Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009813.1 Kokia drynarioides strain JFW-HI SEQ_124534, 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: 34973
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Found at i:1157 original size:26 final size:26
Alignment explanation
Indices: 1121--1204 Score: 152
Period size: 26 Copynumber: 3.3 Consensus size: 26
1111 CGCTTCTGTT
*
1121 CAGCACTGTGTGTGCTTCTGTTTCCC
1 CAGCACTGTGTGTGCTTTTGTTTCCC
1147 CAGCACTGTGTGTGCTTTTGTTTCCC
1 CAGCACTGTGTGTGCTTTTGTTTCCC
1173 CAGCACTGTGTGTGCTTTTGTTT-CC
1 CAGCACTGTGTGTGCTTTTGTTTCCC
1198 CAGCACT
1 CAGCACT
1205 TATGTACCTC
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
25 9 0.16
26 48 0.84
ACGTcount: A:0.10, C:0.29, G:0.23, T:0.39
Consensus pattern (26 bp):
CAGCACTGTGTGTGCTTTTGTTTCCC
Found at i:5035 original size:21 final size:21
Alignment explanation
Indices: 5011--5062 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
5001 TTATTTGGGC
*
5011 TTTATTGTTTAGGGTTACATG
1 TTTATGGTTTAGGGTTACATG
5032 TTTATGGTTTAGGGTTACATG
1 TTTATGGTTTAGGGTTACATG
*
5053 TTTAGGGTTT
1 TTTATGGTTT
5063 TTTATTTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.04, G:0.27, T:0.52
Consensus pattern (21 bp):
TTTATGGTTTAGGGTTACATG
Found at i:5042 original size:28 final size:28
Alignment explanation
Indices: 5031--5175 Score: 98
Period size: 28 Copynumber: 5.2 Consensus size: 28
5021 AGGGTTACAT
*
5031 GTTTATGGTTTAGGGTTACATGTTTAGG
1 GTTTATTGTTTAGGGTTACATGTTTAGG
* * * * *
5059 GTTTTTTATTTAGGGTTTA-TTGTCTA-A
1 GTTTATTGTTTAGGG-TTACATGTTTAGG
* * *
5086 GATTACATGTTTAGGGTTTA-TTGTTTAGG
1 GTTTA-TTGTTTAGGG-TTACATGTTTAGG
*** *
5115 GTTTATCACTTAAGGTTACATGTTTAGG
1 GTTTATTGTTTAGGGTTACATGTTTAGG
* *
5143 GTTTATTGTTTAAGATTACATGTTTAGG
1 GTTTATTGTTTAGGGTTACATGTTTAGG
*
5171 ATTTA
1 GTTTA
5176 GGGTTTCATT
Statistics
Matches: 89, Mismatches: 24, Indels: 8
0.74 0.20 0.07
Matches are distributed among these distances:
27 6 0.07
28 76 0.85
29 7 0.08
ACGTcount: A:0.22, C:0.05, G:0.23, T:0.50
Consensus pattern (28 bp):
GTTTATTGTTTAGGGTTACATGTTTAGG
Found at i:5055 original size:14 final size:14
Alignment explanation
Indices: 5038--5170 Score: 60
Period size: 14 Copynumber: 9.5 Consensus size: 14
5028 CATGTTTATG
5038 GTTTAGGGTTACAT
1 GTTTAGGGTTACAT
***
5052 GTTTAGGGTTTTTT
1 GTTTAGGGTTACAT
* *
5066 ATTTAGGGTTTA-TT
1 GTTTAGGG-TTACAT
* * *
5080 GTCTAAGATTACAT
1 GTTTAGGGTTACAT
*
5094 GTTTAGGGTTTA-TT
1 GTTTAGGG-TTACAT
5108 GTTTAGGGTTTATCA-
1 GTTTAGGG-TTA-CAT
* *
5123 -CTTAAGGTTACAT
1 GTTTAGGGTTACAT
*
5136 GTTTAGGGTTTA-TT
1 GTTTAGGG-TTACAT
* *
5150 GTTTAAGATTACAT
1 GTTTAGGGTTACAT
5164 GTTTAGG
1 GTTTAGG
5171 ATTTAGGGTT
Statistics
Matches: 86, Mismatches: 24, Indels: 18
0.67 0.19 0.14
Matches are distributed among these distances:
12 2 0.02
13 9 0.10
14 67 0.78
15 8 0.09
ACGTcount: A:0.22, C:0.05, G:0.24, T:0.49
Consensus pattern (14 bp):
GTTTAGGGTTACAT
Found at i:5092 original size:42 final size:42
Alignment explanation
Indices: 5046--5154 Score: 148
Period size: 42 Copynumber: 2.6 Consensus size: 42
5036 TGGTTTAGGG
* **
5046 TTACATGTTTAGGGTTTTTTATTTAGGGTTTAT-TGTCTAAGA
1 TTACATGTTTAGGGTTTATTATTTAGGGTTTATCACT-TAAGA
* *
5088 TTACATGTTTAGGGTTTATTGTTTAGGGTTTATCACTTAAGG
1 TTACATGTTTAGGGTTTATTATTTAGGGTTTATCACTTAAGA
*
5130 TTACATGTTTAGGGTTTATTGTTTA
1 TTACATGTTTAGGGTTTATTATTTA
5155 AGATTACATG
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 60 0.98
43 1 0.02
ACGTcount: A:0.21, C:0.06, G:0.22, T:0.51
Consensus pattern (42 bp):
TTACATGTTTAGGGTTTATTATTTAGGGTTTATCACTTAAGA
Found at i:5181 original size:28 final size:28
Alignment explanation
Indices: 5124--5181 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
5114 GGTTTATCAC
* * **
5124 TTAAGGTTACATGTTTAGGGTTTATTGT
1 TTAAGATTACATGTTTAGGATTTAGGGT
5152 TTAAGATTACATGTTTAGGATTTAGGGT
1 TTAAGATTACATGTTTAGGATTTAGGGT
5180 TT
1 TT
5182 CATTTTCACT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.48
Consensus pattern (28 bp):
TTAAGATTACATGTTTAGGATTTAGGGT
Found at i:17026 original size:25 final size:24
Alignment explanation
