAAATATA
25376136 TTAGAGGGAT
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
98 13 0.16
99 23 0.28
100 47 0.57
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27
Consensus pattern (99 bp):
CATATTTCGTGTAAAAATTTGCAATTCCAGAAAGAGAAAAAAGACACATTTTTACCCAAAAGAAT
AGGTTAGAGAAAGCAGTGTCAAATATACATAGGT
Found at i:25378914 original size:6 final size:6
Alignment explanation
Indices: 25378903--25378943 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
25378893 CTTTTCTCGG
* *
25378903 TCCCTA TCCCTA TCCCTA TCCTTA TCTCTA TCCCTA TCCCT
1 TCCCTA TCCCTA TCCCTA TCCCTA TCCCTA TCCCTA TCCCT
25378944 GTGGCGATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.15, C:0.46, G:0.00, T:0.39
Consensus pattern (6 bp):
TCCCTA
Found at i:25379091 original size:39 final size:39
Alignment explanation
Indices: 25379047--25379163 Score: 173
Period size: 39 Copynumber: 3.0 Consensus size: 39
25379037 CCCATACAAG
25379047 GTTGCATTTAACTTATATCACTAAGAGACCAAATGTAGA
1 GTTGCATTTAACTTATATCACTAAGAGACCAAATGTAGA
25379086 GTTGCATTTAACTTATATCACTAAGAGACCAAATGTAGA
1 GTTGCATTTAACTTATATCACTAAGAGACCAAATGTAGA
* * * * *
25379125 GTTGCATGTAA-TCCATAACACTAAAAGCCCAAATGTAGA
1 GTTGCATTTAACT-TATATCACTAAGAGACCAAATGTAGA
25379164 ACAGGCATAA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
38 1 0.01
39 71 0.99
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.28
Consensus pattern (39 bp):
GTTGCATTTAACTTATATCACTAAGAGACCAAATGTAGA
Found at i:25380436 original size:21 final size:19
Alignment explanation
Indices: 25380384--25380439 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
25380374 AATATATAAT
25380384 TATATT-TTAAAAATAAAA
1 TATATTATTAAAAATAAAA
25380402 TATA-TATCTAAAAACTAAAA
1 TATATTAT-TAAAAA-TAAAA
25380422 TATTATTATTAAAAATAA
1 TA-TATTATTAAAAATAA
25380440 TTTCTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 1 0.03
18 5 0.15
19 6 0.18
20 10 0.30
21 8 0.24
22 3 0.09
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
TATATTATTAAAAATAAAA
Found at i:25380871 original size:3 final size:3
Alignment explanation
Indices: 25380863--25380902 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
25380853 TACGAATGTG
25380863 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
25380903 CTCATAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:25381551 original size:32 final size:32
Alignment explanation
Indices: 25381515--25381575 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
25381505 TTTTTTGTTC
*
25381515 AATTTGATA-CTCAAACTTGACATTTTTTTCGT
1 AATTTGATATCT-AAACTTGACACTTTTTTCGT
*
25381547 AATTTGGTATCTAAACTTGACACTTTTTT
1 AATTTGATATCTAAACTTGACACTTTTTT
25381576 ATATTGGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.48
Consensus pattern (32 bp):
AATTTGATATCTAAACTTGACACTTTTTTCGT
Found at i:25381592 original size:29 final size:32
Alignment explanation
Indices: 25381515--25381593 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 32
25381505 TTTTTTGTTC
* * * *
25381515 AATTTGATACTCAAACTTGACATTTTTTTCGT
1 AATTTGGTACTTAAACTTGACACTTTTTTCAT
25381547 AATTTGGTA-TCTAAACTTGACACTTTTTT-AT
1 AATTTGGTACT-TAAACTTGACACTTTTTTCAT
25381578 -A-TTGGTACTTAAACTT
1 AATTTGGTACTTAAACTT
25381594 TTTGGGGTCC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
