Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013244.1 Kokia drynarioides strain JFW-HI SEQ_128263, 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: 192555
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:5227 original size:25 final size:25
Alignment explanation
Indices: 5195--5247 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
5185 TGAATAATAT
5195 ATATTTAATAAAGTTACTTTATAAA
1 ATATTTAATAAAGTTACTTTATAAA
* * *
5220 ATATTTAATAGATTTATTTTATAAA
1 ATATTTAATAAAGTTACTTTATAAA
5245 ATA
1 ATA
5248 ATTGAAGTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (25 bp):
ATATTTAATAAAGTTACTTTATAAA
Found at i:5486 original size:20 final size:20
Alignment explanation
Indices: 5449--5486 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5439 TAATATTTTA
*
5449 AAATATTTATTTTGAAACTC
1 AAATATTTATATTGAAACTC
5469 AAATATATTATATT-AAAC
1 AAATAT-TTATATTGAAAC
5487 CTAAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (20 bp):
AAATATTTATATTGAAACTC
Found at i:5493 original size:21 final size:20
Alignment explanation
Indices: 5447--5493 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
5437 GTTAATATTT
*
5447 TAAAATATTTATTTTGAAAC
1 TAAAATATTTATATTGAAAC
*
5467 TCAAATATATTATATT-AAACC
1 TAAAATAT-TTATATTGAAA-C
5488 TAAAAT
1 TAAAAT
5494 TAAATGACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (20 bp):
TAAAATATTTATATTGAAAC
Found at i:7975 original size:24 final size:24
Alignment explanation
Indices: 7930--7976 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
7920 ATTTAGTAGT
*
7930 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATTGATTAGC
* *
7954 ATAATATATTTTGTATTGATTAG
1 ATAATATATTTAGCATTGATTAG
7977 AATTAGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (24 bp):
ATAATATATTTAGCATTGATTAGC
Found at i:12386 original size:24 final size:24
Alignment explanation
Indices: 12341--12387 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
12331 ATTTAGTAGT
* *
12341 ATAATTTATTTAGAATTTATTAGC
1 ATAATATATTTAGAATTGATTAGC
* *
12365 ATAATATATTTTGTATTGATTAG
1 ATAATATATTTAGAATTGATTAG
12388 AATTAGGCTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (24 bp):
ATAATATATTTAGAATTGATTAGC
Found at i:18128 original size:2 final size:2
Alignment explanation
Indices: 18121--18162 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
18111 TAACTTTCAT
*
18121 CA CA CA CA CA CA CA CA CA CA CA CA CA CA TA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
18163 TAGATACAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:20251 original size:28 final size:28
Alignment explanation
Indices: 20219--20303 Score: 68
Period size: 28 Copynumber: 3.0 Consensus size: 28
20209 ATAGCTCTAC
20219 CCGAGTTGTACATGGCATTACGCTTTAA
1 CCGAGTTGTACATGGCATTACGCTTTAA
* * * *
20247 CCGAGTCGTAAACAAAT-CCA-TA-GCTATAC
1 CCGAGTTGT--AC--ATGGCATTACGCTTTAA
*
20276 CCGAGCTGTACATGGCATTACGCTTTAA
1 CCGAGTTGTACATGGCATTACGCTTTAA
