Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001075.1 Kokia drynarioides strain JFW-HI SEQ_112331, 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: 45330
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:3270 original size:29 final size:30
Alignment explanation
Indices: 3238--3294 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
3228 TTCCTTTTTC
* *
3238 AAAAATTTATACCTAAAAG-TTTTGAAGTA
1 AAAAACTTACACCTAAAAGTTTTTGAAGTA
*
3267 AAAAACTTACACCTAAAGGTTTTTGAAG
1 AAAAACTTACACCTAAAAGTTTTTGAAG
3295 GGAAAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.32
Consensus pattern (30 bp):
AAAAACTTACACCTAAAAGTTTTTGAAGTA
Found at i:6168 original size:44 final size:43
Alignment explanation
Indices: 6118--6206 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 43
6108 ATTAAAAAAA
* * * *
6118 AATAAAATTTGTGATAATTATATATTTAAAAATAATTATAATTT
1 AATAAAAATTGTGATAACTACATATTT-AAAATAATTACAATTT
6162 AATAAAAATTGTGATAACTACATATTTAAAATAATTACAATTT
1 AATAAAAATTGTGATAACTACATATTTAAAATAATTACAATTT
6205 AA
1 AA
6207 ATTATAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 17 0.41
44 24 0.59
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.40
Consensus pattern (43 bp):
AATAAAAATTGTGATAACTACATATTTAAAATAATTACAATTT
Found at i:6206 original size:16 final size:17
Alignment explanation
Indices: 6175--6207 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6165 AAAAATTGTG
6175 ATAACTACATATTTAAA
1 ATAACTACATATTTAAA
*
6192 ATAATTACA-ATTTAAA
1 ATAACTACATATTTAAA
6208 TTATAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAACTACATATTTAAA
Found at i:8719 original size:17 final size:14
Alignment explanation
Indices: 8689--8748 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 14
8679 AATTTTTTTT
*
8689 AAAAAGAGAAAAAA
1 AAAAAGAAAAAAAA
*
8703 TAAAAGAATGAAAAAA
1 AAAAAGAA--AAAAAA
8719 AAAAGAGAAAAAAAA
1 AAAA-AGAAAAAAAA
8734 ACAAAAGAAAAAAAA
1 A-AAAAGAAAAAAAA
8749 TTTGTTGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 6 0.15
15 17 0.44
16 12 0.31
17 4 0.10
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.03
Consensus pattern (14 bp):
AAAAAGAAAAAAAA
Found at i:8728 original size:29 final size:28
Alignment explanation
Indices: 8689--8748 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
8679 AATTTTTTTT
*
8689 AAAAAGAGAAAAAATAAA-AGAATGAAAAA
1 AAAAAGAGAAAAAA-AAACA-AAAGAAAAA
8718 AAAAAGAGAAAAAAAAACAAAAGAAAAA
1 AAAAAGAGAAAAAAAAACAAAAGAAAAA
8746 AAA
1 AAA
8749 TTTGTTGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.03
Consensus pattern (28 bp):
AAAAAGAGAAAAAAAAACAAAAGAAAAA
Found at i:9483 original size:17 final size:17
Alignment explanation
Indices: 9461--9539 Score: 88
Period size: 17 Copynumber: 4.7 Consensus size: 17
9451 TGCCCAACAG
9461 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
9478 AATTTAAGTTTATATTA
1 AATTTAAATTTATTTTA
* **
9495 AGTTTAAA-TTATTTGG
1 AATTTAAATTTATTTTA
*
9511 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
*
9528 AATTTAAGTTTA
1 AATTTAAATTTA
9540 AATTTATTTA
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
16 12 0.24
17 37 0.76
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:9519 original size:50 final size:49
Alignment explanation
Indices: 9460--9554 Score: 154
Period size: 50 Copynumber: 1.9 Consensus size: 49
9450 GTGCCCAACA
* *
9460 GAATTTAAATTTATTTTAAATTTAAGTTTATATTAAGTTTAAATTATTTG
1 GAATTTAAATTTATTATAAATTTAAGTTTAAATTAA-TTTAAATTATTTG
*
9510 GAATTTAAATTTATTATAAATTTAAGTTTAAATTTATTTAAATTA
1 GAATTTAAATTTATTATAAATTTAAGTTTAAATTAATTTAAATTA
9555 ATAATGTCCA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
49 9 0.21
50 33 0.79
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (49 bp):
GAATTTAAATTTATTATAAATTTAAGTTTAAATTAATTTAAATTATTTG
Found at i:11386 original size:30 final size:30
Alignment explanation
Indices: 11352--11481 Score: 115
Period size: 30 Copynumber: 4.4 Consensus size: 30
11342 AAAAATTACA
11352 TTTTTGACCCCGAACTTTCCAAAAATAATG
1 TTTTTGACCCCGAACTTTCCAAAAATAATG
* *
11382 TTTTTG-CCCTTGAACTTTCCAAAAATGATG
1 TTTTTGACCC-CGAACTTTCCAAAAATAATG
* **
11412 TTTTT-TCCCCTGAAC-TTCCAAAAATAACC
1 TTTTTGACCCC-GAACTTTCCAAAAATAATG
* * * *
11441 ATTTT-ACCCCCAAACTTTCCAAAAATCATA
1 TTTTTGA-CCCCGAACTTTCCAAAAATAATG
*
11471 TTTTTGCCCCC
1 TTTTTGACCCC
11482 AAGTGTTCAA
Statistics
Matches: 80, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
29 21 0.26
30 59 0.74
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (30 bp):