29 13 0.32
30 2 0.05
31 2 0.05
32 24 0.59
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (32 bp):
AATTTGGTACTTAAACTTGACACTTTTTTCAT
Found at i:25382002 original size:29 final size:30
Alignment explanation
Indices: 25381940--25382010 Score: 117
Period size: 29 Copynumber: 2.4 Consensus size: 30
25381930 TTAAGTATAT
* *
25381940 TATAAAATAACTTTTCACCAAAAAAAATAT
1 TATAAAATACCTTTTCACCAAAAAAAATAC
25381970 TATAAAATACCTTTTCA-CAAAAAAAATAC
1 TATAAAATACCTTTTCACCAAAAAAAATAC
25381999 TATAAAATACCT
1 TATAAAATACCT
25382011 AACTATATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 23 0.59
30 16 0.41
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (30 bp):
TATAAAATACCTTTTCACCAAAAAAAATAC
Found at i:25384906 original size:15 final size:15
Alignment explanation
Indices: 25384886--25384915 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25384876 CCTATTTTGA
*
25384886 TTTATTCCCCTTTTC
1 TTTATTACCCTTTTC
25384901 TTTATTACCCTTTTC
1 TTTATTACCCTTTTC
25384916 CTTCGCAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.30, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTATTACCCTTTTC
Found at i:25388339 original size:18 final size:17
Alignment explanation
Indices: 25388314--25388347 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
25388304 ATATATTAAT
*
25388314 TAATAATAATATTATTA
1 TAATAATAATAATATTA
25388331 TAATAAATAATAATATT
1 TAAT-AATAATAATATT
25388348 TTATTATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATAATAATAATATTA
Found at i:25388339 original size:21 final size:20
Alignment explanation
Indices: 25388310--25388351 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
25388300 AATGATATAT
*
25388310 TAATTAATAATAATATTATTA
1 TAATAAATAATAATATT-TTA
25388331 TAATAAATAATAATATTTTA
1 TAATAAATAATAATATTTTA
25388351 T
1 T
25388352 TATTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATAAATAATAATATTTTA
Found at i:25391705 original size:18 final size:18
Alignment explanation
Indices: 25391682--25391717 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
25391672 ACTTCTGCAG
*
25391682 CTCGAGGTCGTGGTAGTA
1 CTCGAGGTCGTGCTAGTA
*
25391700 CTCGAGGTGGTGCTAGTA
1 CTCGAGGTCGTGCTAGTA
25391718 GTAGAGGTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.17, G:0.39, T:0.28
Consensus pattern (18 bp):
CTCGAGGTCGTGCTAGTA
Found at i:25395407 original size:21 final size:20
Alignment explanation
Indices: 25395381--25395424 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 20
25395371 TTTCAAATGA
25395381 TATAATAAATAATAATATTAT
1 TATAATAAATAATAATATT-T
25395402 TATAATAAATAATAATATTT
1 TATAATAAATAATAATATTT
25395422 TAT
1 TAT
25395425 TATTTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAATAAATAATAATATTT
Found at i:25403666 original size:100 final size:99
Alignment explanation
Indices: 25403494--25403685 Score: 273
Period size: 100 Copynumber: 1.9 Consensus size: 99
25403484 AATGCACCTG
* * *
25403494 CATATTTCGTGTAAAAATTTGCGATTCCAGAAAGAGAAAAAAGATACGTTTTTACCCAAAAGAAT
1 CATATTTCGTGTAAAAATTTGCAATTCCAGAAAGAGAAAAAAGACACATTTTTACCCAAAAGAAT
*
25403559 AGGTTAGAGAAAGCATTGTCAAATATACATAGGT
66 AGGTTAGAGAAAGCAGTGTCAAATATACATAGGT
* *