20304 TTGAGTCGTA
Statistics
Matches: 41, Mismatches: 9, Indels: 14
0.64 0.14 0.22
Matches are distributed among these distances:
25 2 0.05
26 2 0.05
27 4 0.10
28 13 0.32
29 12 0.29
30 4 0.10
31 2 0.05
32 2 0.05
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (28 bp):
CCGAGTTGTACATGGCATTACGCTTTAA
Found at i:20257 original size:57 final size:57
Alignment explanation
Indices: 20123--20451 Score: 403
Period size: 57 Copynumber: 5.8 Consensus size: 57
20113 TTCTATAGAC
* * * * *
20123 TTACGCTCTAACCGAGACGTAAACAAAT-CAAAGCTCTACCTGAGCTGTTCGTGGCA
1 TTACGCTCTAACCGAGACGTAAACAAATCCATAGCTCTACCCGAGTTGTACATGGCA
* * *
20179 TTATGCTCTAATCGAGACGTAAGCAAATCCATAGCTCTACCCGAGTTGTACATGGCA
1 TTACGCTCTAACCGAGACGTAAACAAATCCATAGCTCTACCCGAGTTGTACATGGCA
* * * *
20236 TTACGCTTTAACCGAGTCGTAAACAAATCCATAGCTATACCCGAGCTGTACATGGCA
1 TTACGCTCTAACCGAGACGTAAACAAATCCATAGCTCTACCCGAGTTGTACATGGCA
* ** * * *
20293 TTACGCTTTAATTGAGTCGTAAGCAAATCCATAGCTATACCCGAGCTT-TACATGGCA
1 TTACGCTCTAACCGAGACGTAAACAAATCCATAGCTCTACCCGAG-TTGTACATGGCA
* **
20350 TTACGCTCTAACCGAGTCGTAAGA-AAATCCATAGCTCTACTTGAGTTGTACATGGCA
1 TTACGCTCTAACCGAGACGTAA-ACAAATCCATAGCTCTACCCGAGTTGTACATGGCA
* * *
20407 TTACACTCTATCCGAGACGTAAACAAATCCATAGCTTTACCCGAG
1 TTACGCTCTAACCGAGACGTAAACAAATCCATAGCTCTACCCGAG
20452 CTGTCATTCG
Statistics
Matches: 236, Mismatches: 32, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
56 28 0.12
57 207 0.88
58 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (57 bp):
TTACGCTCTAACCGAGACGTAAACAAATCCATAGCTCTACCCGAGTTGTACATGGCA
Found at i:20322 original size:114 final size:114
Alignment explanation
Indices: 20123--20453 Score: 454
Period size: 114 Copynumber: 2.9 Consensus size: 114
20113 TTCTATAGAC
* * * * *
20123 TTACGCTCTAACCGAGACGTAAACAAAT-CAAAGCTCTACCTGAGCTGTTCGTGGCATTATGCTC
1 TTACGCTCTAACCGAGTCGTAAACAAATCCATAGCTCTACCTGAGCTGTACATGGCATTACGCTC
*
20187 TAATCGAGACGTAAGCAAATCCATAGCTCTACCCGAG-TTGTACATGGCA
66 TAATCGAGACGTAAGCAAATCCATAGCTATACCCGAGCTT-TACATGGCA
* * * *
20236 TTACGCTTTAACCGAGTCGTAAACAAATCCATAGCTATACCCGAGCTGTACATGGCATTACGCTT
1 TTACGCTCTAACCGAGTCGTAAACAAATCCATAGCTCTACCTGAGCTGTACATGGCATTACGCTC
* *
20301 TAATTGAGTCGTAAGCAAATCCATAGCTATACCCGAGCTTTACATGGCA
66 TAATCGAGACGTAAGCAAATCCATAGCTATACCCGAGCTTTACATGGCA
* * *
20350 TTACGCTCTAACCGAGTCGTAAGA-AAATCCATAGCTCTACTTGAGTTGTACATGGCATTACACT
1 TTACGCTCTAACCGAGTCGTAA-ACAAATCCATAGCTCTACCTGAGCTGTACATGGCATTACGCT
* *
20414 CT-ATCCGAGACGTAAACAAATCCATAGCTTTACCCGAGCT
65 CTAAT-CGAGACGTAAGCAAATCCATAGCTATACCCGAGCT
20454 GTCATTCGAT
Statistics
Matches: 191, Mismatches: 23, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
113 28 0.15
114 160 0.84
115 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (114 bp):
TTACGCTCTAACCGAGTCGTAAACAAATCCATAGCTCTACCTGAGCTGTACATGGCATTACGCTC
TAATCGAGACGTAAGCAAATCCATAGCTATACCCGAGCTTTACATGGCA
Found at i:27181 original size:30 final size:29
Alignment explanation
