Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015290.1 Kokia drynarioides strain JFW-HI SEQ_130335, 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: 218562
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 61 characters in sequence are not A, C, G, or T
Found at i:7112 original size:18 final size:18
Alignment explanation
Indices: 7089--7124 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
7079 TTTTCAAGAG
*
7089 TTAGACAAGTAGATGAGC
1 TTAGACAAATAGATGAGC
7107 TTAGACAAATAGATGAGC
1 TTAGACAAATAGATGAGC
7125 AAGCTGGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.22
Consensus pattern (18 bp):
TTAGACAAATAGATGAGC
Found at i:22399 original size:22 final size:22
Alignment explanation
Indices: 22361--22404 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
22351 TCAATAATAA
*
22361 ATAAATAAATATAAATAGTATT
1 ATAAATAAATAAAAATAGTATT
*
22383 ATAAA-AAATAAATAATATTATT
1 ATAAATAAATAAA-AATAGTATT
22405 CAAGATAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAAATAAATAAAAATAGTATT
Found at i:26528 original size:79 final size:82
Alignment explanation
Indices: 26437--26596 Score: 272
Period size: 79 Copynumber: 2.0 Consensus size: 82
26427 CTCGTAAAAA
*
26437 TAATAAATTTTGGCCTTGTTTATAT-AAAATAATAATAATTTCAATAAA-AATTTAAATT-AAAT
1 TAATAAATTTTGGCCTTGTTTATATAAAAATAATAATAATTTCAATAAACAAATTAAATTCAAAT
26499 AGGGACTAAATTATAAT
66 AGGGACTAAATTATAAT
* *
26516 TAATAATTTTTGGTCTTGTTTATATAAAAATAATAATAATTTCAATAAACAAATTAAATTCAAAT
1 TAATAAATTTTGGCCTTGTTTATATAAAAATAATAATAATTTCAATAAACAAATTAAATTCAAAT
26581 AGGGACTAAATTATAA
66 AGGGACTAAATTATAA
26597 ATCTAACAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
79 23 0.31
80 23 0.31
81 9 0.12
82 20 0.27
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (82 bp):
TAATAAATTTTGGCCTTGTTTATATAAAAATAATAATAATTTCAATAAACAAATTAAATTCAAAT
AGGGACTAAATTATAAT
Found at i:27163 original size:19 final size:19
Alignment explanation
Indices: 27126--27175 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
27116 TAGATATTAT
27126 TATAAA-ATTAAAAAAAGAA
1 TATAAAGATT-AAAAAAGAA
*
27145 TATAAAGATTAAAAGAGAA
1 TATAAAGATTAAAAAAGAA
*
27164 -AGAAAGA-TAAAA
1 TATAAAGATTAAAA
27176 TAAAATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 5 0.18
18 6 0.21
19 14 0.50
20 3 0.11
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (19 bp):
TATAAAGATTAAAAAAGAA
Found at i:28908 original size:29 final size:29
Alignment explanation
Indices: 28813--28916 Score: 102
Period size: 29 Copynumber: 3.5 Consensus size: 29
28803 ATTTAATACA
* *
28813 TTTAGGTACCAAATTGAATCTAAAAAAAG
1 TTTAGGTACCAAATTGAGTCAAAAAAAAG
* * **
28842 CTTAGGTGCCAAATT-AGGAAAAAATGTAAAG
1 TTTAGGTACCAAATTGAGTCAAAAA---AAAG
* *
28873 TTCAGGTACCAAATTGAGTCCAAAAAAAG
1 TTTAGGTACCAAATTGAGTCAAAAAAAAG
28902 TTTAGGTACCAAATT
1 TTTAGGTACCAAATT
28917 AGGAAAAATG
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
28 5 0.09
29 31 0.53
31 16 0.28
32 6 0.10
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.26
Consensus pattern (29 bp):
TTTAGGTACCAAATTGAGTCAAAAAAAAG
Found at i:28933 original size:59 final size:60
Alignment explanation
Indices: 28816--28947 Score: 203
Period size: 60 Copynumber: 2.2 Consensus size: 60
28806 TAATACATTT
* *
28816 AGGTACCAAATTGAATCTAAAAAAAGCTTAGGTGCCAAATTAGGAAAAAATGTAAAGTTC
1 AGGTACCAAATTGAATCCAAAAAAAGCTTAGGTACCAAATTAGGAAAAAATGTAAAGTTC
* * *
28876 AGGTACCAAATTGAGTCCAAAAAAAGTTTAGGTACCAAATTAGG-AAAAATGTCAAGTTC
1 AGGTACCAAATTGAATCCAAAAAAAGCTTAGGTACCAAATTAGGAAAAAATGTAAAGTTC
*
28935 AGGTACTAAATTG
1 AGGTACCAAATTG
28948 GGTCAAATTA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
59 26 0.39
60 40 0.61
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (60 bp):
AGGTACCAAATTGAATCCAAAAAAAGCTTAGGTACCAAATTAGGAAAAAATGTAAAGTTC
Found at i:30196 original size:8 final size:8
Alignment explanation
Indices: 30179--30209 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
30169 ACCAAAAAAA
30179 AAATCCTT
1 AAATCCTT
*
30187 AAATCATT
1 AAATCCTT
30195 AAATCCTT
1 AAATCCTT
30203 AAATCCT
1 AAATCCT
30210 CATTGCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (8 bp):
AAATCCTT
Found at i:30269 original size:15 final size:15
Alignment explanation
Indices: 30235--30283 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
30225 CAAGCAGTAA
*
30235 AAGATGGAAAGAAGAAG
1 AAGAAGGAAAG-A-AAG
*
30252 AAGAGGGAAAGAAAG
1 AAGAAGGAAAGAAAG
*
30267 AAGAAGAAAAGAAAG
1 AAGAAGGAAAGAAAG
30282 AA
1 AA
30284 TTGGCTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 18 0.62
16 1 0.03
17 10 0.34
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (15 bp):
AAGAAGGAAAGAAAG
Found at i:30269 original size:18 final size:17
Alignment explanation
Indices: 30235--30273 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
30225 CAAGCAGTAA
*
30235 AAGATGGAAAGAAGAAG
1 AAGAGGGAAAGAAGAAG
30252 AAGAGGGAAAGAAAGAAG
1 AAGAGGGAAAG-AAGAAG
30270 AAGA
1 AAGA
30274 AAAGAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.03
Consensus pattern (17 bp):
AAGAGGGAAAGAAGAAG
Found at i:30929 original size:94 final size:94
Alignment explanation
Indices: 30728--30915 Score: 358
Period size: 94 Copynumber: 2.0 Consensus size: 94
30718 TACCTCTCCC
30728 TATAATTTAATTTTGGCACACAGGGTGAAAAGAATAAAAATTTTAAGCAATGATTTTTTAAAAAA
1 TATAATTTAATTTTGGCACACAGGGTGAAAAGAATAAAAATTTTAAGCAATGATTTTTTAAAAAA
*
30793 TATTATCAATAATAAAAAATAAATAATTT
66 TATAATCAATAATAAAAAATAAATAATTT
*
30822 TATAATTTAATTTTGGCACACAGGGTGAAAAGAATAAAAATTTTAAGCAATGATTTTTTTAAAAA
1 TATAATTTAATTTTGGCACACAGGGTGAAAAGAATAAAAATTTTAAGCAATGATTTTTTAAAAAA
30887 TATAATCAATAATAAAAAATAAATAATTT
66 TATAATCAATAATAAAAAATAAATAATTT
30916 GTTAATTATA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (94 bp):
TATAATTTAATTTTGGCACACAGGGTGAAAAGAATAAAAATTTTAAGCAATGATTTTTTAAAAAA
TATAATCAATAATAAAAAATAAATAATTT
Found at i:34552 original size:28 final size:28
Alignment explanation
Indices: 34495--34552 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
34485 TATAAAATAC
* * *
34495 GAAATGTATTAATTTAATGGAAATATAG
1 GAAATGTATTAATATAATAGAAATAGAG
34523 GAAATGTATTAATATAA-AGAAAGTAGAG
1 GAAATGTATTAATATAATAGAAA-TAGAG
34551 GA
1 GA
34553 TTATACCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (28 bp):
GAAATGTATTAATATAATAGAAATAGAG
Found at i:35102 original size:24 final size:22
Alignment explanation
Indices: 35075--35135 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
35065 ACGTTAACCA
*
35075 AAATAACCCTAAACCAAAATATAT
1 AAATAACCCTAAA-CAAAAAAT-T
**
35099 AAATAACAAATCAAACAAAAAATT
1 AAATAAC-CCT-AAACAAAAAATT
35123 AAATAACCCTAAA
1 AAATAACCCTAAA
35136 TCCCAAACAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
22 3 0.10
23 1 0.03
24 15 0.50
25 8 0.27
26 3 0.10
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (22 bp):
AAATAACCCTAAACAAAAAATT
Found at i:35200 original size:35 final size:37
Alignment explanation
Indices: 35123--35201 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 37