Indices: 16972--17032 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
16962 TTGGAAAAAT
* *
16972 TAAATAGAACAATTAAGCAGATAAA
1 TAAATACAAAAATTAAGCA-ATAAA
*
16997 TAAATGCAAAAATTAAGC-ATAAGA
1 TAAATACAAAAATTAAGCAATAA-A
17021 TAAAATACAAAA
1 T-AAATACAAAA
17033 TATGATAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 4 0.13
24 2 0.07
25 24 0.80
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.20
Consensus pattern (24 bp):
TAAATACAAAAATTAAGCAATAAA
Found at i:17260 original size:30 final size:29
Alignment explanation
Indices: 17197--17540 Score: 113
Period size: 29 Copynumber: 11.7 Consensus size: 29
17187 TTTGGGGGTA
* ** * *
17197 AAAATATGGTTTTGAAAAAGTTTAGGTTC
1 AAAATGTGGTTTTGGGAAAGTTAAGGATC
17226 AAAATGTGGTTTTGGGAAAGTGTAAGGATC
1 AAAATGTGGTTTTGGGAAAGT-TAAGGATC
*** * * * *
17256 AAAATGAAATTTTAGAAAAATTTAGGCATC
1 AAAATGTGGTTTTGGGAAAGTTAAGG-ATC
* *
17286 AAAATGTGATTTTGGGAAAGTTTAGAGG-TT
1 AAAATGTGGTTTTGGGAAAG-TTA-AGGATC
* ** * *
17316 AAAATGTAGTTTTGGGAAAGTTTGGGGTT
1 AAAATGTGGTTTTGGGAAAGTTAAGGATC
* * * * *
17345 AAACTGTGATTTTGGGAAAGGTAGGGGTC
1 AAAATGTGGTTTTGGGAAAGTTAAGGATC
** ** * *
17374 AAAAAATAATTTTGGAAAAGCTTAAGGTTC
1 AAAATGTGGTTTTGGGAAAG-TTAAGGATC
** * *
17404 AAAATGTAATTTTGGAAAAGATCAAGG-T-
1 AAAATGTGGTTTTGGGAAAG-TTAAGGATC
* * * * * *
17432 TAAATGTGATTTTTGGAAAAGTTCGAGGGTA
1 AAAATGTG-GTTTTGGGAAAGTT-AAGGATC
** *
17463 AAAATGTAATTTTTGGGAAAGTTTAAGG-TT
1 AAAATGT-GGTTTTGGGAAAG-TTAAGGATC
** * *
17493 AAAATGTAATTTTAGGAAAGTTTAA-GATT
1 AAAATGTGGTTTTGGGAAAG-TTAAGGATC
**
17522 AAAATGTAATTTTGGGAAA
1 AAAATGTGGTTTTGGGAAA
17541 CTTTGAGGGT
Statistics
Matches: 248, Mismatches: 54, Indels: 26
0.76 0.16 0.08
Matches are distributed among these distances:
28 10 0.04
29 115 0.46
30 96 0.39
31 22 0.09
32 5 0.02
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (29 bp):
AAAATGTGGTTTTGGGAAAGTTAAGGATC
Found at i:17572 original size:59 final size:59
Alignment explanation
Indices: 17173--17574 Score: 264
Period size: 59 Copynumber: 6.8 Consensus size: 59
17163 GGTGAAAACA
* * * * **
17173 TAATTTTGGAAAAGTTTGGGGGTAAAAATATGGTTTTGAAAAAGTTT-AGGTTCAAAATG
1 TAATTTTGGGAAAGTTTGAGGGTTAAAATGTAATTTTGAAAAAGTTTAAGGTT-AAAATG
** * * * * * *
17232 TGGTTTTGGGAAAGTGTAAGGATCAAAATGAAATTTTAGAAAAA-TTT-AGGCATCAAAATG
1 TAATTTTGGGAAAGTTTGAGGGTTAAAATGTAATTTT-GAAAAAGTTTAAGG--TTAAAATG
* * ** ** *
17292 TGATTTTGGGAAAGTTT-AGAGGTTAAAATGTAGTTTTGGGAAAGTTTGGGGTTAAACTG
1 TAATTTTGGGAAAGTTTGAG-GGTTAAAATGTAATTTTGAAAAAGTTTAAGGTTAAAATG
* * * * ** * *
17351 TGATTTTGGGAAAGGTAG-GGGTCAAAAAATAATTTTGGAAAAGCTTAAGGTTCAAAATG
1 TAATTTTGGGAAAGTTTGAGGGTTAAAATGTAATTTTGAAAAAGTTTAAGGTT-AAAATG
* * * * * * * * *
17410 TAATTTTGGAAAAG-ATCAAGGTT-AAATGTGATTTTTGGAAAAGTTCGAGGGTAAAAATG
1 TAATTTTGGGAAAGTTTGAGGGTTAAAATGT-AATTTTGAAAAAGTT-TAAGGTTAAAATG
* * *
17469 TAATTTTTGGGAAAGTTT-AAGGTTAAAATGTAATTTT-AGGAAAGTTTAAGATTAAAATG
1 TAA-TTTTGGGAAAGTTTGAGGGTTAAAATGTAATTTTGA-AAAAGTTTAAGGTTAAAATG
* *
17528 TAATTTTGGGAAACTTTGAGGGTTAAAATGTGATTTTGAAAAAGTTT
1 TAATTTTGGGAAAGTTTGAGGGTTAAAATGTAATTTTGAAAAAGTTT
17575 GAGGATTGAT
Statistics
Matches: 264, Mismatches: 62, Indels: 34
0.73 0.17 0.09
Matches are distributed among these distances:
58 42 0.16
59 137 0.52
60 75 0.28
61 10 0.04
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (59 bp):
TAATTTTGGGAAAGTTTGAGGGTTAAAATGTAATTTTGAAAAAGTTTAAGGTTAAAATG
Found at i:17578 original size:30 final size:29
Alignment explanation
Indices: 17173--17574 Score: 263
Period size: 30 Copynumber: 13.6 Consensus size: 29
17163 GGTGAAAACA
* * *
17173 TAATTTTGGAAAAGTTTGGGGGTAAAAATA
1 TAATTTTGGAAAAGTTT-AGGGTTAAAATG
** *
17203 TGGTTTTGAAAAAGTTTA-GGTTCAAAATG
1 TAATTTTGGAAAAGTTTAGGGTT-AAAATG
** * * * *
17232 TGGTTTTGGGAAAGTGTAAGGATCAAAATG
1 TAATTTTGGAAAAGT-TTAGGGTTAAAATG
* * * * *
17262 AAATTTTAGAAAAATTTAGGCATCAAAATG
1 TAATTTTGGAAAAGTTTAGG-GTTAAAATG
* *
17292 TGATTTTGGGAAAGTTTAGAGGTTAAAATG
1 TAATTTTGGAAAAGTTTAG-GGTTAAAATG
* * * *
17322 TAGTTTTGGGAAAGTTTGGGGTTAAACTG
1 TAATTTTGGAAAAGTTTAGGGTTAAAATG
* * * * **
17351 TGATTTTGGGAAAG-GTAGGGGTCAAAAAA
1 TAATTTTGGAAAAGTTTA-GGGTTAAAATG