Indices: 27139--27195 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
27129 TATTTTGGAA
* * *
27139 ATTTTAGGAAATTTAGGGATTAAATTGTG
1 ATTTTAGAAAATTTAGGAACTAAATTGTG
27168 ATTTTAGTAAAATTTAGGAACTAAATTG
1 ATTTTAG-AAAATTTAGGAACTAAATTG
27196 AGTATTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.39, C:0.02, G:0.19, T:0.40
Consensus pattern (29 bp):
ATTTTAGAAAATTTAGGAACTAAATTGTG
Found at i:39191 original size:12 final size:12
Alignment explanation
Indices: 39174--39233 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 12
39164 CTATGAGGAG
39174 AAAGAAGAAGAA
1 AAAGAAGAAGAA
39186 AAAGAAGAA-AA
1 AAAGAAGAAGAA
*
39197 GAAAGAGGATGAAGGA
1 -AAAGA--A-GAAGAA
39213 AAAGAAAGAAG-A
1 AAAG-AAGAAGAA
39225 AAAGAAGAA
1 AAAGAAGAA
39234 CCTAATGTCG
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
11 7 0.17
12 19 0.46
13 4 0.10
14 2 0.05
15 7 0.17
16 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (12 bp):
AAAGAAGAAGAA
Found at i:42710 original size:76 final size:76
Alignment explanation
Indices: 42617--42770 Score: 283
Period size: 76 Copynumber: 2.0 Consensus size: 76
42607 GTAACACCCA
*
42617 AAACCCGTAACCATCACCAGTTTAAAGTCTCAGGGGTTTA-AGTACTTTACAGATTTTAAAAAAA
1 AAACCCGTAACCATCACCAGTTTAAAGTCTCAAGGGTTTACAGTACTTTACAGATTTTAAAAAAA
42681 AATACCAAATC
66 AATACCAAATC
42692 ANAACCCGTAACCATCACCAGTTTAAAGTCTCAAGGGTTTACAGTACTTTACAGATTTTAAAAAA
1 A-AACCCGTAACCATCACCAGTTTAAAGTCTCAAGGGTTTACAGTACTTTACAGATTTTAAAAAA
42757 AAATACCAAATC
65 AAATACCAAATC
42769 AA
1 AA
42771 TCACAAGTCC
Statistics
Matches: 76, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
75 1 0.01
76 39 0.51
77 36 0.47
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.26
Consensus pattern (76 bp):
AAACCCGTAACCATCACCAGTTTAAAGTCTCAAGGGTTTACAGTACTTTACAGATTTTAAAAAAA
AATACCAAATC
Found at i:44358 original size:50 final size:50
Alignment explanation
Indices: 44293--44450 Score: 199
Period size: 50 Copynumber: 3.1 Consensus size: 50
44283 ACAGAGTTTA
* * *
44293 GCTCTTAGGAGCCCAGACAAAATATCGCTCTTATGAGCCAGTTGGAACATC
1 GCTCTTACGA-CCCAGACAAAATATCGCTCTTACGAGCCAGTTAGAACATC
* * * *
44344 GCTCTTACGACCCAGACAAAATATCGCTCTTACGAGCCGGATAAAATATC
1 GCTCTTACGACCCAGACAAAATATCGCTCTTACGAGCCAGTTAGAACATC
* * * * *
44394 TCTCTTACGAGCCAGACAAAATATTGCTCTTACAAGCCAGTCAGAACATC
1 GCTCTTACGACCCAGACAAAATATCGCTCTTACGAGCCAGTTAGAACATC
44444 GCTCTTA
1 GCTCTTA
44451 AAAACCAGAT
Statistics
Matches: 90, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 81 0.90
51 9 0.10
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (50 bp):
GCTCTTACGACCCAGACAAAATATCGCTCTTACGAGCCAGTTAGAACATC
Found at i:44369 original size:25 final size:25
Alignment explanation
Indices: 44293--44525 Score: 165
Period size: 25 Copynumber: 9.6 Consensus size: 25
44283 ACAGAGTTTA
*
44293 GCTCTTAGGAGCCCAGACAAAATATC
1 GCTCTTACGAG-CCAGACAAAATATC
* **** *
44319 GCTCTTATGAGCCAGTTGGAACATC
1 GCTCTTACGAGCCAGACAAAATATC
*