35113 ACAAAAAATT
* *
35123 AAATAACCCTAAATCCCAAACAATAGCAATCAAAATCG
1 AAATAACCCTAAAT-CCAAACAATAGAAATCAAAATCC
*
35161 AAATAACCCTAAAT-CAAA-AAT-GAAAATCAGAATCC
1 AAATAACCCTAAATCCAAACAATAG-AAATCAAAATCC
35196 AAATAA
1 AAATAA
35202 AAAATGAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
34 1 0.03
35 18 0.49
36 4 0.11
38 14 0.38
ACGTcount: A:0.57, C:0.22, G:0.05, T:0.16
Consensus pattern (37 bp):
AAATAACCCTAAATCCAAACAATAGAAATCAAAATCC
Found at i:36950 original size:18 final size:18
Alignment explanation
Indices: 36912--36950 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
36902 AATATTTTTT
* **
36912 AAAAGTGTTTTTGAGCTA
1 AAAAGTATTTTTGAGAAA
36930 AAAAGTATTTTTGAGAAA
1 AAAAGTATTTTTGAGAAA
36948 AAA
1 AAA
36951 CTAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.33
Consensus pattern (18 bp):
AAAAGTATTTTTGAGAAA
Found at i:37314 original size:11 final size:11
Alignment explanation
Indices: 37271--37328 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
37261 TCAAGTTTTG
*
37271 ATTTTAAAATT
1 ATTTTAAATTT
*
37282 AGGTTTAAA-TT
1 A-TTTTAAATTT
*
37293 AGTTTAAATTT
1 ATTTTAAATTT
37304 ATTTTAAATTT
1 ATTTTAAATTT
37315 AAATTTTAAATTT
1 --ATTTTAAATTT
37328 A
1 A
37329 ATCAAATTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 7 0.17
11 17 0.41
12 6 0.15
13 11 0.27
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:37322 original size:13 final size:13
Alignment explanation
Indices: 37295--37329 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
37285 TTTAAATTAG
37295 TTTAAATTT--AT
1 TTTAAATTTAAAT
37306 TTTAAATTTAAAT
1 TTTAAATTTAAAT
37319 TTTAAATTTAA
1 TTTAAATTTAA
37330 TCAAATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 9 0.41
13 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTAAATTTAAAT
Found at i:37392 original size:24 final size:23
Alignment explanation
Indices: 37363--37408 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
37353 CTTAATATTA
37363 AAATTAAAAGCCCAAATAAAAATT
1 AAATTAAAAGCCCAAA-AAAAATT
*
37387 AAATTAAAAGTCCAAAAAAAAT
1 AAATTAAAAGCCCAAAAAAAAT
37409 ACAAAGTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.65, C:0.11, G:0.04, T:0.20
Consensus pattern (23 bp):
AAATTAAAAGCCCAAAAAAAATT
Found at i:38157 original size:24 final size:24
Alignment explanation
Indices: 38128--38173 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
38118 ATATATATTA
*
38128 AATAATTTCATTAATGATAATAAT
1 AATAATTTCATTAAAGATAATAAT
*
38152 AATAATTTTATTAAAGATAATA
1 AATAATTTCATTAAAGATAATA
38174 TTTATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (24 bp):
AATAATTTCATTAAAGATAATAAT
Found at i:38190 original size:18 final size:17
Alignment explanation
Indices: 38149--38191 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
38139 TAATGATAAT
38149 AATAATAAT-TTTATTA
1 AATAATAATATTTATTA
*
38165 AA-GATAATATTTATTA
1 AATAATAATATTTATTA
38181 AATAATTAATA
1 AATAA-TAATA
38192 ATAATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 5 0.23
16 11 0.50
17 1 0.05
18 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AATAATAATATTTATTA
Found at i:39352 original size:29 final size:29
Alignment explanation
Indices: 39314--39683 Score: 165
Period size: 30 Copynumber: 12.9 Consensus size: 29
39304 GAGGTCCCTA
39314 AACTATCCAAAAATTACATTTTTACCCTCG
1 AACT-TCCAAAAATTACATTTTTACCCTCG
*
39344 AACTTCCAAAAATTCCA-TTTT----T--
1 AACTTCCAAAAATTACATTTTTACCCTCG
* * *
39366 AAC-CCCAAAAATTCCATTTTTAACCC-CAA
1 AACTTCCAAAAATTACATTTTT-ACCCTC-G
* *
39395 AACTTCCAAAAATT-CTATTTTAACCCTCAA
1 AACTTCCAAAAATTAC-ATTTTTACCCTC-G
*
39425 AACTTCCAAAAATT-CAATTTTTCCCCTCG
1 AACTTCCAAAAATTAC-ATTTTTACCCTCG
* **
39454 AACTTCCAAAAAATTCCATTTTTGACCCTAA
1 AACTTCC-AAAAATTACATTTTT-ACCCTCG
*
39485 AACTTCCAAAAATTACATTTTTACCC-CC
1 AACTTCCAAAAATTACATTTTTACCCTCG
* * * * *
39513 AACCTCCAAAATTTCCATTTTGACCC-CAA
1 AACTTCCAAAAATTACATTTTTACCCTC-G
* * *
39542 AACTTTCAAAAATTACCA--TTTGCCCCCG
1 AACTTCCAAAAATTA-CATTTTTACCCTCG
* *
39570 AA-TGTCCAAAAACT-CTGTTTTTGA-CCTCG
1 AACT-TCCAAAAATTAC-ATTTTT-ACCCTCG
** *
39599 AAAC-TCTC-AAAATTACCCTTTTACCCCCG
1 -AACTTC-CAAAAATTACATTTTTACCCTCG
* *
39628 AA-TGTCTAAAAATTACATTTTAAACCC-CG
1 AACT-TCCAAAAATTACATTTT-TACCCTCG
*
39657 AACTTTCCCAAAATTACCA-TTTTACCC
1 AAC-TTCCAAAAATTA-CATTTTTACCC
39684 CCGAGAATCC
Statistics
Matches: 263, Mismatches: 42, Indels: 71
0.70 0.11 0.19
Matches are distributed among these distances:
21 12 0.05
22 7 0.03
24 1 0.00
26 1 0.00
27 1 0.00
28 45 0.17
29 86 0.33
30 95 0.36
31 15 0.06
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTACCCTCG
Found at i:39375 original size:21 final size:21
Alignment explanation
Indices: 39349--39402 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
39339 CCTCGAACTT
39349 CCAAAAATTCCATTTTTAACC
1 CCAAAAATTCCATTTTTAACC
39370 CCAAAAATTCCATTTTTAACC
1 CCAAAAATTCCATTTTTAACC
*
39391 CCAAAACTTCCA
1 CCAAAAATTCCA
39403 AAAATTCTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.39, C:0.31, G:0.00, T:0.30
Consensus pattern (21 bp):
CCAAAAATTCCATTTTTAACC
Found at i:39375 original size:50 final size:50
Alignment explanation
Indices: 39320--39426 Score: 146
Period size: 50 Copynumber: 2.1 Consensus size: 50
39310 CCTAAACTAT
*
39320 CCAAAAATTACATTTTT-ACCCTC-GAACTTCCAAAAATTCCATTTTTAACC
1 CCAAAAATTACATTTTTAACCC-CAAAACTTCCAAAAATTCCA-TTTTAACC
* *
39370 CCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCTATTTTAACC
1 CCAAAAATTACATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTAACC
39420 CTCAAAA
1 C-CAAAA
39427 CTTCCAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
50 26 0.51
51 25 0.49
ACGTcount: A:0.39, C:0.28, G:0.01, T:0.32
Consensus pattern (50 bp):
CCAAAAATTACATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTAACC
Found at i:39404 original size:30 final size:29
Alignment explanation
Indices: 39370--39562 Score: 210
Period size: 30 Copynumber: 6.5 Consensus size: 29
39360 ATTTTTAACC
39370 CCAAAAATTCCATTTTTAACCCCAAAACTT
1 CCAAAAATTCCATTTTT-ACCCCAAAACTT
* *
39400 CCAAAAATTCTATTTTAACCCTCAAAACTT
1 CCAAAAATTCCATTTTTACCC-CAAAACTT
* **
39430 CCAAAAATTCAATTTTT-CCCCTCGAACTT
1 CCAAAAATTCCATTTTTACCCC-AAAACTT
*
39459 CCAAAAAATTCCATTTTTGACCCTAAAACTT
1 CC-AAAAATTCCATTTTT-ACCCCAAAACTT
* * *
39490 CCAAAAATTACATTTTTACCCC-CAACCT
1 CCAAAAATTCCATTTTTACCCCAAAACTT
* *
39518 CCAAAATTTCCATTTTGACCCCAAAACTT
1 CCAAAAATTCCATTTTTACCCCAAAACTT
*
39547 TCAAAAATTACCATTT
1 CCAAAAATT-CCATTT
39563 GCCCCCGAAT
Statistics
Matches: 135, Mismatches: 21, Indels: 14
0.79 0.12 0.08
Matches are distributed among these distances:
28 24 0.18
29 29 0.21
30 72 0.53
31 7 0.05
32 3 0.02
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.32
Consensus pattern (29 bp):
CCAAAAATTCCATTTTTACCCCAAAACTT
Found at i:39415 original size:51 final size:49
Alignment explanation
Indices: 39320--39432 Score: 147
Period size: 51 Copynumber: 2.2 Consensus size: 49
39310 CCTAAACTAT
* *