TTTTTGACCCCGAACTTTCCAAAAATAATG
Found at i:11457 original size:59 final size:59
Alignment explanation
Indices: 11394--11522 Score: 163
Period size: 59 Copynumber: 2.2 Consensus size: 59
11384 TTTGCCCTTG
* * * *
11394 AACTTTCCAAAAATGATGTTTTTTCCCCTGAACT-TCCAAAAATAACCATTTTACCCCCA
1 AACTTTCCAAAAATCATATTTTTGCCCC-CAACTGTCCAAAAATAACCATTTTACCCCCA
* * * *
11453 AACTTTCCAAAAATCATATTTTTGCCCCCAAGTGTTCAAAAATTACCATTTTACCCCCG
1 AACTTTCCAAAAATCATATTTTTGCCCCCAACTGTCCAAAAATAACCATTTTACCCCCA
11512 AAC-TTCCAAAA
1 AACTTTCCAAAA
11523 GTTATTACGT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
58 11 0.18
59 50 0.82
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (59 bp):
AACTTTCCAAAAATCATATTTTTGCCCCCAACTGTCCAAAAATAACCATTTTACCCCCA
Found at i:11482 original size:30 final size:30
Alignment explanation
Indices: 11342--11699 Score: 151
Period size: 29 Copynumber: 12.2 Consensus size: 30
11332 CTTGAACCTA
*
11342 AAAAATTACATTTTTGA-CCCCGAACTTTCC
1 AAAAATAACATTTTT-ACCCCCGAACTTTCC
** * **
11372 AAAAATAATGTTTTTGCCCTTGAACTTTCC
1 AAAAATAACATTTTTACCCCCGAACTTTCC
* ** * *
11402 AAAAATGATGTTTTTTCCCCTGAAC-TTCC
1 AAAAATAACATTTTTACCCCCGAACTTTCC
*
11431 AAAAATAACCA-TTTTACCCCCAAACTTTCC
1 AAAAATAA-CATTTTTACCCCCGAACTTTCC
* * * *
11461 AAAAATCATATTTTTGCCCCC-AAGTGTT-C
1 AAAAATAACATTTTTACCCCCGAACT-TTCC
*
11490 AAAAATTACCA-TTTTACCCCCGAAC-TTCC
1 AAAAA-TAACATTTTTACCCCCGAACTTTCC
* * * * *
11519 AAAAGT--TATTACGTTA-CCCCTAAGCTATCC
1 AAAAATAACATT--TTTACCCCCGAA-CTTTCC
* * * * *
11549 AAAAATCACATTTTTA-CCTCAAACATTCA
1 AAAAATAACATTTTTACCCCCGAACTTTCC
* **
11578 AAAAATCACA-TTTTACCCCTAAACTTTCC
1 AAAAATAACATTTTTACCCCCGAACTTTCC
* * *
11607 AAAAATAATATTTTTGCTCCCGAAC-TTCC
1 AAAAATAACATTTTTACCCCCGAACTTTCC
* * *
11636 AAAAAT--TATTAATTTACCCCTGAAC-TTCA
1 AAAAATAACATT--TTTACCCCCGAACTTTCC
*
11665 AAAAAT-ACATTTTTGA-CCTCGAAC-TTCC
1 AAAAATAACATTTTT-ACCCCCGAACTTTCC
11693 TAAAAAT
1 -AAAAAT
11700 TACTGTTGGA
Statistics
Matches: 251, Mismatches: 55, Indels: 45
0.72 0.16 0.13
Matches are distributed among these distances:
26 1 0.00
27 5 0.02
28 26 0.10
29 116 0.46
30 100 0.40
32 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.33
Consensus pattern (30 bp):
AAAAATAACATTTTTACCCCCGAACTTTCC
Found at i:11552 original size:59 final size:58
Alignment explanation
Indices: 11428--11614 Score: 132
Period size: 59 Copynumber: 3.2 Consensus size: 58
11418 CCCCTGAACT
* * *
11428 TCCAAAAATAACCATTTTACCCCCAAACTTTCCAAAAATCATATTTTTGCCCCCAAGTG
1 TCCAAAAATAACCATTTTACCCCCAAACTTTCCAAAAAT-ATATTGTTACCCCCAAGTA
* * * * *
11487 TTCAAAAATTACCATTTTACCCCCGAAC-TTCCAAAAGT-TATTACGTTACCCCTAAGCTA
1 TCCAAAAATAACCATTTTACCCCCAAACTTTCCAAAAATATATT--GTTACCCCCAAG-TA
* * * * * * * *
11546 TCCAAAAATCA-CATTTTTA-CCTCAAACATTCAAAAAATCACATT-TTACCCCTAAACTT
1 TCCAAAAATAACCA-TTTTACCCCCAAACTTTCCAAAAAT-ATATTGTTACCCC-CAAGTA
11604 TCCAAAAATAA
1 TCCAAAAATAA
11615 TATTTTTGCT
Statistics
Matches: 101, Mismatches: 19, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
56 4 0.04
58 44 0.44
59 50 0.50
61 3 0.03
ACGTcount: A:0.39, C:0.28, G:0.04, T:0.29
Consensus pattern (58 bp):
TCCAAAAATAACCATTTTACCCCCAAACTTTCCAAAAATATATTGTTACCCCCAAGTA
Found at i:11787 original size:17 final size:17
Alignment explanation
Indices: 11765--11847 Score: 94
Period size: 17 Copynumber: 4.9 Consensus size: 17
11755 TCTAGATTGT
*
11765 TTTTAAATTTTAATTTA
1 TTTTAAATTTAAATTTA
* *
11782 TTTTAAATATAAACTTA
1 TTTTAAATTTAAATTTA
* * *
11799 CTTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
*
11816 TTTTAAATTTGAATTTA
1 TTTTAAATTTAAATTTA
*
11833 TTTTAAATTAAAATT
1 TTTTAAATTTAAATT
11848 AAAAGTGTCC
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 52 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:12536 original size:3 final size:3
Alignment explanation
Indices: 12528--12593 Score: 105
Period size: 3 Copynumber: 21.7 Consensus size: 3
12518 TTAAAACGTC
12528 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
12576 AACA AAT AAT AGT AAT AA
1 AA-T AAT AAT AAT AAT AA
12594 ATTGCATTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 56 0.97
4 2 0.03
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:13918 original size:29 final size:28
Alignment explanation
Indices: 13852--14305 Score: 151
Period size: 29 Copynumber: 15.6 Consensus size: 28
13842 ACCTCTATTT
* *
13852 TTCCAAAAATTACCATTCT-ACCCTCGAAC
1 TTCCAAAAATT-CCATTTTAACCC-CAAAC
13881 ATTCC-AAAATTCCATTTTTAACCCCAAAC
1 -TTCCAAAAATTCCA-TTTTAACCCCAAAC
* * *