* *
17380 TAATTTTGGAAAAGCTTAAGGTTCAAAATG
1 TAATTTTGGAAAAGTTTAGGGTT-AAAATG
* * *
17410 TAATTTTGGAAAAGATCAAGGTT-AAATG
1 TAATTTTGGAAAAGTTTAGGGTTAAAATG
* * *
17438 TGATTTTTGGAAAAGTTCGAGGGTAAAAATG
1 T-AATTTTGGAAAAGTT-TAGGGTTAAAATG
* *
17469 TAATTTTTGGGAAAGTTTAAGGTTAAAATG
1 TAA-TTTTGGAAAAGTTTAGGGTTAAAATG
* *
17499 TAATTTTAGG-AAAGTTTAAGATTAAAATG
1 TAATTTT-GGAAAAGTTTAGGGTTAAAATG
* *
17528 TAATTTTGGGAAACTTTGAGGGTTAAAATG
1 TAATTTTGGAAAAGTTT-AGGGTTAAAATG
* *
17558 TGATTTTGAAAAAGTTT
1 TAATTTTGGAAAAGTTT
17575 GAGGATTGAT
Statistics
Matches: 293, Mismatches: 64, Indels: 30
0.76 0.17 0.08
Matches are distributed among these distances:
28 12 0.04
29 113 0.39
30 147 0.50
31 21 0.07
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (29 bp):
TAATTTTGGAAAAGTTTAGGGTTAAAATG
Found at i:17601 original size:22 final size:23
Alignment explanation
Indices: 17558--17601 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
17548 GGTTAAAATG
17558 TGATTTTGAAAAAGTTTGAGGAT
1 TGATTTTGAAAAAGTTTGAGGAT
17581 TGATTTTGAAAAAGTTT-AGGA
1 TGATTTTGAAAAAGTTTGAGGA
17602 GTAAAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (23 bp):
TGATTTTGAAAAAGTTTGAGGAT
Found at i:19546 original size:58 final size:58
Alignment explanation
Indices: 19377--20513 Score: 384
Period size: 57 Copynumber: 20.1 Consensus size: 58
19367 AAATTATCTC
** * ** *
19377 ATAAAAAAAGTAATGTCGGTCAAGCATT-TACAACACCAAAAA-AAATAATTTTTATCTA-
1 ATAAAAAAAGTGGTGTCGGCCAAGCATTGGCCAACACCAAAAATATAT-A-TTTTATC-AG
* * * ** * * *
19435 ATAAAAACAA-TGGTGTTGGCCAATACA-TGGCTAACACCAAATTTTTTTTTTTTATCAG
1 ATAAAAA-AAGTGGTGTCGGCCAA-GCATTGGCCAACACCAAAAATATATATTTTATCAG
* * *
19493 GTAAAAAAAGTGATGTCGGCTAAGCATTGGCCAACACCAAAAATATATATTTTATCTA-
1 ATAAAAAAAGTGGTGTCGGCCAAGCATTGGCCAACACCAAAAATATATATTTTATC-AG
* * * * * * * *
19551 AT-AAAAAGGTGTTATCGGCTAAGCATTGACTAATA-TAAAAA-A-A-A-TTTAT-ATG
1 ATAAAAAAAGTGGTGTCGGCCAAGCATTGGCCAACACCAAAAATATATATTTTATCA-G
* * *
19603 AT-AAAAAAGATGGTGTCGACCAAGCATTTGCCAACA-CAAAAAAATA-ATTTTTATCTA-
1 ATAAAAAAAG-TGGTGTCGGCCAAGCATTGGCCAACACCAAAAATATATA-TTTTATC-AG
* * ** * * * * *
19660 AT-AAAAAAGTAGTGTCGGTCAATGCA-TGGCCAGTAACAAAATTTTATTTTTTTATCAA
1 ATAAAAAAAGTGGTGTCGGCCAA-GCATTGGCCAACACCAAAAATATA-TATTTTATCAG
* ** * *
19718 ATAAAAAAGGTGGT-TCGGCCAAGCATTGATCAACACCAAAAAAATATTTTTTATCAG
1 ATAAAAAAAGTGGTGTCGGCCAAGCATTGGCCAACACCAAAAATATATATTTTATCAG
* * * ** * * * * *
19775 ATAAAAATTA-TGATGCCGGCCAATGCA-TGATCAACACTAAAAAATTTGTTTTTTTTTTATCAA
1 ATAAAAA-AAGTGGTGTCGGCCAA-GCATTGGCCAACAC-CAAAAA----TATATATTTTATCAG
** * * * * *
19838 ATAAAAATGGTGGTGTCAGCCAAGCATTGGTCAACACAAAAAAAATAT-TTTTATCTG
1 ATAAAAAAAGTGGTGTCGGCCAAGCATTGGCCAACACCAAAAATATATATTTTATCAG
* * * * * * *
19895 ATAAAAAAGGTGGTGTTGGCCAATGTA-TGGCCAACACTAAAAAATTTTGTTTTTTTATCAG
1 ATAAAAAAAGTGGTGTCGGCCAA-GCATTGGCCAACAC-CAAAAA-TAT-ATATTTTATCAG
*** *
19956 AT-AAAAAAGTGGTGTCGATTAAGCATTGGCCAACACCAAAAAAATATATTTTATC--
1 ATAAAAAAAGTGGTGTCGGCCAAGCATTGGCCAACACCAAAAATATATATTTTATCAG
* * ** *
20011 -TAAGAAAAAGTTGGTGTCGACCAAGAATTAACCAACACCAAAAATAT-T-TTTTGT--G
1 ATAA-AAAAAG-TGGTGTCGGCCAAGCATTGGCCAACACCAAAAATATATATTTTATCAG
* ** *
20066 AT-AAAAAAGATAGTGTCGGCCAAGCATTGATCAACACCCAAAAA-ATAT-TTTTATCTG
1 ATAAAAAAAG-TGGTGTCGGCCAAGCATTGGCCAACA-CCAAAAATATATATTTTATCAG
* * * * * * *
20123 ATACAACAAGTGGTGTCGGTC-A--A-TGGTCAACA-CAAAAA-A-AAATTTAATTAG
1 ATAAAAAAAGTGGTGTCGGCCAAGCATTGGCCAACACCAAAAATATATATTTTATCAG
* * * *
20174 ATAAAAAAAGTGGTGTCGGTCAAGCATTGACCAATACCAAAAA-ATATTTTTTATCAG
1 ATAAAAAAAGTGGTGTCGGCCAAGCATTGGCCAACACCAAAAATATATATTTTATCAG
* * * *
20231 ATAAAAAAAG-AG-GT----CAATGCA-TGGCCAACA-CTAAAAT-TTTTTTTTATCAG
1 ATAAAAAAAGTGGTGTCGGCCAA-GCATTGGCCAACACCAAAAATATATATTTTATCAG
** ** ** * * * **
20281 ATAAAATGA-TGGTGTCGGCCAAAAATTGGTAAACACAAAAAAAATATTTTTTATCTT
1 ATAAAAAAAGTGGTGTCGGCCAAGCATTGGCCAACACCAAAAATATATATTTTATCAG
* ** * * * * *
20338 AT-AATATGGTGCTGTCAGCCAATGCA-TGACCAACACC-AAAAT-T-TTTTTTATCTG
1 ATAAAAAAAGTGGTGTCGGCCAA-GCATTGGCCAACACCAAAAATATATATTTTATCAG
* * * * * * * * *
20392 AT-AAAATAGTTAGTGTCGACTAAGAATTGACCAACATCAAAAAAAATATTTTTTATCAG
1 ATAAAAAAAG-TGGTGTCGGCCAAGCATTGGCCAACA-CCAAAAATATATATTTTATCAG