39320 CCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACC
1 CCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCA-TTTTAACC
*
39370 CCAAAAATTCCATTTTTAACCC-CAAAACTTCCAAAAATTCTATTTTAACC
1 CCAAAAATTCCATTTTT-ACCCTC-AAACTTCCAAAAATTCCATTTTAACC
*
39420 CTCAAAACTTCCA
1 C-CAAAAATTCCA
39433 AAAATTCAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
50 26 0.46
51 30 0.54
ACGTcount: A:0.38, C:0.29, G:0.01, T:0.32
Consensus pattern (49 bp):
CCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTAACC
Found at i:39603 original size:58 final size:58
Alignment explanation
Indices: 39530--39639 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 58
39520 AAAATTTCCA
* *
39530 TTTTGACCCCAAAACTTTCAAAAATTA-CCATTTGCCCCCGAATGTCCAAAAACTCTGT
1 TTTTGACCCCAAAACTCTC-AAAATTACCCATTTACCCCCGAATGTCCAAAAACTCTGT
* * * *
39588 TTTTGACCTCGAAACTCTCAAAATTACCCTTTTACCCCCGAATGTCTAAAAA
1 TTTTGACCCCAAAACTCTCAAAATTACCCATTTACCCCCGAATGTCCAAAAA
39640 TTACATTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 7 0.16
58 38 0.84
ACGTcount: A:0.33, C:0.29, G:0.08, T:0.30
Consensus pattern (58 bp):
TTTTGACCCCAAAACTCTCAAAATTACCCATTTACCCCCGAATGTCCAAAAACTCTGT
Found at i:39684 original size:29 final size:28
Alignment explanation
Indices: 39606--39684 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 28
39596 TCGAAACTCT
* *
39606 CAAAATTACCCTTTTACCCCCGAATGTCT
1 CAAAATTACCATTTTA-CCCCGAATGTCC
* *
39635 AAAAATTA-CATTTTAAACCCCGAACTTTCC
1 CAAAATTACCATTTT--ACCCCGAA-TGTCC
39665 CAAAATTACCATTTTACCCC
1 CAAAATTACCATTTTACCCC
39685 CGAGAATCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
28 5 0.12
29 19 0.46
30 11 0.27
31 6 0.15
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (28 bp):
CAAAATTACCATTTTACCCCGAATGTCC
Found at i:40678 original size:35 final size:34
Alignment explanation
Indices: 40638--40712 Score: 80
Period size: 35 Copynumber: 2.2 Consensus size: 34
40628 GTATTTTTAT
*
40638 AAATTT-GAAATTTAATTTTTTATTTTTATTTTCA
1 AAATTTAGAAATTTAA-TTTTTATTTTTAATTTCA
*** *
40672 AGAATTTAGTCTTTTTATTTTTATTTTTAATTTCA
1 A-AATTTAGAAATTTAATTTTTATTTTTAATTTCA
40707 AAATTT
1 AAATTT
40713 TAGATCTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
34 6 0.18
35 23 0.68
36 5 0.15
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (34 bp):
AAATTTAGAAATTTAATTTTTATTTTTAATTTCA
Found at i:40726 original size:36 final size:35
Alignment explanation
Indices: 40654--40726 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
40644 GAAATTTAAT
* **
40654 TTTTTATTTTTATTTTCAAGAATTTAGTCTTTTTA
1 TTTTTATTTTTAATTTCAAGAATTTAGTCTAATTA
40689 TTTTTATTTTTAATTTCAA-AATTTTAGATCTAATTA
1 TTTTTATTTTTAATTTCAAGAA-TTTAG-TCTAATTA
40725 TT
1 TT
40727 AACACTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 2 0.06
35 23 0.70
36 8 0.24
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.63
Consensus pattern (35 bp):
TTTTTATTTTTAATTTCAAGAATTTAGTCTAATTA
Found at i:40906 original size:24 final size:24
Alignment explanation
Indices: 40878--40924 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
40868 AATCTAAATT
40878 TTAAAATTTGAAAAATAAAAAAAA
1 TTAAAATTTGAAAAATAAAAAAAA
*
40902 TTAAAATTTTAAAAATAAAAAAA
1 TTAAAATTTGAAAAATAAAAAAA
40925 TAGAGACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (24 bp):
TTAAAATTTGAAAAATAAAAAAAA
Found at i:48759 original size:34 final size:35
Alignment explanation
Indices: 48721--48789 Score: 113
Period size: 34 Copynumber: 2.0 Consensus size: 35
48711 CCATACTCCC
48721 TTTAAATTTATTTTAAATTAAATTT-GTTTAAAAA
1 TTTAAATTTATTTTAAATTAAATTTAGTTTAAAAA
*
48755 TTTAAATTTATTTTAAATTTAATTTAAGTTTAAAA
1 TTTAAATTTATTTTAAATTAAATTT-AGTTTAAAA
48790 TTATTTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 24 0.75
36 8 0.25
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTAAATTTAGTTTAAAAA
Found at i:48771 original size:11 final size:11
Alignment explanation
Indices: 48753--48787 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
48743 TTTGTTTAAA
48753 AATTTAAATTT
1 AATTTAAATTT
*
48764 ATTTTAAATTT
1 AATTTAAATTT
*
48775 AATTTAAGTTT
1 AATTTAAATTT
48786 AA
1 AA
48788 AATTATTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:48786 original size:17 final size:17
Alignment explanation
Indices: 48721--48788 Score: 61
Period size: 17 Copynumber: 4.0 Consensus size: 17
48711 CCATACTCCC
*
48721 TTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAA
*
48738 -TTAAATTT-GTTTAAAAA
1 TTTAAATTTAATTT--AAA
*
48755 TTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAA
48772 TTT-AATTTAAGTTTAAA
1 TTTAAATTTAA-TTTAAA
48789 ATTATTTTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
15 3 0.07
16 14 0.33
17 15 0.35
18 8 0.19
19 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Found at i:50408 original size:18 final size:19
Alignment explanation
Indices: 50385--50430 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
50375 TATTATCATT
50385 TATAAAATAATTTAA-TTA
1 TATAAAATAATTTAACTTA
50403 TATAAAAT-ATTTAACTTTA
1 TATAAAATAATTTAAC-TTA
*
50422 AATAAAATA
1 TATAAAATA
50431 CTAAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 6 0.25
18 8 0.33
19 10 0.42
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TATAAAATAATTTAACTTA
Found at i:50483 original size:15 final size:15
Alignment explanation
Indices: 50465--50517 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
50455 CAAGAATCAA
50465 TTTTTCAACACTTAT
1 TTTTTCAACACTTAT
* * *
50480 TTTTTCAATATTTTTT
1 TTTTTCAACA-CTTAT
* *
50496 TTTTTAAACACTTAA
1 TTTTTCAACACTTAT
50511 TTTTTCA
1 TTTTTCA
50518 GTCTAAGGAA
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTCAACACTTAT
Found at i:50562 original size:25 final size:25
Alignment explanation
Indices: 50533--50592 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
50523 AGGAACAATT
50533 TTGACATTTTGAAAATGTTATTATG
1 TTGACATTTTGAAAATGTTATTATG
50558 TTGACATTTTGAAAATGTTATTATG
1 TTGACATTTTGAAAATGTTATTATG
*
50583 TTAACATTTT
1 TTGACATTTT
50593 CTTATATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (25 bp):
TTGACATTTTGAAAATGTTATTATG
Found at i:50735 original size:6 final size:6
Alignment explanation
Indices: 50684--50733 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
50674 TTCTGCAACT
* * *
50684 CGACAC CGACAC CGACAC CGACAC CGACAC CGTCAC CGTCAC CGTCAC
1 CGACAC CGACAC CGACAC CGACAC CGACAC CGACAC CGACAC CGACAC
50732 CG
1 CG
50734 TCGCCTCTCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.26, C:0.50, G:0.18, T:0.06
Consensus pattern (6 bp):
CGACAC
Found at i:58820 original size:70 final size:70
Alignment explanation
Indices: 58742--59027 Score: 482
Period size: 70 Copynumber: 4.1 Consensus size: 70
58732 AAAGTCAACC
*
58742 ATACTTTTTTATTTAATTTATTGAATGAAATTTATTAATAACCTTGTTTACCACATGCGGAACCA
1 ATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATAACCTTGTTTACCACATGCGGAACCA
58807 ATCAA
66 ATCAA
* * *
58812 ATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGGAACCT
1 ATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATAACCTTGTTTACCACATGCGGAACCA
58877 ATCAA
66 ATCAA
* *
58882 ATACTTTTTTATTTAATTTATTAAATGAAATTTATTAGTAACCTTGTTTGCCACATGCGGAACCA
1 ATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATAACCTTGTTTACCACATGCGGAACCA
58947 ATCAA
66 ATCAA
* * * *
58952 ATACTTTTTTATTTAATTCATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGGAACCT
1 ATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATAACCTTGTTTACCACATGCGGAACCA
59017 ATCAA
66 ATCAA
59022 ATACTT
1 ATACTT
59028 CATGACGCTG
Statistics
Matches: 201, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 201 1.00
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (70 bp):
ATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATAACCTTGTTTACCACATGCGGAACCA
ATCAA
Found at i:58936 original size:140 final size:140
Alignment explanation
Indices: 58742--59027 Score: 536
Period size: 140 Copynumber: 2.0 Consensus size: 140
58732 AAAGTCAACC
*
58742 ATACTTTTTTATTTAATTTATTGAATGAAATTTATTAATAACCTTGTTTACCACATGCGGAACCA
1 ATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATAACCTTGTTTACCACATGCGGAACCA
*
58807 ATCAAATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGG
66 ATCAAATACTTTTTTATTTAATTCATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGG
58872 AACCTATCAA
131 AACCTATCAA
* *
58882 ATACTTTTTTATTTAATTTATTAAATGAAATTTATTAGTAACCTTGTTTGCCACATGCGGAACCA
1 ATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATAACCTTGTTTACCACATGCGGAACCA
58947 ATCAAATACTTTTTTATTTAATTCATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGG
66 ATCAAATACTTTTTTATTTAATTCATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGG
59012 AACCTATCAA
131 AACCTATCAA
59022 ATACTT
1 ATACTT
59028 CATGACGCTG
Statistics
Matches: 142, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 142 1.00
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (140 bp):
ATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATAACCTTGTTTACCACATGCGGAACCA
ATCAAATACTTTTTTATTTAATTCATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGG
AACCTATCAA
Found at i:59491 original size:29 final size:31
Alignment explanation
Indices: 59440--59498 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
59430 GGCCATTGCT
59440 AAAAAATTTAAATTTATTATTATATTTTTTG
1 AAAAAATTTAAATTTATTATTATATTTTTTG
* * *
59471 AAAATATTTATATTT-TT-TTATTTTTTTT
1 AAAAAATTTAAATTTATTATTATATTTTTT
59499 ATTTTTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.40
30 2 0.08
31 13 0.52
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (31 bp):
AAAAAATTTAAATTTATTATTATATTTTTTG
Found at i:59497 original size:9 final size:9
Alignment explanation
Indices: 59477--59506 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
59467 TTTGAAAATA
59477 TTTATATTTT
1 TTTAT-TTTT
59487 TTTATTTTT
1 TTTATTTTT
59496 TTTATTTTT
1 TTTATTTTT
59505 TT
1 TT
59507 GAATTAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 15 0.75
10 5 0.25
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTATTTTT
Found at i:65963 original size:16 final size:16
Alignment explanation
Indices: 65944--65994 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
65934 AAATAAATAA
*
65944 TTTTTTAAATGTTTAT
1 TTTTTTAAATATTTAT
*
65960 TTTTAT-AATATTTAT
1 TTTTTTAAATATTTAT
* *
65975 TTTTCTTAACTTTTTAT
1 TTTT-TTAAATATTTAT
65992 TTT
1 TTT
65995 AAATTATATC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 12 0.43
16 6 0.21
17 10 0.36
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTTTTAAATATTTAT
Found at i:65964 original size:14 final size:15
Alignment explanation
Indices: 65945--65978 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
65935 AATAAATAAT
*
65945 TTTTTA-AATGTTTA
1 TTTTTATAATATTTA
65959 TTTTTATAATATTTA
1 TTTTTATAATATTTA
65974 TTTTT
1 TTTTT
65979 CTTAACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TTTTTATAATATTTA
Found at i:72281 original size:69 final size:69
Alignment explanation
Indices: 72208--72341 Score: 160
Period size: 69 Copynumber: 1.9 Consensus size: 69
72198 TTTCAAGTCT
* ** ** * *
72208 AAAAAATTCAATAAAATTAGGCATCAATGTTTACAAAAATTATCATTTTAGTTCTAATTCTAAAA
1 AAAAAACTCAATAAAATTAACCATCAACATTTACAAAAATTATCAATTTAATTCTAATTCTAAAA
72273 AAAA
66 AAAA
* * * * *
72277 AAAAAACTCAATAAATTTAACCCTCAACATTTACAAAATTTGTGAATTTAATTCTAATTCTAAAA
1 AAAAAACTCAATAAAATTAACCATCAACATTTACAAAAATTATCAATTTAATTCTAATTCTAAAA
72342 GTTTAAAAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
69 53 1.00
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (69 bp):
AAAAAACTCAATAAAATTAACCATCAACATTTACAAAAATTATCAATTTAATTCTAATTCTAAAA
AAAA
Found at i:77174 original size:16 final size:16
Alignment explanation
Indices: 77153--77190 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
77143 TGAATTACCG
*
77153 ATTACAACTCTATTTC
1 ATTACAAATCTATTTC
*
77169 ATTACAAATTTATTTC
1 ATTACAAATCTATTTC
77185 ATTACA
1 ATTACA
77191 GTCCTATTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTACAAATCTATTTC
Found at i:79424 original size:19 final size:19
Alignment explanation
Indices: 79400--79442 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
79390 ACAAAATAGT
* *
79400 AACAATATAATAATGAAAC
1 AACAATAAAATAATGAAAA
*
79419 AACAATAAAATAGTGAAAA
1 AACAATAAAATAATGAAAA
79438 AACAA
1 AACAA
79443 CAGTAAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.67, C:0.09, G:0.07, T:0.16
Consensus pattern (19 bp):
AACAATAAAATAATGAAAA
Found at i:86506 original size:36 final size:36
Alignment explanation
Indices: 86463--86531 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
86453 TATTGAGGTA
86463 GAGGAGGTCGATGGAAGCA-ATGTTGAGATATTAATG
1 GAGGAGGTCGATGGAAG-AGATGTTGAGATATTAATG
*
86499 GAGGAGGTGGATGGAAGAGATGTTGAGATATTA
1 GAGGAGGTCGATGGAAGAGATGTTGAGATATTA
86532 TAGTTACTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 1 0.03
36 30 0.97
ACGTcount: A:0.33, C:0.03, G:0.39, T:0.25
Consensus pattern (36 bp):
GAGGAGGTCGATGGAAGAGATGTTGAGATATTAATG
Found at i:88467 original size:23 final size:23
Alignment explanation
Indices: 88437--88507 Score: 106
Period size: 23 Copynumber: 3.1 Consensus size: 23
88427 AAATCTGTAG
* * *
88437 GCACACGAGGTGTGAAACAATAA
1 GCACACGAAGTGCGAAACAGTAA
*
88460 GCACACGAAGTGCGAAATAGTAA
1 GCACACGAAGTGCGAAACAGTAA
88483 GCACACGAAGTGCGAAACAGTAA
1 GCACACGAAGTGCGAAACAGTAA
88506 GC
1 GC
88508 GCGCTAGCGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.42, C:0.20, G:0.27, T:0.11
Consensus pattern (23 bp):
GCACACGAAGTGCGAAACAGTAA
Found at i:92179 original size:39 final size:38
Alignment explanation
Indices: 92146--92235 Score: 112
Period size: 38 Copynumber: 2.4 Consensus size: 38
92136 ATATTATGAT
92146 TTTTATT-AATTCATATTTTAATAATAATTATATTAAAAA
1 TTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAAA
* *
92185 TTTTATTAAATTGTATTTAATAATAATTATGTT-AAAA
1 TTTTATTAAATTATATTTAATAATAATTATATTAAAAA
* *
92222 TATAATTAAATTAT
1 TTTTATTAAATTAT
92236 TTATTATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