13910 TTCAAAAAATTACATTTTGACCCTCAAAC
1 TTCCAAAAATTCCATTTTAACCC-CAAAC
** * *
13939 TTCCAAAAATTAGATTTCAACACCCCGAAC
1 TTCCAAAAATTCCATTT-TA-ACCCCAAAC
*
13969 TTTCCAAAAATTACATTTT-ACCCCTAAAC
1 -TTCCAAAAATTCCATTTTAACCCC-AAAC
* * * * * **
13998 -TACTAATATTCCATTTTGACCCCGATT
1 TTCCAAAAATTCCATTTTAACCCCAAAC
* * *
14025 TTCCAAAAATTATCATATTACCCCCAAA-
1 TTCCAAAAATT-CCATTTTAACCCCAAAC
*
14053 TGTCTAAAAATTCCATTTTTAACCCCAAAC
1 T-TCCAAAAATTCCA-TTTTAACCCCAAAC
* *
14083 TTTCTAAAAATTACCATTTT-ACCCCTGAAC
1 -TTCCAAAAATT-CCATTTTAACCCC-AAAC
* * * * ** *
14113 ATCTAAAAATTTCATTTTTGACATCGAAC
1 TTCCAAAAATTCCA-TTTTAACCCCAAAC
* * * *
14142 TTTCCCAAAATTATCATTTTATCCCCGAA-
1 -TTCCAAAAATT-CCATTTTAACCCCAAAC
* * ***
14171 TGTCTAAAAATTCCATTTTAAAGCTTGAAC
1 T-TCCAAAAATTCCATTTT-AACCCCAAAC
14201 TTTCC-AAAATTACCA-TTT-ACCCCTAAA-
1 -TTCCAAAAATT-CCATTTTAACCCC-AAAC
* * *
14228 TGTCTAAAAATTCCATTTTTGACCCTAAAC
1 T-TCCAAAAATTCCA-TTTTAACCCCAAAC
* * *
14258 TTTCCCAAAATTACAATTTTACCCCCAAA-
1 -TTCCAAAAATT-CCATTTTAACCCCAAAC
14287 TGTCC-AAAATTACCATTTT
1 T-TCCAAAAATT-CCATTTT
14306 GCCCCCGGGT
Statistics
Matches: 322, Mismatches: 66, Indels: 74
0.70 0.14 0.16
Matches are distributed among these distances:
26 1 0.00
27 21 0.07
28 65 0.20
29 128 0.40
30 76 0.24
31 31 0.10
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (28 bp):
TTCCAAAAATTCCATTTTAACCCCAAAC
Found at i:14305 original size:28 final size:28
Alignment explanation
Indices: 14203--14311 Score: 98
Period size: 28 Copynumber: 3.8 Consensus size: 28
14193 GCTTGAACTT
*
14203 TCCAAAATTACCA-TTTACCCCTAAATG
1 TCCAAAATTACCATTTTACCCCCAAATG
* * *
14230 TCTAAAAATT-CCATTTTTGA-CCCTAAACTT
1 TC-CAAAATTACCA-TTTT-ACCCCCAAA-TG
*
14260 TCCCAAAATTACAATTTTACCCCCAAATG
1 T-CCAAAATTACCATTTTACCCCCAAATG
*
14289 TCCAAAATTACCATTTTGCCCCC
1 TCCAAAATTACCATTTTACCCCC
14312 GGGTATCCAA
Statistics
Matches: 66, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
27 5 0.08
28 26 0.39
29 13 0.20
30 19 0.29
31 3 0.05
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (28 bp):
TCCAAAATTACCATTTTACCCCCAAATG
Found at i:14305 original size:59 final size:57
Alignment explanation
Indices: 13784--14305 Score: 328
Period size: 59 Copynumber: 8.9 Consensus size: 57
13774 TCTCAAAGGT
* * * **
13784 CCCTGAACTGTCCATAAATTACTATTTTACCCCTGAATGTCTAAAAATTCCATTTTTGA
1 CCCTAAACTTTCCAAAAATTAC-ATTTTACCCCCAAATGTC-AAAAATTCCATTTTTGA
** * * * *
13843 CCTCT-ATTTTTCCAAAAATTACCATTCTACCCTCGAACAT-TCCAAAATTCCATTTTTAA
1 CC-CTAAACTTTCCAAAAATTA-CATTTTACCC-CCAA-ATGTCAAAAATTCCATTTTTGA
* * * ** ***
13902 CCCCAAAC-TTCAAAAAATTACATTTTGACCCTCAAACT-TCCAAAAATTAGATTTCAACA
1 CCCTAAACTTTCCAAAAATTACATTTT-ACCCCCAAA-TGT-CAAAAATTCCATTT-TTGA
** * * * *
13961 CCCCGAACTTTCCAAAAATTACATTTTACCCCTAAACT-ACTAATATTCCA-TTTTGA
1 CCCTAAACTTTCCAAAAATTACATTTTACCCCCAAA-TGTCAAAAATTCCATTTTTGA
** * * *
14017 CCC-CGATTTTCCAAAAATTATCATATTACCCCCAAATGTCTAAAAATTCCATTTTTAA
1 CCCTAAACTTTCCAAAAATTA-CATTTTACCCCCAAATGTC-AAAAATTCCATTTTTGA
* * * * *
14075 CCCCAAACTTTCTAAAAATTACCATTTTACCCCTGAACATCT-AAAAATTTCATTTTTGA
1 CCCTAAACTTTCCAAAAATTA-CATTTTACCCC-CAA-ATGTCAAAAATTCCATTTTTGA
* * * * * **
14134 -CATCGAACTTTCCCAAAATTATCATTTTATCCCCGAATGTCTAAAAATTCCATTTTAAA
1 CCCT-AAACTTTCCAAAAATTA-CATTTTACCCCCAAATGTC-AAAAATTCCATTTTTGA
* * * *
14193 GCTTGAACTTTCC-AAAATTACCA-TTTACCCCTAAATGTCTAAAAATTCCATTTTTGA
1 CCCTAAACTTTCCAAAAATTA-CATTTTACCCCCAAATGTC-AAAAATTCCATTTTTGA
* *
14250 CCCTAAACTTTCCCAAAATTACAATTTTACCCCCAAATGTCCAAAATTACCATTTT
1 CCCTAAACTTTCCAAAAATTAC-ATTTTACCCCCAAATGTCAAAAATT-CCATTTT
14306 GCCCCCGGGT
Statistics
Matches: 360, Mismatches: 78, Indels: 50
0.74 0.16 0.10
Matches are distributed among these distances:
55 15 0.04
56 19 0.05
57 62 0.17
58 67 0.19
59 164 0.46
60 28 0.08
61 5 0.01
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (57 bp):
CCCTAAACTTTCCAAAAATTACATTTTACCCCCAAATGTCAAAAATTCCATTTTTGA
Found at i:18348 original size:48 final size:49
Alignment explanation
Indices: 18272--18375 Score: 174
Period size: 48 Copynumber: 2.1 Consensus size: 49
18262 ACACTTTACC
18272 ATTCTTTCCATTCGGTCATACCACAATTAATCATTCTTT-AGTTCAATT
1 ATTCTTTCCATTCGGTCATACCACAATTAATCATTCTTTAAGTTCAATT
* * *
18320 ATTCTTTTCATTCGTTCATACCATAATTAATCATTCTTTAAGTTCAATT
1 ATTCTTTCCATTCGGTCATACCACAATTAATCATTCTTTAAGTTCAATT
18369 ATTCTTT
1 ATTCTTT
18376 GGACCTCTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
48 36 0.69
49 16 0.31
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (49 bp):
ATTCTTTCCATTCGGTCATACCACAATTAATCATTCTTTAAGTTCAATT