* * * * * *
20451 AT-AAAAAAGATGGTGTCGGCTAATGCA-TGGTCAATACC-ATAAT-TTTTTTTTATCAG
1 ATAAAAAAAG-TGGTGTCGGCCAA-GCATTGGCCAACACCAAAAATATATATTTTATCAG
20507 ATAAAAA
1 ATAAAAA
20514 TGGTGGCCAA
Statistics
Matches: 810, Mismatches: 191, Indels: 157
0.70 0.16 0.14
Matches are distributed among these distances:
50 27 0.03
51 44 0.05
52 17 0.02
53 32 0.04
54 54 0.07
55 59 0.07
56 63 0.08
57 225 0.28
58 128 0.16
59 75 0.09
60 29 0.04
61 10 0.01
62 10 0.01
63 37 0.05
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (58 bp):
ATAAAAAAAGTGGTGTCGGCCAAGCATTGGCCAACACCAAAAATATATATTTTATCAG
Found at i:19878 original size:120 final size:117
Alignment explanation
Indices: 19603--20479 Score: 459
Period size: 120 Copynumber: 7.7 Consensus size: 117
19593 AATTTATATG
* * *
19603 ATAAAAAAGATGGTGTCGACCAAGCATTTGCCAACA-CAAAAAAATAATTTTTATCTA-ATAAAA
1 ATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACCAAAAAAATATTTTTTATC-AGATAAAA
* * *
19666 AAGTA-GTGTCGGTCAATGCATGGC--CAGTAACAAAATTTTATTTTTTTATCAA
65 AA-TATGTGTCGGCCAATGCATGCCAACACTAA-AAAATTTTATTTTTTTATCAA
* **
19718 ATAAAAAAGGTGGT-TCGGCCAAGCATTGATCAACACCAAAAAAATATTTTTTATCAGATAAAAA
1 ATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACCAAAAAAATATTTTTTATCAGATAAAAA
* * * *
19782 TTATGATGCCGGCCAATGCATGATCAACACTAAAAAATTTGTTTTTTTTTTATCAA
66 ATATG-TGTCGGCCAATGCATG-CCAACACTAAAAAA-TT-TTATTTTTTTATCAA
* * * *
19838 ATAAAAATGGTGGTGTC-AGCCAAGCATTGGTCAACACAAAAAAAATA-TTTTTATCTGATAAAA
1 ATAAAAAAGGTGGTGTCGA-CCAAGCATTGGCCAACACCAAAAAAATATTTTTTATCAGATAAAA
** * * * *
19901 AAGGTGGTGTTGGCCAATGTATGGCCAACACTAAAAAATTTTGTTTTTTTATCAG
65 AATAT-GTGTCGGCCAATGCAT-GCCAACACTAAAAAATTTTATTTTTTTATCAA
** * *
19956 ATAAAAAA-GTGGTGTCGATTAAGCATTGGCCAACACCAAAAAAATATATTTTATCTA-AGAAAA
1 ATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACCAAAAAAATATTTTTTATC-AGATAAAA
* * * * * * *
20019 AGT-TGGTGTCGACCAA-GAATTAACCAACAC-CAAAAA---TA-TTTTTTGT--G
65 AATAT-GTGTCGGCCAATGCA-T-GCCAACACTAAAAAATTTTATTTTTTTATCAA
* * * ** * *
20066 ATAAAAAAGATAGTGTCGGCCAAGCATTGATCAACACCCAAAAAATA-TTTTTATCTGATACAAC
1 ATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACCAAAAAAATATTTTTTATCAGATA-AA-
* * * * ** * * *
20130 AAGT-GGTGTCGGTCAATG---GTCAACAC-AAAAAA----A-AATTTAATTAG
64 AAATATGTGTCGGCCAATGCATGCCAACACTAAAAAATTTTATTTTTTTATCAA
* ** * *
20174 ATAAAAAAAGTGGTGTCGGTCAAGCATTGACCAATACC-AAAAAATATTTTTTATCAGATAAAAA
1 ATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACCAAAAAAATATTTTTTATCAGATAAAAA
* * *
20238 A-A---G-AGGTCAATGCATGGCCAACACT--AAAA--TT-TTTTTTTATCAG
66 ATATGTGTCGGCCAATGCAT-GCCAACACTAAAAAATTTTATTTTTTTATCAA
* * * ** ** * * * *
20281 AT-AAAATGATGGTGTCGGCCAAAAATTGGTAAACACAAAAAAAATATTTTTTATC--TTATAAT
1 ATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACCAAAAAAATATTTTTTATCAGATAAAAA
* * * **
20343 ATGGTGCTGTCAGCCAATGCATGACCAACAC--CAAAA---T-TTTTTTTATCTG
66 AT-ATG-TGTCGGCCAATGCATG-CCAACACTAAAAAATTTTATTTTTTTATCAA
* * * * * * *
20392 ATAAAATAGTTAGTGTCGACTAAGAATTGACCAACATCAAAAAAAATATTTTTTATCAGATAAAA
1 ATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACA-CCAAAAAAATATTTTTTATCAGATAAAA
* *
20457 AAGATGGTGTCGGCTAATGCATG
65 AATAT-GTGTCGGCCAATGCATG
20480 GTCAATACCA
Statistics
Matches: 598, Mismatches: 115, Indels: 99
0.74 0.14 0.12
Matches are distributed among these distances:
102 8 0.01
103 1 0.00
105 9 0.02
106 38 0.06
107 47 0.08
108 45 0.08
110 18 0.03
111 57 0.10
112 55 0.09
113 21 0.04
114 35 0.06
115 45 0.08
116 21 0.04
117 52 0.09
118 38 0.06
119 9 0.02
120 69 0.12
121 30 0.05
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (117 bp):
ATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACCAAAAAAATATTTTTTATCAGATAAAAA
ATATGTGTCGGCCAATGCATGCCAACACTAAAAAATTTTATTTTTTTATCAA
Found at i:20246 original size:51 final size:50
Alignment explanation
Indices: 20191--20286 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
20181 AAGTGGTGTC
*
20191 GGTCAA-GCATTGACCAATACCAAAAAATATTTTTTATCAGATAAAAAAAGA
1 GGTCAATGCA-TGACCAACA-CAAAAAATATTTTTTATCAGATAAAAAAAGA
* * * *
20242 GGTCAATGCATGGCCAACACTAAAATTTTTTTTTATCAGATAAAA