37 15 0.33
38 17 0.38
39 9 0.20
40 4 0.09
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (38 bp):
TTTTATTAAATTATATTTAATAATAATTATATTAAAAA
Found at i:93349 original size:39 final size:39
Alignment explanation
Indices: 93292--93371 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 39
93282 TCGATTCAAG
* *
93292 TCGTTTTTCAACCGGTTTCATAATCGTCATTAGAAACGT
1 TCGTTTTTCAACCAGTTTCATAATCGCCATTAGAAACGT
* *
93331 TCGTTTTTCAACTAGTTTCATAATTGCCATTAGAAACGT
1 TCGTTTTTCAACCAGTTTCATAATCGCCATTAGAAACGT
93370 TC
1 TC
93372 TTAATCATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (39 bp):
TCGTTTTTCAACCAGTTTCATAATCGCCATTAGAAACGT
Found at i:94361 original size:44 final size:44
Alignment explanation
Indices: 94295--94476 Score: 163
Period size: 46 Copynumber: 4.1 Consensus size: 44
94285 TTGACAGTGT
* * * * * *
94295 ATCTGCA-AAATTTGTTATGTATCCACAGCTAGAGGCAGATTCC
1 ATCTGCAGATATTCGTTGTGTATCCACAGCCAAAGGCAAATTCC
* *
94338 ATCTGC-GAGTATTCGTTGTGTATCCACAACCAAAGGCAGATTCC
1 ATCTGCAGA-TATTCGTTGTGTATCCACAGCCAAAGGCAAATTCC
* * * * *
94382 ATCTGCAGGTTATTTGTTGTGTAATCCATAGTCAAAGGCAAATTTC
1 ATCTGCA-GATATTCGTTGTGT-ATCCACAGCCAAAGGCAAATTCC
* *
94428 ATCTGCAAGATTTTCGTTGTGTACCCACAGCCAGAA-GCAAATTCC
1 ATCTGC-AGATATTCGTTGTGTATCCACAGCCA-AAGGCAAATTCC
94473 ATCT
1 ATCT
94477 ACTGGGATTT
Statistics
Matches: 112, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
43 7 0.06
44 35 0.31
45 31 0.28
46 38 0.34
47 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
ATCTGCAGATATTCGTTGTGTATCCACAGCCAAAGGCAAATTCC
Found at i:96185 original size:19 final size:19
Alignment explanation
Indices: 96163--96234 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 19
96153 ATAAAAAATA
96163 AAAAAATCATTAAAATTAT
1 AAAAAATCATTAAAATTAT
*
96182 -AAAAA--ATTAACATT-T
1 AAAAAATCATTAAAATTAT
* *
96197 AACAAAATTATTAGAAATTAA
1 AA-AAAATCATTA-AAATTAT
96218 ATAAAAATCA-TAAAATT
1 A-AAAAATCATTAAAATT
96235 TCTAATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
15 1 0.02
16 9 0.21
17 4 0.10
18 5 0.12
19 9 0.21
20 6 0.14
21 7 0.17
22 1 0.02
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (19 bp):
AAAAAATCATTAAAATTAT
Found at i:101582 original size:209 final size:205
Alignment explanation
Indices: 101217--102230 Score: 1106
Period size: 207 Copynumber: 5.0 Consensus size: 205
101207 TATAGCTTGC
* * * * * *
101217 GACAATTCTTCAATCATACGCCTTATCTCTGACAATTCTATTTCTTGGATTTGA-TTTTCTT-CT
1 GACAATTCTTCTATCATA-GCCTCATCTCTAACAACTCTATTTGTTGGCTTTGATTTTTCTTCCT
* * * * *
101280 TGACCTCTTATATGT---GAATTCATGGCTTAAAAGTGATTTCTAATATAAGTCTTAGGATCTAA
65 TGACCTCTTGTATGTCCAGCA-T-ATAGCTTAAAAGTGATTTCCAATATAAGTCTTAAGATCTAA
* ** * *
101342 TTA-AGCTTTGATACTAAAACCGATTTGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAG-TT
128 TTAGA-CTTTGATACCAAAAATGATGTGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAGCTA
101405 AAAAAATT-AATGT
192 AAAAAATTAAATGT
* * *
101418 GACAATTCTTCTATCATAGTCTCATCTCTGACAACTCTATTTGTTGGCTTTTATTTTTCTTCCTT
1 GACAATTCTTCTATCATAGCCTCATCTCTAACAACTCTATTTGTTGGCTTTGATTTTTCTTCCTT
**
101483 GACCTCTTGTATGTCCAGTCATGCATCATGCTTTAAAAGTGATTTTTAATATAAGTCTTAAGATC
66 GACCTCTTGTATGTCCAG-CAT--AT-A-GC-TTAAAAGTGATTTCCAATATAAGTCTTAAGATC
*
101548 TAATTAGACTTT-AGTACCAAAATTGATGTGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAG
125 TAATTAGACTTTGA-TACCAAAAATGATGTGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAG
*
101612 CTAAAAAAATTAAAATGC
189 CTAAAAAAATT-AAATGT
* * * * * *
101630 GACAATTCTTCTATCACAAGCCTAATCTCAAACAATTTTATTTGTTGGCTTTGATTTTCTCTTAC
1 GACAATTCTTCTATCA-TAGCCTCATCTCTAACAACTCTATTTGTTGGCTTTGATTTT-TCTTCC
* *
101695 TTGACCTCTTATATGTCCAGC-TAT-GACTTAAAAGTGACTTCCAATATAAGTC-------CT-A
64 TTGACCTCTTGTATGTCCAGCATATAG-CTTAAAAGTGATTTCCAATATAAGTCTTAAGATCTAA
101750 --AGA-----ATACCAAAAATGATGTGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAGCTAA
128 TTAGACTTTGATACCAAAAATGATGTGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAGCTAA
101808 AAAAACTTAAATGT
193 AAAAA-TTAAATGT
* *
101822 GACAATTCTTTTATCATAGTCTCATCTCTAACAACTCTATTTGTTGGCTTTGATTTTCTCTTCCT
1 GACAATTCTTCTATCATAGCCTCATCTCTAACAACTCTATTTGTTGGCTTTGATTTT-TCTTCCT
* * * * *
101887 TGACCTCTTGTATGTCTAG--TCATGGCTTAAAAGCGATTTCCAATATAAATCCTAAGATCTAAT
65 TGACCTCTTGTATGTCCAGCAT-ATAGCTTAAAAGTGATTTCCAATATAAGTCTTAAGATCTAAT
* * *
101950 TA-AGCTTTGATAACAAAATTGATGTGGTAAATTATTAGGTTTGAGTGGAAAATCTAAATAGCTA
129 TAGA-CTTTGATACCAAAAATGATGTGGTAAATTATTAGG-TTGAGTGAAAAATCTAAATAGCT-
*
102014 AAAAAAAATAAAATGT
191 -AAAAAAATTAAATGT
*
102030 GACAATT-TTCTATCATACGCCTCATCTCTAACAACTTTATTTGTTGGCTTTGA-TTTTCTTTCC
1 GACAATTCTTCTATCATA-GCCTCATCTCTAACAACTCTATTTGTTGGCTTTGATTTTTC-TTCC
*
102093 TTGACCTCTTGTATGTCCAG--TCATAGCTTAAAAGTGATTTTCAATATAAGTCCTT-AGATCTA
64 TTGACCTCTTGTATGTCCAGCAT-ATAGCTTAAAAGTGATTTCCAATATAAGT-CTTAAGATCTA
* * * * *
102155 ATTAGACTCTGATACCAAAAATAATGTGATAAATTATTAAGTTGAGTGGAAAATCTAAATAGCTA
127 ATTAGACTTTGATACCAAAAATGATGTGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAGCT-
102220 AAAAAAATTAA
191 AAAAAAATTAA
102231 GAGATACGTT
Statistics
Matches: 703, Mismatches: 66, Indels: 84
0.82 0.08 0.10
Matches are distributed among these distances:
190 1 0.00
191 84 0.12
192 79 0.11
193 3 0.00
197 3 0.00
198 2 0.00
199 2 0.00
200 32 0.05
201 25 0.04
202 16 0.02
205 13 0.02
206 57 0.08
207 147 0.21
208 54 0.08
209 94 0.13
210 12 0.02
212 21 0.03
213 34 0.05
214 24 0.03
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (205 bp):
GACAATTCTTCTATCATAGCCTCATCTCTAACAACTCTATTTGTTGGCTTTGATTTTTCTTCCTT
GACCTCTTGTATGTCCAGCATATAGCTTAAAAGTGATTTCCAATATAAGTCTTAAGATCTAATTA
GACTTTGATACCAAAAATGATGTGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAGCTAAAAA
AATTAAATGT
Found at i:102110 original size:398 final size:396
Alignment explanation
Indices: 101367--102146 Score: 1162
Period size: 398 Copynumber: 2.0 Consensus size: 396
101357 AAAACCGATT
*
101367 TGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAGTTAAAAAATTAATGTGACAATTCTTCTAT
1 TGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAGTAAAAAAATTAATGTGACAATTCTTCTAT
* *
101432 CATAGTCTCATCTCTGACAACTCTATTTGTTGGCTTTTATTTTTCTTCCTTGACCTCTTGTATGT
66 CATAGTCTCATCTCTAACAACTCTATTTGTTGGCTTTGATTTTTCTTCCTTGACCTCTTGTATGT
* ** * *
101497 CCAGTCATGCATCATGCTTTAAAAGTGATTTTTAATATAAGTCTTAAGATCTAATTAGACTTTAG
131 CCAGTCATG----A-GCTTTAAAAGCGATTTCCAATATAAATCCTAAGATCTAATTAGACTTTAG
* *
101562 TACCAAAATTGATGTGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAGCTAAAAAAATTAAAA
191 TAACAAAATTGATGTGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAGCTAAAAAAAATAAAA
*
101627 TGCGACAATTCTTCTATCACAAGCCTAATCTCAAACAATTTTATTTGTTGGCTTTGATTTTCTCT
256 TGCGACAATTCTTCTATCACAAGCCTAATCTCAAACAACTTTATTTGTTGGCTTTGATTTTCTCT
101692 TACTTGACCTCTTATATGTCCAG-C-TATGACTTAAAAGTGACTTCCAATATAAGTCCTAAGAAT
321 TACTTGACCTCTTATATGTCCAGTCATA-G-CTTAAAAGTGACTTCCAATATAAGTCCTAAGAAT
101755 ACCAAAAATGATG
384 ACCAAAAATGATG
*