25403593 CATATTTTC-TGTAAAAATTT-CAATTCCAGAAAGACCGGAAAAA-ACACATTTTTGTCCCAAAA
1 CATA-TTTCGTGTAAAAATTTGCAATTCCAGAAAGA--GAAAAAAGACACATTTTT-ACCCAAAA
25403655 GAATAGGTTAGAGAAAGCAGTGTCAAATATA
62 GAATAGGTTAGAGAAAGCAGTGTCAAATATA
25403686 TTAGAGGGAT
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
98 13 0.16
99 23 0.28
100 47 0.57
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27
Consensus pattern (99 bp):
CATATTTCGTGTAAAAATTTGCAATTCCAGAAAGAGAAAAAAGACACATTTTTACCCAAAAGAAT
AGGTTAGAGAAAGCAGTGTCAAATATACATAGGT
Found at i:25407923 original size:19 final size:19
Alignment explanation
Indices: 25407893--25407949 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 19
25407883 GTAATATATA
25407893 ATTATATTTAAAAATAAAAT
1 ATTATA-TTAAAAATAAAAT
25407913 A-TATATCTAAAAACTAAAAT
1 ATTATAT-TAAAAA-TAAAAT
25407933 ATTATTATTAAAAATAA
1 ATTA-TATTAAAAATAA
25407950 TTTCTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 1 0.03
19 10 0.30
20 11 0.33
21 8 0.24
22 3 0.09
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTATATTAAAAATAAAAT
Found at i:25408423 original size:21 final size:20
Alignment explanation
Indices: 25408399--25408445 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
25408389 TTGATAACTC
25408399 ATTTTATATTTTTAAAATTTA
1 ATTTTATATTTTTAAAA-TTA
* *
25408420 ATTTGT-TTTTTTTAATATTA
1 ATTT-TATATTTTTAAAATTA
25408440 ATTTTA
1 ATTTTA
25408446 GTTTTTTCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
19 1 0.05
20 7 0.32
21 13 0.59
22 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
ATTTTATATTTTTAAAATTA
Found at i:25409445 original size:45 final size:44
Alignment explanation
Indices: 25409382--25409466 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 44
25409372 AATATTTGCA
* *
25409382 AATATACGAATTTGTATTATTATTATTATTAGTAA-AATATGCT
1 AATATACGAATGTGTATTATTATTATTATTACTAATAATATGCT
25409425 AATATACGAATGTGATTATTATTATTATTATTACTAATAATA
1 AATATACGAATGTG--TATTATTATTATTATTACTAATAATA
25409467 ATAAAGGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
43 13 0.35
45 20 0.54
46 4 0.11
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (44 bp):
AATATACGAATGTGTATTATTATTATTATTACTAATAATATGCT
Found at i:25410129 original size:33 final size:33
Alignment explanation
Indices: 25410059--25410130 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
25410049 GTTTCTAAAT
*
25410059 TTTTTTTGCTCAATTTGATACTCAAACTTGACA
1 TTTTTTTCCTCAATTTGATACTCAAACTTGACA
*
25410092 TTTTTTTCCT-AATTTGGTA-TCTAAACTTGACA
1 TTTTTTTCCTCAATTTGATACTC-AAACTTGACA
*
25410124 CTTTTTT
1 TTTTTTT
25410131 ATATTGGTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 2 0.06
32 24 0.69
33 9 0.26
ACGTcount: A:0.24, C:0.17, G:0.08, T:0.51
Consensus pattern (33 bp):
TTTTTTTCCTCAATTTGATACTCAAACTTGACA
Found at i:25410147 original size:29 final size:32
Alignment explanation
Indices: 25410070--25410148 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 32
25410060 TTTTTTGCTC
* * * *
25410070 AATTTGATACTCAAACTTGACATTTTTTTCCT
1 AATTTGGTACTTAAACTTGACACTTTTTTCAT
25410102 AATTTGGTA-TCTAAACTTGACACTTTTTT-AT
1 AATTTGGTACT-TAAACTTGACACTTTTTTCAT
25410133 -A-TTGGTACTTAAACTT
1 AATTTGGTACTTAAACTT
25410149 TTTGGGTTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