Found at i:19704 original size:23 final size:22
Alignment explanation
Indices: 19675--19719 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
19665 CAGATGCAAT
*
19675 GAAGA-AAAATAAATAAAAAAA
1 GAAGAGAAAATAAAAAAAAAAA
*
19696 GAAGAGAAACTAAAAAAAAAAA
1 GAAGAGAAAATAAAAAAAAAAA
19718 GA
1 GA
19720 GAGGTCAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (22 bp):
GAAGAGAAAATAAAAAAAAAAA
Found at i:20965 original size:97 final size:97
Alignment explanation
Indices: 20799--21307 Score: 781
Period size: 97 Copynumber: 5.2 Consensus size: 97
20789 ACAAAGGAAA
*
20799 AATGGCGAACCTAGTACCTCGGAGACATGAAGGGAAAGATCTAAGTCGCAACGGCGGATCCAGTA
1 AATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAGTCGCAACGGCGGATCCAGTA
20864 CCACGAAGACACAAAGGAAAGGTTTAAGTCGC
66 CCACGAAGACACAAAGGAAAGGTTTAAGTCGC
* * *
20896 AATGGCGAACCTAGTACCTTAGAGACATGAAGGGAAAGATCTAAGTCGCAACGGTGGATCTAGTA
1 AATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAGTCGCAACGGCGGATCCAGTA
*
20961 CCACGAAGACACAAGGGAAAGGTTTAAGTCGC
66 CCACGAAGACACAAAGGAAAGGTTTAAGTCGC
* *
20993 AATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAG-CTGCAACGGCAGATCTAGT
1 AATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAGTC-GCAACGGCGGATCCAGT
21057 ACCACGAAGACACAATA-GAAAGGTTTAAGTCGC
65 ACCACGAAGACACAA-AGGAAAGGTTTAAGTCGC
* *
21090 AATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAGCCGTAACGGCGGATCCAGTA
1 AATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAGTCGCAACGGCGGATCCAGTA
* * *
21155 CCACGAAGACATAAGGGAAATGTTTAAGTCGC
66 CCACGAAGACACAAAGGAAAGGTTTAAGTCGC
* * *
21187 AATGACAAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAGTCGCAACGGCAGATCCAGTA
1 AATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAGTCGCAACGGCGGATCCAGTA
** * *
21252 CCGTGAAAACACAAAGGGAAAGATTTAAGTCGC
66 CCACGAAGACACAAA-GGAAAGGTTTAAGTCGC
*
21285 AATGCCGAACCTTA-TACCTCAGA
1 AATGGCGAACC-TAGTACCTCAGA
21308 AGCATGGGAG
Statistics
Matches: 377, Mismatches: 29, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
96 1 0.00
97 340 0.90
98 34 0.09
99 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (97 bp):
AATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAGTCGCAACGGCGGATCCAGTA
CCACGAAGACACAAAGGAAAGGTTTAAGTCGC
Found at i:22758 original size:3 final size:3
Alignment explanation
Indices: 22750--22788 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
22740 TTAAAACGTC
* *
22750 AAT AAT AAT AAT AAT AAT AAT AACA AAT AAT AGT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AA
22789 ATTTCATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.94
4 2 0.06
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:23210 original size:18 final size:19
Alignment explanation
Indices: 23189--23226 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
23179 AATCAAAACA
23189 AAAAAT-AAAAAAAGAAAG
1 AAAAATCAAAAAAAGAAAG
*
23207 AAAAATCAAAAAATGAAAG
1 AAAAATCAAAAAAAGAAAG
23226 A
1 A
23227 CTAAACTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.79, C:0.03, G:0.11, T:0.08
Consensus pattern (19 bp):
AAAAATCAAAAAAAGAAAG
Found at i:24055 original size:29 final size:29
Alignment explanation
Indices: 24034--24093 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
24024 AAATTCCATT
*
24034 TTTTGA-CCTCGAACTTCTAAAAATCACA
1 TTTTGACCCTCAAACTTCTAAAAATCACA
*
24062 TTTTGACCCTCAAACTTCTAAAAATCAAA
1 TTTTGACCCTCAAACTTCTAAAAATCACA
24091 TTT
1 TTT
24094 CAACTCCCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (29 bp):
TTTTGACCCTCAAACTTCTAAAAATCACA
Found at i:24055 original size:30 final size:30
Alignment explanation
Indices: 24019--24086 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
24009 CGCCCGAATG
*
24019 TCTAAAAATTC-CATTTTTTGA-CCTCGAACT
1 TCTAAAAATTCACA--TTTTGACCCTCAAACT
24049 TCTAAAAA-TCACATTTTGACCCTCAAACT
1 TCTAAAAATTCACATTTTGACCCTCAAACT
24078 TCTAAAAAT
1 TCTAAAAAT
24087 CAAATTTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 6 0.18
29 18 0.53
30 10 0.29
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (30 bp):
TCTAAAAATTCACATTTTGACCCTCAAACT
Found at i:24106 original size:29 final size:29
Alignment explanation
Indices: 24040--24107 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
24030 CATTTTTTGA
* **
24040 CCTCGAACTTCTAAAAATCACATTTTGAC
1 CCTCGAACTTCTAAAAATCAAATTTCAAC
*
24069 CCTCAAACTTCTAAAAATCAAATTTCAAC
1 CCTCGAACTTCTAAAAATCAAATTTCAAC
24098 TCC-CGAACTT
1 -CCTCGAACTT
24108 TCCAAAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 31 0.94