44344 GCTCTTACGACCCAGACAAAATATC
1 GCTCTTACGAGCCAGACAAAATATC
* *
44369 GCTCTTACGAGCCGGATAAAATATC
1 GCTCTTACGAGCCAGACAAAATATC
* *
44394 TCTCTTACGAGCCAGACAAAATATT
1 GCTCTTACGAGCCAGACAAAATATC
* * * *
44419 GCTCTTACAAGCCAGTCAGAACATC
1 GCTCTTACGAGCCAGACAAAATATC
** *
44444 GCTCTTA--A---A-A-ACCAGATC
1 GCTCTTACGAGCCAGACAAAATATC
* * *
44462 GCTCTTACAAGCCAGATAGAATATC
1 GCTCTTACGAGCCAGACAAAATATC
* * *
44487 ACTTTTACGAGCCAAACAAAATATC
1 GCTCTTACGAGCCAGACAAAATATC
**
44512 ATTCTTACGAGCCA
1 GCTCTTACGAGCCA
44526 AATAGAATAT
Statistics
Matches: 159, Mismatches: 41, Indels: 15
0.74 0.19 0.07
Matches are distributed among these distances:
18 12 0.08
20 2 0.01
23 2 0.01
24 1 0.01
25 132 0.83
26 10 0.06
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (25 bp):
GCTCTTACGAGCCAGACAAAATATC
Found at i:44464 original size:18 final size:18
Alignment explanation
Indices: 44441--44478 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
44431 CAGTCAGAAC
44441 ATCGCTCTTAAAAACCAG
1 ATCGCTCTTAAAAACCAG
* *
44459 ATCGCTCTTACAAGCCAG
1 ATCGCTCTTAAAAACCAG
44477 AT
1 AT
44479 AGAATATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.29, G:0.13, T:0.24
Consensus pattern (18 bp):
ATCGCTCTTAAAAACCAG
Found at i:44534 original size:25 final size:26
Alignment explanation
Indices: 44464--44535 Score: 94
Period size: 25 Copynumber: 2.8 Consensus size: 26
44454 ACCAGATCGC
* *
44464 TCTTACAAGCCAGATAGAATATCACT
1 TCTTACGAGCCAAATAGAATATCACT
* *
44490 T-TTACGAGCCAAACAAAATATCA-T
1 TCTTACGAGCCAAATAGAATATCACT
44514 TCTTACGAGCCAAATAGAATAT
1 TCTTACGAGCCAAATAGAATAT
44536 TTCTCTTACG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
24 2 0.05
25 36 0.92
26 1 0.03
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (26 bp):
TCTTACGAGCCAAATAGAATATCACT
Found at i:44542 original size:25 final size:25
Alignment explanation
Indices: 44463--44547 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
44453 AACCAGATCG
* *
44463 CTCTTACAAGCCAGATAGAATATCA-
1 CTCTTACGAGCCAAATAGAATAT-AT
* * *
44488 CTTTTACGAGCCAAACAAAATATCAT
1 CTCTTACGAGCCAAATAGAATAT-AT
*
44514 -TCTTACGAGCCAAATAGAATATTT
1 CTCTTACGAGCCAAATAGAATATAT
44538 CTCTTACGAG
1 CTCTTACGAG
44548 ACAATCTTCA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
24 1 0.02
25 48 0.98
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (25 bp):
CTCTTACGAGCCAAATAGAATATAT
Found at i:47250 original size:13 final size:13
Alignment explanation
Indices: 47205--47275 Score: 63
Period size: 13 Copynumber: 5.2 Consensus size: 13
47195 ATTATTTCAA
47205 AAAAAATAATTTT
1 AAAAAATAATTTT
**
47218 AATAATTTTATATTTT
1 AA-AA-AATA-ATTTT
47234 AAAAAATAA-TTT
1 AAAAAATAATTTT
*
47246 AAAAATTTATATTTT
1 AAAAA-ATA-ATTTT
47261 AAAAAATAATTTT
1 AAAAAATAATTTT
47274 AA
1 AA
47276 TATTTTAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
12 8 0.17
13 12 0.26
14 7 0.15
15 12 0.26
16 7 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAAAAATAATTTT
Found at i:47254 original size:27 final size:28
Alignment explanation
Indices: 47177--47277 Score: 114
Period size: 27 Copynumber: 3.5 Consensus size: 28
47167 TTGAAAATTT
* * *
47177 AAATTATTTAATAATTTTATTATTTCAAAAA
1 AAATAATTTAATAAATTTA-TATTT--TAAA
*
47208 AAATAATTTTAATAATTTTATATTTTAAA
1 AAATAA-TTTAATAAATTTATATTTTAAA
47237 AAATAATTTAA-AAATTTATATTTTAAA
1 AAATAATTTAATAAATTTATATTTTAAA
47264 AAATAATTTTAATA
1 AAATAA-TTTAATA
47278 TTTTAAAATC
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
27 21 0.33
28 10 0.16
29 10 0.16
31 10 0.16
32 13 0.20
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (28 bp):
AAATAATTTAATAAATTTATATTTTAAA
Found at i:47280 original size:27 final size:27
Alignment explanation
Indices: 47205--47280 Score: 116
Period size: 27 Copynumber: 2.7 Consensus size: 27
47195 ATTATTTCAA
47205 AAAAAATAATTTTAATAATTTTATATTTT
1 AAAAAATAATTTTAAT-A-TTTATATTTT
* *
47234 AAAAAATAATTTAAAAATTTATATTTT
1 AAAAAATAATTTTAATATTTATATTTT
47261 AAAAAATAATTTTAATATTT
1 AAAAAATAATTTTAATATTT
47281 TAAAATCATT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 28 0.65
28 1 0.02
29 14 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
AAAAAATAATTTTAATATTTATATTTT
Found at i:51556 original size:75 final size:75
Alignment explanation
Indices: 51466--51666 Score: 233
Period size: 75 Copynumber: 2.7 Consensus size: 75
51456 TCTTATGAGC
* * *
51466 CCAGACAGAATATCGCTCTTACGAGCCAATCCGAACATCGCTCTTACGAGCCAGACAAAATATTA
1 CCAGACAGAATATCGCTCTTACGAGCTAATCAGAACATCGCTCTTACGAGCCAGACAAAATATCA
* *
51531 TTTTTACGAG
66 CTTTTACAAG
* * * * * * * *
51541 CCAGACAAAACATCGCTCTTACGAGCTAGTCAGAACATTGCTCTTATGAGCCAGATAGAATATCG
1 CCAGACAGAATATCGCTCTTACGAGCTAATCAGAACATCGCTCTTACGAGCCAGACAAAATATCA
51606 CTTTTACAAG
66 CTTTTACAAG
* * * *
51616 CAAGACAGAATATCGCTCTTATGAGCTAGA-CGGAATATCGCTCTTACGAGC
1 CCAGACAGAATATCGCTCTTACGAGCTA-ATCAGAACATCGCTCTTACGAGC
51667 TAATCTTCAG
Statistics
Matches: 103, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
75 103 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (75 bp):
CCAGACAGAATATCGCTCTTACGAGCTAATCAGAACATCGCTCTTACGAGCCAGACAAAATATCA
CTTTTACAAG
Found at i:51668 original size:25 final size:25
Alignment explanation
Indices: 51456--51666 Score: 199
Period size: 25 Copynumber: 8.4 Consensus size: 25
51446 AGAGTTTAGA
*
51456 TCTTATGAGCCCAGACAGAATATCGC
1 TCTTACGAG-CCAGACAGAATATCGC
* *
51482 TCTTACGAGCCA-ATCCGAACATCGC
1 TCTTACGAGCCAGA-CAGAATATCGC
* ***
51507 TCTTACGAGCCAGACAAAATATTAT
1 TCTTACGAGCCAGACAGAATATCGC
* * *
51532 TTTTACGAGCCAGACAAAACATCGC
1 TCTTACGAGCCAGACAGAATATCGC
* * * *
51557 TCTTACGAGCTAGTCAGAACATTGC
1 TCTTACGAGCCAGACAGAATATCGC
* *
51582 TCTTATGAGCCAGATAGAATATCGC
1 TCTTACGAGCCAGACAGAATATCGC
* * *
51607 TTTTACAAGCAAGACAGAATATCGC
1 TCTTACGAGCCAGACAGAATATCGC
* * *
51632 TCTTATGAGCTAGACGGAATATCGC
1 TCTTACGAGCCAGACAGAATATCGC
51657 TCTTACGAGC
1 TCTTACGAGC
51667 TAATCTTCAG