1 GGTCAATGCATGACCAACACAAAAAATATTTTTTATCAGATAAAA
20287 TGATGGTGTC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
50 23 0.59
51 13 0.33
52 3 0.08
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (50 bp):
GGTCAATGCATGACCAACACAAAAAATATTTTTTATCAGATAAAAAAAGA
Found at i:20383 original size:112 final size:115
Alignment explanation
Indices: 20212--20512 Score: 318
Period size: 112 Copynumber: 2.7 Consensus size: 115
20202 GACCAATACC
*
20212 AAAAAATATTTTTTATCAGATAAAAAAAGA-G--GT----CAATGCATGGCCAACACTAAAATTT
1 AAAAAATATTTTTTATCAGAT-AAAAAAGATGCTGTCAGCCAATGCATGGCCAACACCAAAATTT
* * **
20270 TTTTTTATCAGATAAAAT-GATGGTGTCGGCCAAAAATTGGTAAACA-CAA
65 TTTTTTATCAGATAAAATAGATAGTGTCGACCAAAAATTGACAAACATCAA
** * * * *
20319 AAAAAATATTTTTTATCTTAT-AATATGGTGCTGTCAGCCAATGCATGACCAACACCAAAA-TTT
1 AAAAAATATTTTTTATCAGATAAAAAAGATGCTGTCAGCCAATGCATGGCCAACACCAAAATTTT
* * * * *
20382 TTTTTATCTGATAAAATAGTTAGTGTCGACTAAGAATTGACCAACATCAA
66 TTTTTATCAGATAAAATAGATAGTGTCGACCAAAAATTGACAAACATCAA
* * * * * *
20432 AAAAAATATTTTTTATCAGATAAAAAAGATGGTGTCGGCTAATGCATGGTCAATACCATAATTTT
1 AAAAAATATTTTTTATCAGATAAAAAAGATGCTGTCAGCCAATGCATGGCCAACACCAAAATTTT
20497 TTTTTATCAGATAAAA
66 TTTTTATCAGATAAAA
20513 ATGGTGGCCA
Statistics
Matches: 154, Mismatches: 29, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
105 4 0.03
106 1 0.01
107 19 0.12
108 2 0.01
111 19 0.12
112 40 0.26
113 22 0.14
114 29 0.19
115 18 0.12
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.33
Consensus pattern (115 bp):
AAAAAATATTTTTTATCAGATAAAAAAGATGCTGTCAGCCAATGCATGGCCAACACCAAAATTTT
TTTTTATCAGATAAAATAGATAGTGTCGACCAAAAATTGACAAACATCAA
Found at i:20552 original size:41 final size:40
Alignment explanation
Indices: 20496--20593 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 40
20486 ACCATAATTT
* *
20496 TTTTTTATCAGATAAAAATGGTGGCCAACACCAAAAAAATA
1 TTTTTTATCTGATAAAAAAGGTGGCCAACACC-AAAAAATA
* *
20537 TTTTTTATCTGATAAAAAAGGTGGTCGACACCAAAAAATA
1 TTTTTTATCTGATAAAAAAGGTGGCCAACACCAAAAAATA
20577 TATTTTTATCTGATAAA
1 T-TTTTTATCTGATAAA
20594 TTTTTTTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 9 0.17
41 43 0.83
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (40 bp):
TTTTTTATCTGATAAAAAAGGTGGCCAACACCAAAAAATA
Found at i:20705 original size:58 final size:57
Alignment explanation
Indices: 20643--21407 Score: 329
Period size: 58 Copynumber: 13.5 Consensus size: 57
20633 CATTGACCTA
** * * *
20643 CAAAAAAAATATTTTTTATTTGATACAAAGGTGGTGTCGGTCAATGCATGATCAACAC
1 CAAAAAAAATATTTTTTATCAGATAAAAAGGTGGTGTCGGCCAA-GCATGACCAACAC
* * *
20701 C---AAAAAT-TTTTTTATCTGATAAAAAAGTTGGTGT-GGACGAA--A--ACCAA-A-
1 CAAAAAAAATATTTTTTATCAGAT-AAAAAGGTGGTGTCGG-CCAAGCATGACCAACAC
* * * * ** *
20749 -AAAAAAAA-A----TTATCAGATAAAAACGTGGTGTCGGCTAATACATGGCTGATAC
1 CAAAAAAAATATTTTTTATCAGATAAAAAGGTGGTGTCGGCCAA-GCATGACCAACAC
* * * * *
20801 C-AAAAAATTATATTTTATCAGATAAAAAAGGTGGTGTTGGCCAAGCATTAGTCAACAC
1 CAAAAAAAATATTTTTTATCAGAT-AAAAAGGTGGTGTCGGCCAAGCATGA-CCAACAC
** * ** * * *
20859 C-AAAAAAATATTTTTTATTTGATAAAAAAGATGGTGTCGATCAAGTATTGGCCAATAC
1 CAAAAAAAATATTTTTTATCAGAT-AAAAAGGTGGTGTCGGCCAAGCA-TGACCAACAC
* * * *
20917 CAAAAAAAATATTTTTTATCTGATAAAAAAGTGGTGTCGACCAATGCAT-AGCCAATA-
1 CAAAAAAAATATTTTTTATCAGATAAAAAGGTGGTGTCGGCCAA-GCATGA-CCAACAC
* * * * * * *
20974 TAAAAAAATTTGTTTTTTATTAGATAAAAAAGGTGTTGTCGACCAAGCATTAGCCAACA-
1 CAAAAAAA-ATATTTTTTATCAGAT-AAAAAGGTGGTGTCGGCCAAGCATGA-CCAACAC
* ** ***
21033 C-AAAAAAATATTTTTTATCAGATAAAAAAGTGGTGTCGGTGAATGCATG-GGGA-A-
1 CAAAAAAAATATTTTTTATCAGATAAAAAGGTGGTGTCGGCCAA-GCATGACCAACAC
** * * * **
21087 CATTAAAATTTTTTTTTATCAGATAAAAGTGGTGGTGTCGAG-CAAGCATTGGTCAACAC
1 CAAAAAAAATATTTTTTATCAGATAAAA-AGGTGGTGTCG-GCCAAGCA-TGACCAACAC
* * * * *
21146 C-AAAAAAATA-TTTTTATCTGATAAAAAGGTGTTGTCGACCAATGCATG-GCATA-AT
1 CAAAAAAAATATTTTTTATCAGATAAAAAGGTGGTGTCGGCCAA-GCATGACCA-ACAC
* * * * * *
21201 TAAAAAAATTTAATTTTTTATCAGATAAAAATAGTGGTGTCGACCAAGCATTAGCCAAAAC
1 CAAAAAAA-AT-ATTTTTTATCAGATAAAAA-GGTGGTGTCGGCCAAGCATGA-CCAACAC
* * * * * **
21262 CAAAAAAAAATATTTTTTATTAGATAAAAAAGTGGTGTCAGCTAATGAATGGTCAACAC