101768 TGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAGCTAAAAAAACTTAAATGTGACAATTCTTT
1 TGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAG-TAAAAAAA-TT-AATGTGACAATTCTTC
101833 TATCATAGTCTCATCTCTAACAACTCTATTTGTTGGCTTTGATTTTCTCTTCCTTGACCTCTTGT
63 TATCATAGTCTCATCTCTAACAACTCTATTTGTTGGCTTTGATTTT-TCTTCCTTGACCTCTTGT
*
101898 ATGTCTAGTCATG-GC-TTAAAAGCGATTTCCAATATAAATCCTAAGATCTAATTA-AGCTTT-G
127 ATGTCCAGTCATGAGCTTTAAAAGCGATTTCCAATATAAATCCTAAGATCTAATTAGA-CTTTAG
*
101959 ATAACAAAATTGATGTGGTAAATTATTAGGTTTGAGTGGAAAATCTAAATAGCTAAAAAAAAATA
191 -TAACAAAATTGATGTGGTAAATTATTAGG-TTGAGTGAAAAATCTAAATAGCT-AAAAAAAATA
* * * * *
102024 AAATGTGACAATT-TTCTATCATACGCCTCATCTCTAACAACTTTATTTGTTGGCTTTGATTTTC
253 AAATGCGACAATTCTTCTATCACAAGCCTAATCTCAAACAACTTTATTTGTTGGCTTTGATTTTC
* * * *
102088 T-TTCCTTGACCTCTTGTATGTCCAGTCATAGCTTAAAAGTGATTTTCAATATAAGTCCT
318 TCTTACTTGACCTCTTATATGTCCAGTCATAGCTTAAAAGTGACTTCCAATATAAGTCCT
102147 TAGATCTAAT
Statistics
Matches: 346, Mismatches: 23, Indels: 23
0.88 0.06 0.06
Matches are distributed among these distances:
397 2 0.01
398 114 0.33
399 73 0.21
400 23 0.07
401 36 0.10
402 7 0.02
403 2 0.01
404 59 0.17
405 30 0.09
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (396 bp):
TGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAGTAAAAAAATTAATGTGACAATTCTTCTAT
CATAGTCTCATCTCTAACAACTCTATTTGTTGGCTTTGATTTTTCTTCCTTGACCTCTTGTATGT
CCAGTCATGAGCTTTAAAAGCGATTTCCAATATAAATCCTAAGATCTAATTAGACTTTAGTAACA
AAATTGATGTGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAGCTAAAAAAAATAAAATGCGA
CAATTCTTCTATCACAAGCCTAATCTCAAACAACTTTATTTGTTGGCTTTGATTTTCTCTTACTT
GACCTCTTATATGTCCAGTCATAGCTTAAAAGTGACTTCCAATATAAGTCCTAAGAATACCAAAA
ATGATG
Found at i:102601 original size:68 final size:68
Alignment explanation
Indices: 102492--102629 Score: 267
Period size: 68 Copynumber: 2.0 Consensus size: 68
102482 AGTTCTAAAA
102492 ATATTGTCTCCTCCGATCTTCATTCTCTCTTTTGTGGGATGTTGTCATTAACCTTCCAACCATCA
1 ATATTGTCTCCTCCGATCTTCATTCTCTCTTTTGTGGGATGTTGTCATTAACCTTCCAACCATCA
102557 ATG
66 ATG
*
102560 ATATTGTCTCTTCCGATCTTCATTCTCTCTTTTGTGGGATGTTGTCATTAACCTTCCAACCATCA
1 ATATTGTCTCCTCCGATCTTCATTCTCTCTTTTGTGGGATGTTGTCATTAACCTTCCAACCATCA
102625 ATG
66 ATG
102628 AT
1 AT
102630 TCCCCTTTAG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.42
Consensus pattern (68 bp):
ATATTGTCTCCTCCGATCTTCATTCTCTCTTTTGTGGGATGTTGTCATTAACCTTCCAACCATCA
ATG
Found at i:108167 original size:20 final size:21
Alignment explanation
Indices: 108133--108181 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
108123 ATAAATATTA
*
108133 AATTAAATTTGATATTAAAAT
1 AATTAAATTTAATATTAAAAT
*
108154 AATT-AATTTAATATTAAATT
1 AATTAAATTTAATATTAAAAT
*
108174 AATAAAAT
1 AATTAAAT
108182 ATTATCAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
AATTAAATTTAATATTAAAAT
Found at i:113722 original size:3 final size:3
Alignment explanation
Indices: 113714--113750 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
113704 AATCTTTCAG
113714 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
113751 ACTCTTGTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:114906 original size:22 final size:24
Alignment explanation
Indices: 114880--114924 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
114870 ACATAAAACA
*
114880 TGAAATCCAACAA-AAAT-ATTAT
1 TGAAAACCAACAATAAATGATTAT
*
114902 TGAAAACTAACAATAAATGATTA
1 TGAAAACCAACAATAAATGATTA
114925 AATGAATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 4 0.21
24 4 0.21
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.27
Consensus pattern (24 bp):
TGAAAACCAACAATAAATGATTAT
Found at i:118891 original size:53 final size:53
Alignment explanation
Indices: 118811--118928 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
118801 AATCTCTTCC
*
118811 ATTTTGGTTTCATACTGCTTTATCTTATACATAAGCATTTTCATATGGACAAA
1 ATTTTGATTTCATACTGCTTTATCTTATACATAAGCATTTTCATATGGACAAA
*
118864 ATTTTGATTTCATACTGCTTTATCTTATACATGAGCATTTTCATATGGACAAA
1 ATTTTGATTTCATACTGCTTTATCTTATACATAAGCATTTTCATATGGACAAA
*
118917 ATTTTGAGTTCA
1 ATTTTGATTTCA
118929 ACGATGCATA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 62 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (53 bp):
ATTTTGATTTCATACTGCTTTATCTTATACATAAGCATTTTCATATGGACAAA
Found at i:123671 original size:39 final size:40
Alignment explanation
Indices: 123617--123693 Score: 129
Period size: 39 Copynumber: 1.9 Consensus size: 40
123607 TTAATAGGGG
*
123617 TATTTTAAGAGTATAAAAAAA-TAATAGGATTATTTTAAA
1 TATTTTAAGAGTATAAAAAAATTAATAGGAGTATTTTAAA
*
123656 TATTTTAGGAGTATAAAAAAATTAATAGGAGTATTTTA
1 TATTTTAAGAGTATAAAAAAATTAATAGGAGTATTTTA
123694 GGTAGAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 20 0.57
40 15 0.43
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (40 bp):
TATTTTAAGAGTATAAAAAAATTAATAGGAGTATTTTAAA
Found at i:123684 original size:20 final size:20
Alignment explanation
Indices: 123625--123689 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
123615 GGTATTTTAA
123625 GAGTATAAAAAAA-TAATAG
1 GAGTATAAAAAAATTAATAG
* ** * *
123644 GATTATTTTAAATATT-TTAG
1 GAGTA-TAAAAAAATTAATAG
123664 GAGTATAAAAAAATTAATAG
1 GAGTATAAAAAAATTAATAG
123684 GAGTAT
1 GAGTAT
123690 TTTAGGTAGA
Statistics
Matches: 33, Mismatches: 10, Indels: 5
0.69 0.21 0.10
Matches are distributed among these distances:
19 11 0.33
20 21 0.64
21 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (20 bp):
GAGTATAAAAAAATTAATAG
Found at i:123708 original size:31 final size:31
Alignment explanation
Indices: 123656--123714 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
123646 TTATTTTAAA
* *
123656 TATTTTAGGAGTATAAAAAAATTAATAGGAG
1 TATTTTAGGAGAATAAAAAAATCAATAGGAG
123687 TATTTTAGGTAGAAT-AAAAAATCAATAG
1 TATTTTAGG-AGAATAAAAAAATCAATAG
123715 ATAATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.49, C:0.02, G:0.17, T:0.32
Consensus pattern (31 bp):
TATTTTAGGAGAATAAAAAAATCAATAGGAG
Found at i:123849 original size:156 final size:169
Alignment explanation
Indices: 123671--124043 Score: 414
Period size: 179 Copynumber: 2.2 Consensus size: 169
123661 TAGGAGTATA
* *
123671 AAAAAATTAATA-GGAGTATTTTAGGTAGAATAAAAAAT-CAA-T-AG-A-T-AA-TAATAAGGA
1 AAAAAATTAATAGGGA-TATTTTAGGTAGAATAAAAAATAAAATTAAGCATTAAATTAATAAGAA
* *
123728 TAATTTAGGGA-TTTGCAAACAAAGTTAATTTATTTATTTATGAACTTT-AATTCTTATTATT-A
65 AAATTTAGGGATTTTGCAAACAAAGTTAATTTATTTATTTATAAACTTTAAATTCTTATTATTAA
** *
123790 -ATTTTTTATTTAATATAAATAAAGGTGGTTTAA-GA-GT
130 TATTTTTTATTTAATATAAATAAAGGTACTTTAACAATGT
*
123827 AAAAAATTAATAGGGATATTTTAGGTAGAAGAGAAAATCAATAGAGAAAATTTAAGCATTACAAA
1 AAAAAATTAATAGGGATATTTTAGGTAG-A-ATAAAA--AAT----AAAA-TTAAGCATT--AAA
* * *
123892 TTAATAAGAAAAATTTAGGTATTTTGTAAACAAAGTTAATTTATTTATTTATAAATTTTAAATTC
55 TTAATAAGAAAAATTTAGGGATTTTGCAAACAAAGTTAATTTATTTATTTATAAACTTTAAATTC
*
123957 TTATTATTAATTATTTTTTATTTAATATAAATAAGGGTACTTTAACAATGT
120 TTATTATTAA-TATTTTTTATTTAATATAAATAAAGGTACTTTAACAATGT
*