Statistics
Matches: 147, Mismatches: 36, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
24 1 0.01
25 137 0.93
26 9 0.06
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (25 bp):
TCTTACGAGCCAGACAGAATATCGC
Found at i:57372 original size:17 final size:18
Alignment explanation
Indices: 57350--57386 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
57340 GGCTTATAAC
*
57350 AATATAAACATG-AATTA
1 AATATAAACAAGCAATTA
57367 AATATAAACAAGCAATTA
1 AATATAAACAAGCAATTA
57385 AA
1 AA
57387 CACAATCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (18 bp):
AATATAAACAAGCAATTA
Found at i:61839 original size:21 final size:21
Alignment explanation
Indices: 61792--61841 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
61782 CTCTATAGGA
* *
61792 TCTTCCTCAGGATCCTCTTCT
1 TCTTCTTCAGGATACTCTTCT
*
61813 TCTTCTTCAGGATATTCTTCT
1 TCTTCTTCAGGATACTCTTCT
61834 TCTTCTTC
1 TCTTCTTC
61842 TTCAACTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.10, C:0.32, G:0.08, T:0.50
Consensus pattern (21 bp):
TCTTCTTCAGGATACTCTTCT
Found at i:64055 original size:18 final size:18
Alignment explanation
Indices: 64032--64099 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
64022 CATTAATTTA
64032 CAATGACAAATGGAAATG
1 CAATGACAAATGGAAATG
* *
64050 CAATGAC-AATGCACATG
1 CAATGACAAATGGAAATG
* * **
64067 GAATGACAATTAAAAATG
1 CAATGACAAATGGAAATG
*
64085 CAATGACAAAGGGAA
1 CAATGACAAATGGAA
64100 TGTGATGACA
Statistics
Matches: 37, Mismatches: 12, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
17 14 0.38
18 23 0.62
ACGTcount: A:0.50, C:0.13, G:0.21, T:0.16
Consensus pattern (18 bp):
CAATGACAAATGGAAATG
Found at i:64575 original size:24 final size:24
Alignment explanation
Indices: 64523--64579 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
64513 ATTTTCCTCT
*
64523 ACTTCTTTTCCTTCCTCTCTTTCT
1 ACTTCTTTTCCTTCCTCTCTTTCC
* *
64547 TCTTCTTTTCCTTCTTCT-TCTTCC
1 ACTTCTTTTCCTTCCTCTCT-TTCC
64571 ACTTCTTTT
1 ACTTCTTTT
64580 ACTCGTGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.04, C:0.35, G:0.00, T:0.61
Consensus pattern (24 bp):
ACTTCTTTTCCTTCCTCTCTTTCC
Found at i:74090 original size:3 final size:3
Alignment explanation
Indices: 74084--74138 Score: 53
Period size: 3 Copynumber: 18.3 Consensus size: 3
74074 GTATCGTAGT
*
74084 AGA AGA AGA AGCA AG- AGA AGA AGA GAGA A-A AG- ACA AGA AGGA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA -AGA AGA AGA AGA AGA A-GA AGA
74129 AGA AGA AGA A
1 AGA AGA AGA A
74139 ATTACCCCGA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
2 5 0.11
3 30 0.68
4 9 0.20
ACGTcount: A:0.64, C:0.04, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:74129 original size:17 final size:18
Alignment explanation
Indices: 74084--74134 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
74074 GTATCGTAGT
*
74084 AGAAGA-AGAAGCAAGAGA
1 AGAAGAGAGAAG-AAGACA
74102 AGAAGAGAGAA-AAGACA