1 C-AAAAAAAATATTTTTTATCAGATAAAAAGGTGGTGTCGGCCAA-GCATGACCAACAC
* * * * * ***
21321 TAAAAAAAAATATTTTTTTATTAGATAAAGAAGGTGATGTTGGCAAAGCATTG-GGTA-A-
1 -CAAAAAAAATA-TTTTTTATCAGATAAA-AAGGTGGTGTCGGCCAAGCA-TGACCAACAC
21379 CAAAAAAAATATTTTTTATCAGATAAAAA
1 CAAAAAAAATATTTTTTATCAGATAAAAA
21408 AAAATGGTGT
Statistics
Matches: 538, Mismatches: 115, Indels: 111
0.70 0.15 0.15
Matches are distributed among these distances:
45 14 0.03
46 10 0.02
48 1 0.00
49 1 0.00
50 11 0.02
51 1 0.00
52 7 0.01
53 1 0.00
54 16 0.03
55 50 0.09
56 64 0.12
57 67 0.12
58 118 0.22
59 98 0.18
60 54 0.10
61 18 0.03
62 7 0.01
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (57 bp):
CAAAAAAAATATTTTTTATCAGATAAAAAGGTGGTGTCGGCCAAGCATGACCAACAC
Found at i:20923 original size:59 final size:58
Alignment explanation
Indices: 20797--21408 Score: 400
Period size: 58 Copynumber: 10.6 Consensus size: 58
20787 TACATGGCTG
* * * * *
20797 ATACC-AAAAAATTATATTTTATCAGATAAAAAAGGTGGTGTTGGCCAAGCATTAGTCA
1 ATACCAAAAAAAATATTTTTTATCAGATAAAAAA-GTGGTGTCGACCAAGCATTAGCCA
* ** * * *
20855 ACACC-AAAAAAATATTTTTTATTTGATAAAAAAGATGGTGTCGATCAAGTATTGGCCA
1 ATACCAAAAAAAATATTTTTTATCAGATAAAAAAG-TGGTGTCGACCAAGCATTAGCCA
*
20913 ATACCAAAAAAAATATTTTTTATCTGATAAAAAAGTGGTGTCGACCAATGCA-TAGCCA
1 ATACCAAAAAAAATATTTTTTATCAGATAAAAAAGTGGTGTCGACCAA-GCATTAGCCA
* * * * *
20971 ATA-TAAAAAAATTTGTTTTTTATTAGATAAAAAAGGTGTTGTCGACCAAGCATTAGCCA
1 ATACCAAAAAAA-ATATTTTTTATCAGATAAAAAA-GTGGTGTCGACCAAGCATTAGCCA
* *** ***
21030 ACA-C-AAAAAAATATTTTTTATCAGATAAAAAAGTGGTGTCGGTGAATGCA-T-GGGG
1 ATACCAAAAAAAATATTTTTTATCAGATAAAAAAGTGGTGTCGACCAA-GCATTAGCCA
** * * ** * * *
21085 A-A-CATTAAAATTTTTTTTTATCAGATAAAAGTGGTGGTGTCGAGCAAGCATTGGTCA
1 ATACCAAAAAAAATATTTTTTATCAGATAAAA-AAGTGGTGTCGACCAAGCATTAGCCA
* * * * * *
21142 ACACC-AAAAAAATA-TTTTTATCTGATAAAAAGGTGTTGTCGACCAATGCA-TGGCATA
1 ATACCAAAAAAAATATTTTTTATCAGATAAAAAAGTGGTGTCGACCAA-GCATTAGC-CA
**
21199 ATTA--AAAAAATTTAATTTTTTATCAGATAAAAATAGTGGTGTCGACCAAGCATTAGCCA
1 A-TACCAAAAAAAAT-ATTTTTTATCAGATAAAAA-AGTGGTGTCGACCAAGCATTAGCCA
* * * * * *
21258 AAACCAAAAAAAAATATTTTTTATTAGATAAAAAAGTGGTGTC-AGCTAATG-AATGGTCA
1 ATACC-AAAAAAAATATTTTTTATCAGATAAAAAAGTGGTGTCGA-CCAA-GCATTAGCCA
* * * * * * * * *
21317 ACACTAAAAAAAAATATTTTTTTATTAGATAAAGAAGGTGATGTTGGCAAAGCATT-G--G
1 ATAC-CAAAAAAAATA-TTTTTTATCAGATAAA-AAAGTGGTGTCGACCAAGCATTAGCCA
* *
21375 GTAACAAAAAAAATATTTTTTATCAGATAAAAAA
1 ATACCAAAAAAAATATTTTTTATCAGATAAAAAA
21409 AAATGGTGTC
Statistics
Matches: 436, Mismatches: 87, Indels: 65
0.74 0.15 0.11
Matches are distributed among these distances:
54 2 0.00
55 29 0.07
56 54 0.12
57 68 0.16
58 107 0.25
59 103 0.24
60 53 0.12
61 20 0.05
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (58 bp):
ATACCAAAAAAAATATTTTTTATCAGATAAAAAAGTGGTGTCGACCAAGCATTAGCCA
Found at i:20945 original size:116 final size:115
Alignment explanation
Indices: 20799--21408 Score: 528
Period size: 116 Copynumber: 5.3 Consensus size: 115
20789 CATGGCTGAT
* * * * * * *
20799 ACCAAAAAATTATATTTTATCAGATAAAAAAGGTGGTGTTGGCCAA-GCATTAGTCAACACCAAA
1 ACCAAAAAAATATTTTTTATCTGATAAAAAA-GTGGTGTCGACCAATGCA-TAGGCAACA-TAAA
** * * * * *
20863 AAAA-TATTTTTTATTTGATAAAAAAGATGGTGTCGATCAAGTATTGGCCAAT
63 AAAATTATTTTTTATCAGATAAAAAAGGTGGTGTCGACCAAGCATTAGCCAAC
* *
20915 ACCAAAAAAAATATTTTTTATCTGATAAAAAAGTGGTGTCGACCAATGCATAGCCAATATAAAAA
1 ACC-AAAAAAATATTTTTTATCTGATAAAAAAGTGGTGTCGACCAATGCATAGGCAACATAAAAA
* * *
20980 AATTTGTTTTTTATTAGATAAAAAAGGTGTTGTCGACCAAGCATTAGCCAAC
65 AA-TTATTTTTTATCAGATAAAAAAGGTGGTGTCGACCAAGCATTAGCCAAC
* *** * * *
21032 A-CAAAAAAATATTTTTTATCAGATAAAAAAGTGGTGTCGGTGAATGCATGGGGAACAT--TAAA
1 ACCAAAAAAATATTTTTTATCTGATAAAAAAGTGGTGTCGACCAATGCATAGGCAACATAAAAAA
* ** * * *
21094 ATTTTTTTTTATCAGATAAAAGTGGTGGTGTCGAGCAAGCATTGGTCAAC
66 ATTATTTTTTATCAGATAAAAAAGGTGGTGTCGACCAAGCATTAGCCAAC
* *
21144 ACCAAAAAAATA-TTTTTATCTGATAAAAAGGTGTTGTCGACCAATGCAT-GGCATA-ATTAAAA
1 ACCAAAAAAATATTTTTTATCTGATAAAAAAGTGGTGTCGACCAATGCATAGGCA-ACA-TAAAA
*
21206 AAATTTAATTTTTTATCAGATAAAAATA-GTGGTGTCGACCAAGCATTAGCCAAA
64 AAA-TT-ATTTTTTATCAGATAAAAA-AGGTGGTGTCGACCAAGCATTAGCCAAC