124008 AAAAAATTAATAGGGGTATTTTAGGTAGAATAAAAA
1 AAAAAATTAATAGGGATATTTTAGGTAGAATAAAAA
124044 GGCAATAGGA
Statistics
Matches: 177, Mismatches: 14, Indels: 31
0.80 0.06 0.14
Matches are distributed among these distances:
156 24 0.14
157 4 0.02
158 5 0.03
160 3 0.02
165 2 0.01
167 1 0.01
168 2 0.01
169 1 0.01
170 1 0.01
173 2 0.01
174 17 0.10
175 34 0.19
176 13 0.07
177 2 0.01
179 35 0.20
180 2 0.01
181 29 0.16
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (169 bp):
AAAAAATTAATAGGGATATTTTAGGTAGAATAAAAAATAAAATTAAGCATTAAATTAATAAGAAA
AATTTAGGGATTTTGCAAACAAAGTTAATTTATTTATTTATAAACTTTAAATTCTTATTATTAAT
ATTTTTTATTTAATATAAATAAAGGTACTTTAACAATGT
Found at i:124124 original size:176 final size:176
Alignment explanation
Indices: 123739--124159 Score: 479
Period size: 181 Copynumber: 2.4 Consensus size: 176
123729 AATTTAGGGA
* * *
123739 TTTGCAAACAAAGTTAATTTATTTATTTATGAACTTT-AATTCTTATTATT-A--ATTTTTTATT
1 TTTGTAAACAAAGTTAATTTATTTATTTATAAATTTTAAATTCTTATTATTAATTATTTTTTATT
** * *
123800 TAATATAAATAAAGGTGGTTTAAGAGTAAAAAATTAATAGGGATATTTTAGGTAGAAGAGAAAAT
66 TAATATAAATAAAGGTACTTTAAAAGTAAAAAATTAATAGGGATATTTTAGGTAGAAGAGAAAAG
123865 CAATAGAGAAAATTTAAGCATTACAAATTAATAAGAAAAATTTAGGTAT
131 CAATAGAGAAAATTTAAGCATTACAAATT-ATAAGAAAAATTT--GTAT
123914 TTTGTAAACAAAGTTAATTTATTTATTTATAAATTTTAAATTCTTATTATTAATTATTTTTTATT
1 TTTGTAAACAAAGTTAATTTATTTATTTATAAATTTTAAATTCTTATTATTAATTATTTTTTATT
* * *
123979 TAATATAAATAAGGGTACTTTAACAATGTAAAAAATTAATAGGGGTATTTTAGGTAGAATA-AAA
66 TAATATAAATAAAGGTACTTTAA-AA-GTAAAAAATTAATAGGGATATTTTAGGTAGAAGAGAAA
* * * **
124043 AGGCAATAG-GAATAATTTAGGCATTAGAAGGCATT-TTAG-TTAA-TT-TAT
129 A-GCAATAGAGAA-AATTTAAGCATTACAA---ATTATAAGAAAAATTTGTAT
* * * *
124091 TTTGTAAACAAACTTAATTT-TTTATTTATAAATTTTAAACTTTATTATGATTAGTTA-TTTTTA
1 TTTGTAAACAAAGTTAATTTATTTATTTATAAATTTTAAA--TTCTTATTATTAATTATTTTTTA
124154 TTTAAT
64 TTTAAT
124160 CTATATCTAT
Statistics
Matches: 214, Mismatches: 19, Indels: 24
0.83 0.07 0.09
Matches are distributed among these distances:
175 34 0.16
176 32 0.15
177 35 0.16
178 13 0.06
179 30 0.14
180 10 0.05
181 54 0.25
182 3 0.01
184 3 0.01
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (176 bp):
TTTGTAAACAAAGTTAATTTATTTATTTATAAATTTTAAATTCTTATTATTAATTATTTTTTATT
TAATATAAATAAAGGTACTTTAAAAGTAAAAAATTAATAGGGATATTTTAGGTAGAAGAGAAAAG
CAATAGAGAAAATTTAAGCATTACAAATTATAAGAAAAATTTGTAT
Found at i:128406 original size:26 final size:26
Alignment explanation
Indices: 128344--128413 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
128334 TCTAATTTCC
*
128344 ATTTAATATTTTATA--TAATTATAA
1 ATTTAAAATTTTATATTTAATTATAA
*
128368 ATATAAAGTATTTTATATTGTAATTA-AA
1 ATTTAAA--ATTTTATATT-TAATTATAA
128396 ATTTAAAATTTTATATTT
1 ATTTAAAATTTTATATTT
128414 CATAAGAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
24 5 0.13
25 1 0.03
26 18 0.47
28 8 0.21
29 6 0.16
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (26 bp):
ATTTAAAATTTTATATTTAATTATAA
Found at i:128699 original size:6 final size:6
Alignment explanation
Indices: 128666--128698 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
128656 TAAAGCAACC
128666 TTTTCT TTTTCT TTTTCT TTTTCT TTTT-T TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
128699 TACGATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTCT
Found at i:135178 original size:6 final size:6
Alignment explanation
Indices: 135146--135177 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
135136 AAAAGAAAAA
*
135146 AACAAT AACAAT AACAAT AACAAT AATAAT AA
1 AACAAT AACAAT AACAAT AACAAT AACAAT AA
135178 TGAGCTGTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (6 bp):
AACAAT
Found at i:158882 original size:203 final size:203
Alignment explanation
Indices: 158522--159005 Score: 636
Period size: 203 Copynumber: 2.4 Consensus size: 203
158512 GGCACCGCCA
*
158522 GGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGTC
1 GGATCCGTGGCGCAAGGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGTC
* * *
158587 GGGTTCAAAACCCCGAATCCTTTCGGATCAATTTTTTCTTTCTTTGCCTCTTCGGATATGGGCCC
66 GGGTTCAAAACCCCGAAACATTTCGGATCAATTTTTTCTTTCTCTGCCTCTTCGGATATGGGCCC
* * ** * * ** * *
158652 ATCTGGGCTAAGCCCGGTCTAAGTTGTTCCTGTA-AGGTCAAAGC-AAAATAGGTGATGTAATAG
131 ATCTCGGCAAAGCCCAATCTAAGTTGTTCCTGTATAGGTAAAAACTAAAATA--CAATGGAA-AC
*
158715 AAAGC-CTCCT
193 AAAGCACACCT
*
158725 GGATCCGTGGTGCAAGGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGTC
1 GGATCCGTGGCGCAAGGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGTC
* * * *
158790 GGGTTCAAAATCCGGAAAGATTTCGGAT-ATTTTCTTTCCTTT-TCTGCCTCTTCGGATATGGGC
66 GGGTTCAAAACCCCGAAACATTTCGGATCAATTT-TTT-CTTTCTCTGCCTCTTCGGATATGGGC
*
158853 CCATCTCGGCAAAGCCCAATCTGAGTTGTTCCTGTATAGGTAAAAACTTTAAAAATACAATGGAA
129 CCATCTCGGCAAAGCCCAATCTAAGTTGTTCCTGTATAGGTAAAAAC--T-AAAATACAATGGAA
***
158918 ACCTTGCATCACCT
191 ACAAAGCA-CACCT
158932 GGATCCGTGGCGCAAGGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGTC
1 GGATCCGTGGCGCAAGGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGTC
158997 GGGTTCAAA
66 GGGTTCAAA
159006 TCCCTTATAT
Statistics
Matches: 247, Mismatches: 25, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
202 4 0.02
203 140 0.57
204 12 0.05
205 3 0.01
206 5 0.02
207 77 0.31
208 6 0.02
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (203 bp):
GGATCCGTGGCGCAAGGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGTC
GGGTTCAAAACCCCGAAACATTTCGGATCAATTTTTTCTTTCTCTGCCTCTTCGGATATGGGCCC
ATCTCGGCAAAGCCCAATCTAAGTTGTTCCTGTATAGGTAAAAACTAAAATACAATGGAAACAAA
GCACACCT
Found at i:162112 original size:31 final size:31
Alignment explanation
Indices: 162074--162142 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
162064 ACTCATTTAT
* *
162074 ATTACTTATTTACTACTACTAA-AAAATTAAA
1 ATTACTTACTAACTACTACTAACAAAA-TAAA
*
162105 CTTACTTACTAACTACTACTAACAAAATAAA
1 ATTACTTACTAACTACTACTAACAAAATAAA
162136 ATTACTT
1 ATTACTT
162143 TAATAACCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.36
Consensus pattern (31 bp):
ATTACTTACTAACTACTACTAACAAAATAAA
Found at i:164202 original size:20 final size:23
Alignment explanation
Indices: 164159--164202 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
164149 AATAGTTTCT
164159 TACTCAAGCATCTAAAATCATAA
1 TACTCAAGCATCTAAAATCATAA
164182 TACTCAAGC-TC-AAAA-CATAA
1 TACTCAAGCATCTAAAATCATAA
164202 T
1 T
164203 CATGAATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 4 0.19
22 2 0.10
23 9 0.43
ACGTcount: A:0.48, C:0.23, G:0.05, T:0.25
Consensus pattern (23 bp):
TACTCAAGCATCTAAAATCATAA
Found at i:165165 original size:18 final size:18
Alignment explanation
Indices: 165125--165159 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
165115 TAAATAATAA
* *
165125 AATATTTTTATTTATTAT
1 AATATTATTATTAATTAT
165143 AATATTATTATTAATTA
1 AATATTATTATTAATTA
165160 ATATATCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AATATTATTATTAATTAT
Found at i:169660 original size:18 final size:18