1 AGAAGAGAGAAGAAGACA
74119 AGAAG-GAAGAAGAAGA
1 AGAAGAG-AGAAGAAGA
74135 AGAAATTACC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 1 0.03
17 14 0.48
18 10 0.34
19 4 0.14
ACGTcount: A:0.63, C:0.04, G:0.33, T:0.00
Consensus pattern (18 bp):
AGAAGAGAGAAGAAGACA
Found at i:74573 original size:17 final size:17
Alignment explanation
Indices: 74535--74567 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
74525 TATAATTTAA
74535 ATTGTCATTGCATTTTT
1 ATTGTCATTGCATTTTT
*
74552 ATTGTCCTTGCATTTT
1 ATTGTCATTGCATTTT
74568 ATTTGTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.58
Consensus pattern (17 bp):
ATTGTCATTGCATTTTT
Found at i:85479 original size:15 final size:16
Alignment explanation
Indices: 85454--85498 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
85444 CTTTTTCTTT
85454 TTCCTTC-TCTTCTC-
1 TTCCTTCTTCTTCTCA
85468 TTCCTTCTTCTTCTCA
1 TTCCTTCTTCTTCTCA
85484 TTTCTCTTCTTCTTC
1 -TTC-CTTCTTCTTC
85499 AATACCCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.26
15 7 0.26
17 3 0.11
18 10 0.37
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (16 bp):
TTCCTTCTTCTTCTCA
Found at i:95060 original size:24 final size:24
Alignment explanation
Indices: 95027--95073 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
95017 GTTAAGAGTA
*
95027 AAAATTGTCAGTGCAAATGTAATAT
1 AAAATTGTCAGAGCAAAT-TAATAT
95052 AAAA-TGTCAGAGCAAATTAATA
1 AAAATTGTCAGAGCAAATTAATA
95074 AAAGATGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.28
Consensus pattern (24 bp):
AAAATTGTCAGAGCAAATTAATAT
Found at i:112242 original size:21 final size:21
Alignment explanation
Indices: 112218--112267 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
112208 TAAGATGCAC
*
112218 CCACAACAAAGTC-AGATGTAG
1 CCACAACAAAATCGA-ATGTAG
*
112239 CCACACCAAAATCGAATGTAG
1 CCACAACAAAATCGAATGTAG
112260 CCACAACA
1 CCACAACA
112268 CTTTTCAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.44, C:0.30, G:0.14, T:0.12
Consensus pattern (21 bp):
CCACAACAAAATCGAATGTAG
Found at i:117232 original size:21 final size:22
Alignment explanation
Indices: 117208--117257 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
117198 CTTTTTCTTT
**
117208 TTCTTCCTTCTC-TTCTTTTTC
1 TTCTTCCTTCTCTTTCTCCTTC
*
117229 TTCTT-CTTTTCTTTCTCCTTC
1 TTCTTCCTTCTCTTTCTCCTTC
117250 TTCTTCCT
1 TTCTTCCT
117258 CAATACCCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.21
21 17 0.71
22 2 0.08
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (22 bp):
TTCTTCCTTCTCTTTCTCCTTC
Found at i:117254 original size:18 final size:17
Alignment explanation
Indices: 117200--117254 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 17
117190 GGCAACGTCT
117200 TTTTCTTTTTCTTCCTTC
1 TTTTCTTTTTCTT-CTTC
*
117218 TCTTCTTTTTCTTCTTC
1 TTTTCTTTTTCTTCTTC
*
117235 TTTTCTTTCTCCTTCTTC
1 TTTTCTTT-TTCTTCTTC
117253 TT
1 TT
117255 CCTCAATACC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 11 0.33