* *
21260 ACCAAAAAAAAATATTTTTTAT-TAGATAAAAAAGTGGTGTC-AGCTAATGAAT-GGTCAACACT
1 ACC--AAAAAAATATTTTTTATCT-GATAAAAAAGTGGTGTCGA-CCAATGCATAGG-CAACA-T
* * * * * * * * **
21322 AAAAAAAAATATTTTTTTATTAGATAAAGAAGGTGATGTTGGCAAAGCATTGGGTAAC
60 -AAAAAAATTA-TTTTTTATCAGATAAAAAAGGTGGTGTCGACCAAGCATTAGCCAAC
*
21380 A--AAAAAAATATTTTTTATCAGATAAAAAA
1 ACCAAAAAAATATTTTTTATCTGATAAAAAA
21409 AAATGGTGTC
Statistics
Matches: 406, Mismatches: 65, Indels: 46
0.79 0.13 0.09
Matches are distributed among these distances:
111 4 0.01
112 75 0.18
113 14 0.03
114 4 0.01
115 57 0.14
116 91 0.22
117 69 0.17
118 11 0.03
119 34 0.08
120 40 0.10
121 7 0.02
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (115 bp):
ACCAAAAAAATATTTTTTATCTGATAAAAAAGTGGTGTCGACCAATGCATAGGCAACATAAAAAA
ATTATTTTTTATCAGATAAAAAAGGTGGTGTCGACCAAGCATTAGCCAAC
Found at i:21169 original size:112 final size:113
Alignment explanation
Indices: 20867--21300 Score: 466
Period size: 112 Copynumber: 3.8 Consensus size: 113
20857 ACCAAAAAAA
** * * * * * *
20867 TATTTTTTATTTGATAAAAAAGATGGTGTCGATCAAGTATTGGCCAATACCAAAAAAAATATTTT
1 TATTTTTTATCAGATAAAAATGGTGGTGTCGACCAAGCATTAGCCAACACCAAAAAAAATATTTT
* *
20932 TTATCTGATAAAAAAGTGGTGTCGACCAATGCATAGCCAATATAAAAAAATT
66 TTATCTGATAAAAAAGTGGTGTCGACCAATGCAT-GGCAA-AT--TAAAATT
* * * *
20984 TGTTTTTTATTAGATAAAAAAGGTGTTGTCGACCAAGCATTAGCCAACA-C-AAAAAAATATTTT
1 TATTTTTTATCAGATAAAAATGGTGGTGTCGACCAAGCATTAGCCAACACCAAAAAAAATATTTT
* *** *
21047 TTATCAGATAAAAAAGTGGTGTCGGTGAATGCATGGGGAACATTAAAATT
66 TTATCTGATAAAAAAGTGGTGTCGACCAATGCAT-GGCAA-ATTAAAATT
* * * *
21097 T-TTTTTTATCAGATAAAAGTGGTGGTGTCGAGCAAGCATTGGTCAACACC-AAAAAAATA-TTT
1 TATTTTTTATCAGATAAAAATGGTGGTGTCGACCAAGCATTAGCCAACACCAAAAAAAATATTTT
* *
21159 TTATCTGATAAAAAGGTGTTGTCGACCAATGCATGGCATAATTAAAAAAATT
66 TTATCTGATAAAAAAGTGGTGTCGACCAATGCATGGCA-AATT---AAAATT
* *
21211 TAATTTTTTATCAGATAAAAATAGTGGTGTCGACCAAGCATTAGCCAAAACCAAAAAAAAATATT
1 T-ATTTTTTATCAGATAAAAATGGTGGTGTCGACCAAGCATTAGCCAACACC-AAAAAAAATATT
21276 TTTTAT-TAGATAAAAAAGTGGTGTC
64 TTTTATCT-GATAAAAAAGTGGTGTC
21301 AGCTAATGAA
Statistics
Matches: 267, Mismatches: 39, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
111 6 0.02
112 72 0.27
113 17 0.06
114 7 0.03
115 48 0.18
116 44 0.16
117 41 0.15
118 10 0.04
119 22 0.08
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (113 bp):
TATTTTTTATCAGATAAAAATGGTGGTGTCGACCAAGCATTAGCCAACACCAAAAAAAATATTTT
TTATCTGATAAAAAAGTGGTGTCGACCAATGCATGGCAAATTAAAATT
Found at i:21386 original size:60 final size:59
Alignment explanation
Indices: 21263--21408 Score: 142
Period size: 60 Copynumber: 2.5 Consensus size: 59
21253 AGCCAAAACC
* * *
21263 AAAAAAAAATATTTTTTATTAGATAAAAAAGTGGTGTCAGCTAATGAATGGTCAACACT
1 AAAAAAAAATATTTTTTATTAGATAAAAAAGTGATGTCAGCTAAAGAATGGTCAACACA
* ** *
21322 AAAAAAAAATATTTTTTTATTAGATAAAGAAGGTGATGTTGGC-AAAGCATTGGGT--A-AC-
1 AAAAAAAAATA-TTTTTTATTAGATAAA-AAAGTGATGTCAGCTAAAG-AAT-GGTCAACACA
*
21380 -AAAAAAAATATTTTTTATCAGATAAAAAA
1 AAAAAAAAATATTTTTTATTAGATAAAAAA
21409 AAATGGTGTC
Statistics
Matches: 75, Mismatches: 8, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
55 2 0.03
56 15 0.20
57 10 0.13
59 13 0.17
60 20 0.27
61 12 0.16
62 3 0.04
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (59 bp):
AAAAAAAAATATTTTTTATTAGATAAAAAAGTGATGTCAGCTAAAGAATGGTCAACACA
Found at i:23699 original size:19 final size:19
Alignment explanation
Indices: 23669--23710 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
23659 TTTTAATTAG
23669 ATTA-AATTTATTTAAAT-
1 ATTATAATTTATTTAAATA
23686 ATTATAATTATATTTAAATA
1 ATTATAATT-TATTTAAATA
23706 ATTAT
1 ATTAT
23711 GGTTAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.18
18 4 0.18
19 9 0.41
20 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTATAATTTATTTAAATA
Found at i:25261 original size:39 final size:40
Alignment explanation
Indices: 25196--25271 Score: 136
Period size: 39 Copynumber: 1.9 Consensus size: 40
25186 ATTTAATGTC
*
25196 GATCTTATTTTTATAATTAAGTTTTAAATATGATTAAGTT
1 GATCTTATTTTTATAATTAAGTTTTAAATATAATTAAGTT
25236 GATCTTATTTTTA-AATTAAGTTTTAAATATAATTAA