29 13 0.32
30 2 0.05
31 2 0.05
32 24 0.59
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (32 bp):
AATTTGGTACTTAAACTTGACACTTTTTTCAT
Found at i:25410194 original size:32 final size:31
Alignment explanation
Indices: 25410082--25410194 Score: 71
Period size: 32 Copynumber: 3.8 Consensus size: 31
25410072 TTTGATACTC
* *
25410082 AAACTTGACATTTTTTTCCTAATTTGGTATCT
1 AAACTTGAC-TTTTTGTCCTAATTTGGTACCT
* *
25410114 AAACTTGACACTTTT-T--T-ATATTGGTACTT
1 AAACTTGAC-TTTTTGTCCTAAT-TTGGTACCT
** *
25410143 AAACTT---TTTGGGTTC-AATTTGGTACCT
1 AAACTTGACTTTTTGTCCTAATTTGGTACCT
25410170 AAACTTGACTCTTTTGTCCTAATTT
1 AAACTTGACT-TTTTGTCCTAATTT
25410195 AATATGTAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
25 2 0.03
26 1 0.02
27 14 0.23
28 4 0.07
29 14 0.23
30 1 0.02
31 6 0.10
32 19 0.31
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.48
Consensus pattern (31 bp):
AAACTTGACTTTTTGTCCTAATTTGGTACCT
Found at i:25410428 original size:3 final size:3
Alignment explanation
Indices: 25410420--25410455 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
25410410 TACATCCCAA
25410420 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
25410456 GAATAGAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:25411516 original size:7 final size:7
Alignment explanation
Indices: 25411504--25411560 Score: 73
Period size: 7 Copynumber: 8.4 Consensus size: 7
25411494 TTTCAAAAAA
25411504 GTCAACG
1 GTCAACG
25411511 GTCAACG
1 GTCAACG
* *
25411518 ATCAA-A
1 GTCAACG
25411524 GTCAACG
1 GTCAACG
25411531 GTCAACG
1 GTCAACG
*
25411538 GTCAA-A
1 GTCAACG
25411544 GTCAACG
1 GTCAACG
25411551 GTCAACG
1 GTCAACG
25411558 GTC
1 GTC
25411561 GGTCAACGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
6 9 0.21
7 33 0.79
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:25411536 original size:27 final size:27
Alignment explanation
Indices: 25411504--25411560 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
25411494 TTTCAAAAAA
*
25411504 GTCAACGGTCAACGATCAA-AGTCAACG
1 GTCAACGGTCAAAG-TCAACAGTCAACG
*
25411531 GTCAACGGTCAAAGTCAACGGTCAACG
1 GTCAACGGTCAAAGTCAACAGTCAACG
25411558 GTC
1 GTC
25411561 GGTCAACGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (27 bp):
GTCAACGGTCAAAGTCAACAGTCAACG
Found at i:25411547 original size:13 final size:13
Alignment explanation
Indices: 25411501--25411555 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
25411491 GTTTTTCAAA
25411501 AAAGTCAACGGTC
1 AAAGTCAACGGTC
* *
25411514 AACGATCAA-AGTC
1 AAAG-TCAACGGTC
*
25411527 AACGGTCAACGGTC
1 AA-AGTCAACGGTC
25411541 AAAGTCAACGGTC
1 AAAGTCAACGGTC
25411554 AA
1 AA
25411556 CGGTCGGTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 24 0.71
14 10 0.29
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:25411558 original size:20 final size:20
Alignment explanation
Indices: 25411501--25411560 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
25411491 GTTTTTCAAA
*
25411501 AAAGTCAACGGTCAACGATC
1 AAAGTCAACGGTCAACGGTC
25411521 AAAGTCAACGGTCAACGGTC
1 AAAGTCAACGGTCAACGGTC
25411541 AAAGTCAACGGTCAACGGTC
1 AAAGTCAACGGTCAACGGTC
25411561 GGTCAACGTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (20 bp):
AAAGTCAACGGTCAACGGTC
Done.