30 2 0.06
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.29
Consensus pattern (29 bp):
CCTCGAACTTCTAAAAATCAAATTTCAAC
Found at i:24208 original size:59 final size:58
Alignment explanation
Indices: 24134--24330 Score: 225
Period size: 59 Copynumber: 3.3 Consensus size: 58
24124 TTGACCCGAT
* * * *
24134 TTTCCAAAAACTACCATTTTACCCCCAGATGTCTAAAAATTCTATTTTAAACCTTGAAC
1 TTTCCAAAAATTACCATTTTACCCTC-GATGTCTAAAAATTCTATTTTTAACCTTAAAC
* ** ** *
24193 TTTCCGAAAATTACCATTTTACCCTCGAACATCTAAAAATTCTATTTTTGTCCTCAAAC
1 TTTCCAAAAATTACCATTTTACCCTCG-ATGTCTAAAAATTCTATTTTTAACCTTAAAC
* * *
24252 TTTCCAAAAATTACCATTTTACCTTCGGATGTCTAAAAATT-TCATTTTTTACCCTAAAC
1 TTTCCAAAAATTACCATTTTACCCTC-GATGTCTAAAAATTCT-ATTTTTAACCTTAAAC
*
24311 TTTCCTAAAATTACCATTTT
1 TTTCCAAAAATTACCATTTT
24331 GTCCCCGGGT
Statistics
Matches: 116, Mismatches: 19, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
58 2 0.02
59 113 0.97
60 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.39
Consensus pattern (58 bp):
TTTCCAAAAATTACCATTTTACCCTCGATGTCTAAAAATTCTATTTTTAACCTTAAAC
Found at i:24233 original size:29 final size:29
Alignment explanation
Indices: 24199--24292 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
24189 GAACTTTCCG
24199 AAAATTACCATTTTACCCTCGAACATCTA
1 AAAATTACCATTTTACCCTCGAACATCTA
* ** * * *
24228 AAAATT-CTATTTTTGTCCTCAAACTTTCCA
1 AAAATTACCA-TTTTACCCTCGAAC-ATCTA
* * **
24258 AAAATTACCATTTTACCTTCGGATGTCTA
1 AAAATTACCATTTTACCCTCGAACATCTA
24287 AAAATT
1 AAAATT
24293 TCATTTTTTA
Statistics
Matches: 47, Mismatches: 15, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
28 2 0.04
29 26 0.55
30 17 0.36
31 2 0.04
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.37
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAACATCTA
Found at i:25454 original size:30 final size:30
Alignment explanation
Indices: 25400--25485 Score: 97
Period size: 29 Copynumber: 2.9 Consensus size: 30
25390 TTCGATAATT
*
25400 ACATTTTT-ATCCTCAAAC-TTCCAAAAATC
1 ACATTTTTGA-CCCCAAACTTTCCAAAAATC
*
25429 ACATTTTTGACCCCAAACTTTCCAAAAATT
1 ACATTTTTGACCCCAAACTTTCCAAAAATC
** *
25459 ACATTTTTG-CCCCCGAGTTTCCAAAAA
1 ACATTTTTGACCCCAAACTTTCCAAAAA
25486 ATACCATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
29 30 0.60
30 20 0.40
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (30 bp):
ACATTTTTGACCCCAAACTTTCCAAAAATC
Found at i:25495 original size:29 final size:29
Alignment explanation
Indices: 25418--25638 Score: 155
Period size: 29 Copynumber: 7.6 Consensus size: 29
25408 ATCCTCAAAC
* * *
25418 TTCCAAAAATCACATTTTTGACCC-CAAACT
1 TTCCAAAAATTACATTTTTG-CCCTC-GAGT
*
25448 TTCCAAAAATTACATTTTTGCCCCCGAGT
1 TTCCAAAAATTACATTTTTGCCCTCGAGT
* * * *
25477 TTCCAAAAAATACCA-TTTTACCCTCTAAT
1 TTCCAAAAATTA-CATTTTTGCCCTCGAGT
*
25506 ATCCAAAAATTACATTTTTGCCCTCGAGT
1 TTCCAAAAATTACATTTTTGCCCTCGAGT
* *
25535 GTT-CAAAAATTAC-TATTTTACCCTCGAAT
1 -TTCCAAAAATTACAT-TTTTGCCCTCGAGT
* * * *
25564 CTCTAAAAATTACATTTTT-CCGTCTAGT
1 TTCCAAAAATTACATTTTTGCCCTCGAGT
* ** * * *
25592 GTCCAAAAATTACCGTTTTACACTCGAAT
1 TTCCAAAAATTACATTTTTGCCCTCGAGT
*
25621 CTCCAAAAATTACCATTT
1 TTCCAAAAATTA-CATTT
25639 ACCCCCAAGC
Statistics
Matches: 150, Mismatches: 32, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
28 25 0.17
29 98 0.65
30 27 0.18
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.35
Consensus pattern (29 bp):
TTCCAAAAATTACATTTTTGCCCTCGAGT
Found at i:25618 original size:57 final size:58
Alignment explanation
Indices: 25449--25638 Score: 256
Period size: 58 Copynumber: 3.3 Consensus size: 58
25439 CCCCAAACTT
* * * * *
25449 TCCAAAAATTACATTTTTGCCCCCGAGTTTCCAAAAAATACCATTTTACCCTCTAATA
1 TCCAAAAATTACATTTTTGCCCTCGAGTGTCCAAAAATTACCATTTTACCCTCGAATC
* *
25507 TCCAAAAATTACATTTTTGCCCTCGAGTGTTCAAAAATTACTATTTTACCCTCGAATC
1 TCCAAAAATTACATTTTTGCCCTCGAGTGTCCAAAAATTACCATTTTACCCTCGAATC
* * * * *
25565 TCTAAAAATTACATTTTT-CCGTCTAGTGTCCAAAAATTACCGTTTTACACTCGAATC
1 TCCAAAAATTACATTTTTGCCCTCGAGTGTCCAAAAATTACCATTTTACCCTCGAATC
25622 TCCAAAAATTACCATTT
1 TCCAAAAATTA-CATTT
25639 ACCCCCAAGC
Statistics
Matches: 116, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
57 43 0.37
58 73 0.63
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (58 bp):
TCCAAAAATTACATTTTTGCCCTCGAGTGTCCAAAAATTACCATTTTACCCTCGAATC
Found at i:35717 original size:210 final size:210
Alignment explanation
Indices: 35338--36554 Score: 1808
Period size: 210 Copynumber: 5.8 Consensus size: 210
35328 TGCGATTATC
* * * *