1 GATCTTATTTTTATAATTAAGTTTTAAATATAATTAA
25272 ATAAATCATA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 22 0.63
40 13 0.37
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (40 bp):
GATCTTATTTTTATAATTAAGTTTTAAATATAATTAAGTT
Found at i:29235 original size:21 final size:21
Alignment explanation
Indices: 29211--29266 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
29201 GAGTCTGTTG
29211 CATCACTCTCTTAGCCTCTTC
1 CATCACTCTCTTAGCCTCTTC
*
29232 CATCACTCTCTTAGCCTTTTC
1 CATCACTCTCTTAGCCTCTTC
* *
29253 CACCACTCTTTTAG
1 CATCACTCTCTTAG
29267 TTGCTTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.16, C:0.39, G:0.05, T:0.39
Consensus pattern (21 bp):
CATCACTCTCTTAGCCTCTTC
Found at i:32089 original size:16 final size:16
Alignment explanation
Indices: 32056--32085 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32046 TGAAAGCAAT
32056 AATAAATAAACATTTA
1 AATAAATAAACATTTA
32072 AATAAATAAA-ATTT
1 AATAAATAAACATTT
32086 TAAAGTACGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAATAAACATTTA
Found at i:33337 original size:16 final size:16
Alignment explanation
Indices: 33316--33348 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
33306 CTAAGTTGGT
33316 ATCTACTGCTAAATTA
1 ATCTACTGCTAAATTA
33332 ATCTACTGCTAAATTA
1 ATCTACTGCTAAATTA
33348 A
1 A
33349 CCTGTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (16 bp):
ATCTACTGCTAAATTA
Found at i:33610 original size:82 final size:82
Alignment explanation
Indices: 33473--33624 Score: 241
Period size: 82 Copynumber: 1.9 Consensus size: 82
33463 TCATAATTTT
* * *
33473 CGTCAATTCATGGCACCCGGTGCCTAGCGGATAAACCGCAATAAGTGAGCGCAGCTCTAGCTGGA
1 CGTCAATTCATGGCACCCAGTGCCTAGCGGATAAACCGCAATAAGTGAGCCCAGCTATAGCTGGA
33538 TTAACTAATGATAATTC
66 TTAACTAATGATAATTC
* * * *
33555 CGTCAATTCCTGGCACCTAGTGCCTAGTGGATAAACCGCAATAAGTGAGCCCAGCTATAGTTGGA
1 CGTCAATTCATGGCACCCAGTGCCTAGCGGATAAACCGCAATAAGTGAGCCCAGCTATAGCTGGA
33620 TTAAC
66 TTAAC
33625 CAACGGTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 63 1.00
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (82 bp):
CGTCAATTCATGGCACCCAGTGCCTAGCGGATAAACCGCAATAAGTGAGCCCAGCTATAGCTGGA
TTAACTAATGATAATTC
Found at i:33803 original size:79 final size:78
Alignment explanation
Indices: 33668--33884 Score: 310
Period size: 79 Copynumber: 2.7 Consensus size: 78
33658 CCGACGATCC
* * * *
33668 TGGCACCTAGTGCCTAGCGAATAAATCGCAAAAGTGAGCACAGCTCTAGTTAGATTAACCAACAA
1 TGGCACCTAGTGCCTAACGAATAAA-CGTAAAAGTGAGCCCAGCTCTAGTTGGATTAACCAACAA
33733 TGTCCATCAAATCT
65 TGTCCATCAAATCT
33747 TGGCACCTAGTGCCTAAC-AGATAAACCGTAAAAGTGAGCCCAGCTCTAGTTGGATTAACCAACA
1 TGGCACCTAGTGCCTAACGA-ATAAA-CGTAAAAGTGAGCCCAGCTCTAGTTGGATTAACCAACA
33811 ATGTCCATCAAATCT
64 ATGTCCATCAAATCT
* * * * *
33826 TGACACCCAGTACCTACCGAATAAACTTCAAAAGTGAGCCCAGCTCTAGTTGGATTAAC
1 TGGCACCTAGTGCCTAACGAATAAACGT-AAAAGTGAGCCCAGCTCTAGTTGGATTAAC
33885 TAACGGTTTT
Statistics
Matches: 125, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
78 3 0.02
79 121 0.97
80 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (78 bp):
TGGCACCTAGTGCCTAACGAATAAACGTAAAAGTGAGCCCAGCTCTAGTTGGATTAACCAACAAT
GTCCATCAAATCT
Found at i:34011 original size:102 final size:102
Alignment explanation
Indices: 33829--34030 Score: 305
Period size: 102 Copynumber: 2.0 Consensus size: 102
33819 CAAATCTTGA
** * *
33829 CACCCAGTACCTACCGAATAAACTTCAAAAGTGAGCCCAGCTCTAGTTGGATTAACTAACGGTTT
1 CACCCAGTACCTACCGAATAAACAGCAAAAGTGAGCCCAGCTCTAGTTGGATTAACCAAAGGTTT
*
33894 TGCGCCCAGCCCTAGTCAGATAAACCGACGATCCTGG
66 TGCGCCCAACCCTAGTCAGATAAACCGACGATCCTGG
* * *
33931 CACCCAGTGCCTAGCGGATAAACAGCAAAAGTGAGCCCAGCTCTAGTTGGATTAACCAAAGGTTT
1 CACCCAGTACCTACCGAATAAACAGCAAAAGTGAGCCCAGCTCTAGTTGGATTAACCAAAGGTTT
* * *
33996 TGCGCCCAACGCTAGTCGGATAAACCGATGATCCT
66 TGCGCCCAACCCTAGTCAGATAAACCGACGATCCT
34031 TTAATAATTC
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
102 89 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (102 bp):
CACCCAGTACCTACCGAATAAACAGCAAAAGTGAGCCCAGCTCTAGTTGGATTAACCAAAGGTTT
TGCGCCCAACCCTAGTCAGATAAACCGACGATCCTGG
Done.