Alignment explanation
Indices: 169637--169673 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
169627 ACAATTCATA
169637 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
*
169655 TCACTTTCACTTCCAATT
1 TCACTTTCAATTCCAATT
169673 T
1 T
169674 TGATCACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.30, G:0.00, T:0.46
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:182575 original size:23 final size:24
Alignment explanation
Indices: 182534--182588 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
182524 TTAACTAACT
*
182534 TATTTAAAATATTATAAAAT-ATA
1 TATTTAAAATATGATAAAATAATA
182557 TATTTAAAATAATGA-AAAATAAATA
1 TATTTAAAAT-ATGATAAAAT-AATA
182582 TATTTAA
1 TATTTAA
182589 GTGACTTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 15 0.54
24 3 0.11
25 10 0.36
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
TATTTAAAATATGATAAAATAATA
Found at i:196316 original size:42 final size:41
Alignment explanation
Indices: 196250--196355 Score: 149
Period size: 42 Copynumber: 2.5 Consensus size: 41
196240 ATAAAGAAAG
*
196250 TTAAAAATCAAAATACAATACTAATTTCACTATTATTTCAA
1 TTAAAAATCAAAATACAATACTAATTTAACTATTATTTCAA
* *
196291 TTAAAGAATCAAAATATAATTCTAATTTAACTATTATTTCAAA
1 TTAAA-AATCAAAATACAATACTAATTTAACTATTATTTC-AA
**
196334 AAAAAAATCAAAATACAATACT
1 TTAAAAATCAAAATACAATACT
196356 TTTTTGATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
41 5 0.09
42 46 0.82
43 5 0.09
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (41 bp):
TTAAAAATCAAAATACAATACTAATTTAACTATTATTTCAA
Found at i:197118 original size:25 final size:25
Alignment explanation
Indices: 197090--197139 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
197080 GAGATAACGA
*
197090 AAATCTTCATCATAAAACAATGCAT
1 AAATCTTCATCACAAAACAATGCAT
197115 AAATCTTCATCACAAAACAATGCAT
1 AAATCTTCATCACAAAACAATGCAT
197140 TGTAACATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.48, C:0.22, G:0.04, T:0.26
Consensus pattern (25 bp):
AAATCTTCATCACAAAACAATGCAT
Found at i:199965 original size:243 final size:245
Alignment explanation
Indices: 199519--200007 Score: 865
Period size: 243 Copynumber: 2.0 Consensus size: 245
199509 CCCAAATCAG
*
199519 TCCTGCACCCAAAGAATAAACAAGTGAAGCAGTGAGTCTATAAATCCATGATATATAACCTGAGT
1 TCCTACACCCAAAGAATAAACAAGTGAAGCAGTGAGTCTATAAATCCATGATATATAACCTGAGT
*
199584 TCCAAAACATTAACCCTCAAGAGTAATTGATAAGCATAGCTCCAGAATAAAGAAAACCCTAACGA
66 TCCAAAACATTAACCCTCAAGAGTAATTGATAAGCATAGCACCAGAATAAAGAAAACCCTAACGA
* *
199649 CTATAGTTTACATGACAATTCTAAGAGAAAGTTGGTTTGAATATTAATAAAAAAGTAACTGCTTT
131 CTATAGTTTACATGACAATTCTAACAGAAAGTTGGCTTGAATATTAATAAAAAAGTAACTGCTTT
* * *
199714 CTATTTATTTTCTAAGTAGTCACAATTAGAA-GGAAAAAACCCTAAACCC
196 CCATTTATTTTCTAAGTAGTCACAATTAGAATGAAAAAAACCCCAAACCC
199763 TCCTACACCCAAAGAA-AAACAAGTGAAGCAGTGAGTCTATAAATCCATGATATATAACCTGAGT
1 TCCTACACCCAAAGAATAAACAAGTGAAGCAGTGAGTCTATAAATCCATGATATATAACCTGAGT
* *
199827 TCCTAAACATTAACCCTCAAGAGTAATTGATAAGCATAGCACTAGAATAAAGAAAACCCTAACGA
66 TCCAAAACATTAACCCTCAAGAGTAATTGATAAGCATAGCACCAGAATAAAGAAAACCCTAACGA
* *
199892 CTATCGTTTATATGACAATTCTAACAGAAAGTTGGCTTGAATATTAATAAAAAAGTAACTGCTTT
131 CTATAGTTTACATGACAATTCTAACAGAAAGTTGGCTTGAATATTAATAAAAAAGTAACTGCTTT
199957 CCATTTATTTTCTAAGTAGTCACAATTAGAATGAAAAAAACCCCAAACCC
196 CCATTTATTTTCTAAGTAGTCACAATTAGAATGAAAAAAACCCCAAACCC
200007 T
1 T
200008 GAACCCTGAA
Statistics
Matches: 233, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
243 201 0.86
244 32 0.14
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (245 bp):
TCCTACACCCAAAGAATAAACAAGTGAAGCAGTGAGTCTATAAATCCATGATATATAACCTGAGT
TCCAAAACATTAACCCTCAAGAGTAATTGATAAGCATAGCACCAGAATAAAGAAAACCCTAACGA
CTATAGTTTACATGACAATTCTAACAGAAAGTTGGCTTGAATATTAATAAAAAAGTAACTGCTTT
CCATTTATTTTCTAAGTAGTCACAATTAGAATGAAAAAAACCCCAAACCC
Found at i:202719 original size:20 final size:20
Alignment explanation
Indices: 202679--202719 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
202669 TTATGTAATT
*
202679 AATTTTATTACTAAATTTTA
1 AATTTTATTACTAAATATTA
* *
202699 AATTTTATTAGTCAATATTA
1 AATTTTATTACTAAATATTA
202719 A
1 A
202720 TGTGTTTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (20 bp):
AATTTTATTACTAAATATTA
Found at i:202973 original size:27 final size:26
Alignment explanation
Indices: 202926--202988 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 26
202916 AAAATATTCA
*
202926 TTTATATTATTTTTTAATATTTAATATT
1 TTTATA-TATTTTTTAATA-TTAAAATT
*
202954 TTTATATA-TTTTTATTTATTAAAATT
1 TTTATATATTTTTTA-ATATTAAAATT
202980 TTATATATA
1 TT-TATATA
202989 GTCCCCTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 15 0.48
27 10 0.32
28 6 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTATATATTTTTTAATATTAAAATT
Found at i:205775 original size:19 final size:18
Alignment explanation
Indices: 205751--205802 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
205741 TTTTTTAGAT
205751 AATTAAGTTTATTTCTTTA
1 AATTAAGTTTATTT-TTTA
*
205770 AATTAAGAGTTATTTTTTA
1 AATTAAG-TTTATTTTTTA
205789 AATTTAA-TTTATTT
1 AA-TTAAGTTTATTT
205803 ATTTTTTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 6 0.21
19 13 0.45
20 10 0.34
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (18 bp):
AATTAAGTTTATTTTTTA
Found at i:207677 original size:24 final size:23
Alignment explanation
Indices: 207648--207713 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
207638 ATGTTTCATG
* *
207648 TGACGGCAAATAAGAGAATGAGGT
1 TGACGGCAAATAAGAGAATCA-AT
*
207672 TGACGG-AAAAAAG-GAACTCAAT
1 TGACGGCAAATAAGAGAA-TCAAT
*
207694 TGACGCCAAATAAGAGAATC
1 TGACGGCAAATAAGAGAATC
207714 CTCCAAAGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
22 9 0.26
23 16 0.47
24 9 0.26
ACGTcount: A:0.45, C:0.14, G:0.26, T:0.15
Consensus pattern (23 bp):
TGACGGCAAATAAGAGAATCAAT
Found at i:216856 original size:40 final size:40
Alignment explanation
Indices: 216780--216876 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
216770 GCGTTTGGAA
* ** *
216780 AGAAAACGCCGCAAAAGGTAAAGTACTAGCGACGCTTATG
1 AGAAAGCGCCGCAAAAGGTAAAACACTAACGACGCTTATG
* * *
216820 GGAAAGCGCCGCAAAAGGTAAAACATTAACGGCGCTTATG
1 AGAAAGCGCCGCAAAAGGTAAAACACTAACGACGCTTATG
* *
216860 AGAAAGCGTCGCTAAAG
1 AGAAAGCGCCGCAAAAG
216877 ATCGGAACAT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (40 bp):
AGAAAGCGCCGCAAAAGGTAAAACACTAACGACGCTTATG
Found at i:216917 original size:41 final size:41
Alignment explanation
Indices: 216841--216930 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 41
216831 CAAAAGGTAA
* *
216841 AACATTAACGGCGCTTATGAGAAAGCGTCGCTAAAGATCGG
1 AACATTAACGGCGCTTATGAGAAAACGCCGCTAAAGATCGG
* * * *
216882 AACATTAGCTGCGCTTATG-GAAAAACGCCGTTAAAGGTCGG
1 AACATTAACGGCGCTTATGAG-AAAACGCCGCTAAAGATCGG
*
216923 AGCATTAA
1 AACATTAA
216931 GCATTAGCGA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
40 1 0.03
41 39 0.98
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (41 bp):
AACATTAACGGCGCTTATGAGAAAACGCCGCTAAAGATCGG
Done.