35338 CAAAAGAAGTGATGCGGTCATATTCCTGATGAGATATTGAGAAGTAGACCAAATCAATGAAACCA
1 CAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
* * * * * * *
35403 AAGCTCGATGTGAGTGAAACTTCAAACCCTAGCTTCATGATGAGATACTAAGAAGTAGGTCGAAG
66 AAGCTCGATGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAA
* * * *
35468 CAATAAAACGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGA
131 CAATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGA
*
35533 CACATAGAAGTGGAT
196 CACAGAGAAGTGGAT
* * *
35548 CAAAACAAGTGATGCAATCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCGATGAAACCA
1 CAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
* *
35613 AAGCTCGATGTGAGTGAAACTTCGAACCCCAGCTTCCTGATGATATACTGAGAAGCAGGTCGAAA
66 AAGCTCGATGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAA
* * * *
35678 CAATAAAATGGTTAGCTTCCTTATGAGGTACAAAGAAGTGGACCAAATCCATCTTCCTGATGAGA
131 CAATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGA
35743 CACAGAGAAGTGGAT
196 CACAGAGAAGTGGAT
35758 CAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
1 CAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
* * *
35823 AAGCTCGATGTGAGTGAAACTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGCAAGTCGAAA
66 AAGCTCGATGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAA
35888 CAATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGA
131 CAATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGA
35953 CACAGAGAAGTGGAT
196 CACAGAGAAGTGGAT
* * * *
35968 CAAAACAAGTGATGCAGTCATGTTCCTGATGAGATACTGAGAAGTAGACTAAAACAATGAAA-TA
1 CAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
** * * *
36032 AAGCTTAATATGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGATCAAAA
66 AAGCTCGATGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAA
** * *
36097 CAATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGGGTCAAATCCGTTTTCCTGATGAAA
131 CAATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGA
*
36162 CACAAAGAAGTGGAT
196 CACAGAGAAGTGGAT
* * * *
36177 CAAAACAAGTGATGCGGTCATCTTCTTGGTGAGATATTGAGAAGTAGACCAAATCAATGAAA-CA
1 CAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
* * * * * *
36241 AAGCTCAATATGAGCGAAACTTCGAACCCTAGCTTCTTGATGAGATATTGAGAAGCAGGTCGAAG
66 AAGCTCGATGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAA
* * * * *
36306 CAATAAGATGATTAGCTTCTTGGTGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTAATGAGA
131 CAATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGA
*
36371 CATAGAGAAGTGGAT
196 CACAGAGAAGTGGAT
* *
36386 CAAAACAAGTGATGCAATCATCTTCCTGATAAGATACTGAGAAGTAGACCAAATCAATGAAACCA
1 CAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
* ** * * *
36451 AAGTTATATGTGAGCAAAACTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
66 AAGCTCGATGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAA
*
36516 CAATAAAAATAGTTAGCTTCCTGATGAGATACAGAGAAG
131 CAAT-AAAATGGTTAGCTTCCTGATGAGATACAGAGAAG
36555 CAGATTGAAA
Statistics
Matches: 909, Mismatches: 96, Indels: 3
0.90 0.10 0.00
Matches are distributed among these distances:
209 372 0.41
210 508 0.56
211 29 0.03
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (210 bp):
CAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
AAGCTCGATGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAA
CAATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGA
CACAGAGAAGTGGAT
Found at i:36916 original size:17 final size:17
Alignment explanation
Indices: 36894--36973 Score: 88
Period size: 17 Copynumber: 4.7 Consensus size: 17
36884 GGCCTAACAG
36894 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
36911 AATTTAAGTTTATATTA
1 AATTTAAATTTATTTTA
* * **
36928 AGTTTAAATCTATTTGG
1 AATTTAAATTTATTTTA
*
36945 AATTTAAATTTATTGTA
1 AATTTAAATTTATTTTA
*
36962 AATTTAAGTTTA
1 AATTTAAATTTA
36974 AATTAATAAT
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 49 1.00
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:38768 original size:29 final size:29
Alignment explanation
Indices: 38729--39279 Score: 312
Period size: 29 Copynumber: 18.9 Consensus size: 29
38719 TAGGTCCCTG
* *
38729 AACTGTCCAAAAATCACATTTTTACCCTCG
1 AACT-TCCAAAAATTACATTTTTACCCTCA
* * *
38759 AACTTAC-AAAATTACCA-TTTTACCCCCG
1 AACTTCCAAAAATTA-CATTTTTACCCTCA
*
38787 AACCTCCAAAAATTACATTTTTGA-CCTCA
1 AACTTCCAAAAATTACATTTTT-ACCCTCA
* ** * *
38816 AATTTTCCAAAAATTATGTTTTTGCCCCCA
1 AA-CTTCCAAAAATTACATTTTTACCCTCA
*
38846 AACTTCCAAAAATTATCA-TTTTACCCTCG
1 AACTTCCAAAAATTA-CATTTTTACCCTCA
* * * **
38875 AAGTTCCAAAAATCACATTTTTACACTTG
1 AACTTCCAAAAATTACATTTTTACCCTCA
* * **
38904 AACTTTCCAAAAATCACATTTTTGCCCTTG
1 AAC-TTCCAAAAATTACATTTTTACCCTCA
* * *
38934 AACTTCTAAAAATTAC-TGTTTTACCTTTA
1 AACTTCCAAAAATTACAT-TTTTACCCTCA
* * * *
38963 AACTT-TAGAAAACTCACATTATTACACTCA
1 AACTTCCA-AAAA-TTACATTTTTACCCTCA
* *
38993 AACTTTCAAAAAATCACATTTTT-CCC-CA
1 AAC-TTCCAAAAATTACATTTTTACCCTCA
39021 AACTTCCAAAAATTACCA-TTTTACCC-CTA
1 AACTTCCAAAAATTA-CATTTTTACCCTC-A
* * * *
39050 AACTTCCAAAAAATACTTTTTTAACCTCG
1 AACTTCCAAAAATTACATTTTTACCCTCA
** *
39079 AACTTCCTAAAAATTATGTTTTTA-TCTCCA
1 AACTTCC-AAAAATTACATTTTTACCCT-CA
* * **
39109 AACATCAAAAAATTACCGTTTTACCC-CAA
1 AACTTCCAAAAATTACATTTTTACCCTC-A
* *
39138 AACTT-CTAAAATCACATTTTTAACCCT-A
1 AACTTCCAAAAATTACATTTTT-ACCCTCA
* *
39166 AACTTTCCAAAAATTACATTTTTTCCC-CTG
1 AAC-TTCCAAAAATTACATTTTTACCCTC-A
** *
39196 AGTTTCCAAAAATTACCA-TTTTACCCTCG
1 AACTTCCAAAAATTA-CATTTTTACCCTCA
*
39225 AA-TGTCCAAAAATTACATTTTTGCCCTC-
1 AACT-TCCAAAAATTACATTTTTACCCTCA
* *
39253 GAGTGTCCAAAAATTA-ATGTTTTACCC
1 AACT-TCCAAAAATTACAT-TTTTACCC
39280 CTGAATCTCC
Statistics
Matches: 412, Mismatches: 73, Indels: 73
0.74 0.13 0.13
Matches are distributed among these distances:
27 14 0.03
28 62 0.15
29 213 0.52
30 115 0.28
31 7 0.02
32 1 0.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTACCCTCA
Found at i:38779 original size:28 final size:28
Alignment explanation
Indices: 38736--38807 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
38726 CTGAACTGTC
* * *
38736 CAAAAATCACATTTTTACCCTCGAACTTA
1 CAAAAATTACA-TTTTACCCCCGAACCTA
*
38765 C-AAAATTACCATTTTACCCCCGAACCTC
1 CAAAAATTA-CATTTTACCCCCGAACCTA
38793 CAAAAATTACATTTT
1 CAAAAATTACATTTT
38808 TGACCTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 27 0.73
29 10 0.27
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.31
Consensus pattern (28 bp):
CAAAAATTACATTTTACCCCCGAACCTA
Found at i:38885 original size:88 final size:87
Alignment explanation
Indices: 38729--39307 Score: 405
Period size: 88 Copynumber: 6.6 Consensus size: 87
38719 TAGGTCCCTG
* * * * * * * *
38729 AACTGTCCAAAAATCACATTTTTACCCTCGAACTTAC-AAAATTACCATTTTACCCCCGAACCTC
1 AACTTTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTACCATTTTACCCTCAAACTTC
*
38793 CAAAAATTACATTTTTGACCTCA
66 CAAAAATCACATTTTT-ACCTCA
* ** * * * *
38816 AATTTTCCAAAAATTATGTTTTTGCCCCCAAACTTCCAAAAATTATCATTTTACCCTCGAAGTTC
1 AACTTTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTACCATTTTACCCTCAAACTTC
**
38881 CAAAAATCACATTTTTACACTTG
66 CAAAAATCACATTTTTAC-CTCA
* * *** * ** * *
38904 AACTTTCCAAAAATCACATTTTTGCCCTTGAACTTCTAAAAATTACTGTTTTACCTTTAAACTT-
1 AACTTTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTACCATTTTACCCTCAAACTTC
* *
38968 TAGAAAACTCACATTATTACACTCA
66 CA-AAAA-TCACATTTTTAC-CTCA
* *
38993 AACTTTCAAAAAATCACATTTTT--CCCCAAACTTCCAAAAATTACCATTTTACCC-CTAAACTT
1 AACTTTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTACCATTTTACCCTC-AAACTT
* *
39055 CCAAAAAAT-ACTTTTTTAACCTCG
65 CC-AAAAATCACATTTTT-ACCTCA
** * * * * *
39079 AAC-TTCCTAAAAATTATGTTTTTATCTCCAAACATCAAAAAATTACCGTTTTACCC-CAAAACT
1 AACTTTCC-AAAAATTACATTTTTACCCCCAAACTTCCAAAAATTACCATTTTACCCTC-AAACT
*
39142 T-CTAAAATCACATTTTTAACC-CTA
64 TCCAAAAATCACATTTTT-ACCTC-A
* ** ** *
39166 AACTTTCCAAAAATTACATTTTTTCCCCTGAGTTTCCAAAAATTACCATTTTACCCTCGAA-TGT
1 AACTTTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTACCATTTTACCCTCAAACT-T
* *
39230 CCAAAAATTACATTTTTGCCCTC-
65 CCAAAAATCACATTTTT-ACCTCA
* * * ** *
39253 GAGTGTCCAAAAATTA-ATGTTTTACCCCTGAA-TCTCC-AAAATTATCATTTTACCC
1 AACTTTCCAAAAATTACAT-TTTTACCCCCAAACT-TCCAAAAATTACCATTTTACCC
39308 CCAGGCATCA
Statistics
Matches: 389, Mismatches: 83, Indels: 41
0.76 0.16 0.08
Matches are distributed among these distances:
85 3 0.01
86 51 0.13
87 145 0.37
88 152 0.39
89 38 0.10
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (87 bp):
AACTTTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTACCATTTTACCCTCAAACTTC
CAAAAATCACATTTTTACCTCA
Found at i:38967 original size:59 final size:59
Alignment explanation
Indices: 38729--39061 Score: 170
Period size: 59 Copynumber: 5.7 Consensus size: 59
38719 TAGGTCCCTG
* * * * ***
38729 AACTGTCCAAAAATCACATTTTTACCCTCGAACTTAC-AAAATTACCA-TTTTACCCCCG
1 AACTTTCCAAAAATCACATTTTTACCCTCGAACTTCCAAAAATCA-CATTTTTACACTTA
* * * * * ** * * **
38787 AAC-CTCCAAAAATTACATTTTTGA-CCTCAAATTTTCCAAAAATTATGTTTTTGCCCCCA
1 AACTTTCCAAAAATCACATTTTT-ACCCTCGAA-CTTCCAAAAATCACATTTTTACACTTA
* * *
38846 AAC-TTCCAAAAATTATCA-TTTTACCCTCGAAGTTCCAAAAATCACATTTTTACACTTG
1 AACTTTCCAAAAATCA-CATTTTTACCCTCGAACTTCCAAAAATCACATTTTTACACTTA
* * * *
38904 AACTTTCCAAAAATCACATTTTTGCCCTTGAACTTCTAAAAATTAC-TGTTTTAC-CTTTA
1 AACTTTCCAAAAATCACATTTTTACCCTCGAACTTCCAAAAATCACAT-TTTTACAC-TTA
** * * * * * **
38963 AACTTTAGAAAACTCACATTATTACACTCAAACTTTCAAAAAATCACATTTTT-C-CCCA
1 AACTTTCCAAAAATCACATTTTTACCCTCGAAC-TTCCAAAAATCACATTTTTACACTTA
* *
39021 AAC-TTCCAAAAATTACCA-TTTTACCC-CTAAACTTCCAAAAA
1 AACTTTCCAAAAATCA-CATTTTTACCCTC-GAACTTCCAAAAA
39062 ATACTTTTTT
Statistics
Matches: 215, Mismatches: 46, Indels: 30
0.74 0.16 0.10
Matches are distributed among these distances:
56 9 0.04
57 41 0.19
58 39 0.18
59 108 0.50
60 17 0.08
61 1 0.00
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (59 bp):
AACTTTCCAAAAATCACATTTTTACCCTCGAACTTCCAAAAATCACATTTTTACACTTA
Found at i:39030 original size:175 final size:172
Alignment explanation
Indices: 38841--39246 Score: 414
Period size: 175 Copynumber: 2.3 Consensus size: 172
38831 ATGTTTTTGC
* *
38841 CCCCAAACTTCCAAAAATTATCATTTTACCCTCGAAGTTCCAAAAATCACATTTTT-ACACTTGA
1 CCCCAAACTTCCAAAAATTACCATTTTACCCTCGAA-TTCCAAAAAT-ACATTTTTAAC-CTCGA
* * * * ***
38905 ACTTTCC-AAAAATCACATTTTT-GC-CCTTGAACTTCTAAAAATTACTGTTTTACCTTTAAACT
63 AC-TTCCTAAAAATCACATTTTTAGCTCC--AAACATCAAAAAATTACCGTTTTACCCCAAAACT
*
38967 T-TAGAAAACTCACATTATT-ACACTCAAACTTTCAAAAAATCACA-TTTTT
125 TCT--AAAA-TCACATTATTAACCCT-AAACTTTCAAAAAATCACATTTTTT
* *
39016 CCCCAAACTTCCAAAAATTACCATTTTACCC-CTAAACTTCCAAAAAATACTTTTTTAACCTCGA
1 CCCCAAACTTCCAAAAATTACCATTTTACCCTC-GAA-TTCC-AAAAATACATTTTTAACCTCGA
* ** *
39080 ACTTCCTAAAAATTATGTTTTTATCTCCAAACATCAAAAAATTACCGTTTTACCCCAAAACTTCT
63 ACTTCCTAAAAATCACATTTTTAGCTCCAAACATCAAAAAATTACCGTTTTACCCCAAAACTTCT
* * *
39145 AAAATCACATTTTTAACCCTAAACTTTCCAAAAATTACATTTTTT
128 AAAATCACATTATTAACCCTAAACTTTCAAAAAATCACATTTTTT
* **
39190 CCCCTGAGTTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAATTACATTTTT
1 CCCC-AAACTTCCAAAAATTACCATTTTACCCTCGAAT-TCCAAAAA-TACATTTTT
39247 GCCCTCGAGT
Statistics
Matches: 193, Mismatches: 25, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
173 26 0.13
174 28 0.15
175 126 0.65
176 11 0.06
177 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35
Consensus pattern (172 bp):
CCCCAAACTTCCAAAAATTACCATTTTACCCTCGAATTCCAAAAATACATTTTTAACCTCGAACT
TCCTAAAAATCACATTTTTAGCTCCAAACATCAAAAAATTACCGTTTTACCCCAAAACTTCTAAA
ATCACATTATTAACCCTAAACTTTCAAAAAATCACATTTTTT
Found at i:39233 original size:58 final size:59
Alignment explanation
Indices: 39171--39303 Score: 166
Period size: 58 Copynumber: 2.3 Consensus size: 59
39161 CCCTAAACTT
* * *
39171 TCCAAAAATTACATTTTTTCCCCT-GAGTTTCCAAAAATTACCATTTTA-CCCTCGAATG
1 TCCAAAAATTACATTTTTTCCCCTCGAGTGTCCAAAAATTAACATTTTACCCCT-GAATC
* **
39229 TCCAAAAATTACA-TTTTTGCCCTCGAGTGTCCAAAAATTAATGTTTTACCCCTGAATC
1 TCCAAAAATTACATTTTTTCCCCTCGAGTGTCCAAAAATTAACATTTTACCCCTGAATC
39287 TCC-AAAATTATCATTTT
1 TCCAAAAATTA-CATTTT
39304 ACCCCCAGGC
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
57 16 0.25
58 42 0.65
59 7 0.11
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.37
Consensus pattern (59 bp):
TCCAAAAATTACATTTTTTCCCCTCGAGTGTCCAAAAATTAACATTTTACCCCTGAATC
Found at i:39290 original size:29 final size:30
Alignment explanation
Indices: 39145--39308 Score: 139
Period size: 29 Copynumber: 5.6 Consensus size: 30
39135 CAAAACTTCT
* * * *
39145 AAAATCACATTTTTAACCCT-AAACTTTCCA
1 AAAATTACATTTTTACCCCTCGAA-TGTCCA
* * *
39175 AAAATTACATTTTTTCCCCT-GAGTTTCCA
1 AAAATTACATTTTTACCCCTCGAATGTCCA
39204 AAAATTACCA-TTTTA-CCCTCGAATGTCCA
1 AAAATTA-CATTTTTACCCCTCGAATGTCCA
* *
39233 AAAATTACATTTTT-GCCCTCGAGTGTCCA
1 AAAATTACATTTTTACCCCTCGAATGTCCA
*
39262 AAAATTA-ATGTTTTACCCCT-GAATCTCC-
1 AAAATTACAT-TTTTACCCCTCGAATGTCCA
39290 AAAATTATCA-TTTTACCCC
1 AAAATTA-CATTTTTACCCC
39309 CAGGCATCAT
Statistics
Matches: 114, Mismatches: 12, Indels: 18
0.79 0.08 0.12
Matches are distributed among these distances:
28 24 0.21
29 65 0.57
30 25 0.22
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTTACCCCTCGAATGTCCA
Found at i:45266 original size:19 final size:19
Alignment explanation
Indices: 45231--45275 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
45221 AGTTAAAAGA
*
45231 AGTTGAATATAGTTACTGTC
1 AGTTG-ATATAGTTACTATC
45251 AGTTGATATACG-TACTATC
1 AGTTGATATA-GTTACTATC
45270 AGTTGA
1 AGTTGA
45276 AGTCAGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (19 bp):
AGTTGATATAGTTACTATC
Done.