18 22 0.67
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCTTTTTCTTCTTC
Found at i:131389 original size:23 final size:22
Alignment explanation
Indices: 131353--131396 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
131343 TAAATATTTC
*
131353 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
131376 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
131397 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:138153 original size:121 final size:121
Alignment explanation
Indices: 137933--138176 Score: 436
Period size: 121 Copynumber: 2.0 Consensus size: 121
137923 GCCTATCGAA
*
137933 CAGCATTTAAGACACCATTAGGAATGACTCCATATCGGTTAGTCTTTGGAAAGGCATGTCATTTG
1 CAGCATTTAAGACACCATTAGGAATGACTCCATATCAGTTAGTCTTTGGAAAGGCATGTCATTTG
137998 CCATTGGAGTTGGAGAATAGAGCTCACTGGGCTTTGAAGCAGTTGAACTTTAATCT
66 CCATTGGAGTTGGAGAATAGAGCTCACTGGGCTTTGAAGCAGTTGAACTTTAATCT
** *
138054 CAGCA-TTAAGACACTGTTAGGAATGACTCCATATCAGTTAGTCTTTGGAAGGGCATGTTCATTT
1 CAGCATTTAAGACACCATTAGGAATGACTCCATATCAGTTAGTCTTTGGAAAGGCATG-TCATTT
138118 GCCATTGGAGTTGGAGAATAGAGCTCACTGGGCTTTGAAGCAGTTGAACTTTAATCT
65 GCCATTGGAGTTGGAGAATAGAGCTCACTGGGCTTTGAAGCAGTTGAACTTTAATCT
138175 CA
1 CA
138177 AGCAAGCCAG
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
120 48 0.41
121 70 0.59
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (121 bp):
CAGCATTTAAGACACCATTAGGAATGACTCCATATCAGTTAGTCTTTGGAAAGGCATGTCATTTG
CCATTGGAGTTGGAGAATAGAGCTCACTGGGCTTTGAAGCAGTTGAACTTTAATCT
Found at i:156449 original size:18 final size:19
Alignment explanation
Indices: 156426--156476 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
156416 GTATTACGGC
*
156426 AGAAGAAGAAGAA-AGAAA
1 AGAAGAAAAAGAAGAGAAA
*
156444 AGAAGAAAAAGAAGAGAAG
1 AGAAGAAAAAGAAGAGAAA
*
156463 A-AAGAAAAACAAGA
1 AGAAGAAAAAGAAGA
156477 AGATGTTGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (19 bp):
AGAAGAAAAAGAAGAGAAA
Found at i:156455 original size:21 final size:21
Alignment explanation
Indices: 156426--156479 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
156416 GTATTACGGC
*
156426 AGAAGAAGAAGA-AAGAAAAGA
1 AGAAAAAGAAGAGAAG-AAAGA
156447 AGAAAAAGAAGAGAAGAAAGA
1 AGAAAAAGAAGAGAAGAAAGA
156468 A-AAACAAGAAGA
1 AGAAA-AAGAAGA
156480 TGTTGCCTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 3 0.10
21 24 0.80
22 3 0.10
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (21 bp):
AGAAAAAGAAGAGAAGAAAGA
Found at i:156896 original size:17 final size:18
Alignment explanation
Indices: 156870--156908 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
156860 GCATGCATTT
156870 TTTTTAATTGTCAT-TGCA
1 TTTTTAATTGTC-TCTGCA
156888 TTTTT-ATTGTCTCTGCA
1 TTTTTAATTGTCTCTGCA
156905 TTTT
1 TTTT
156909 ATTTGTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.05
17 14 0.70
18 5 0.25
ACGTcount: A:0.15, C:0.13, G:0.10, T:0.62
Consensus pattern (18 bp):
TTTTTAATTGTCTCTGCA
Found at i:156914 original size:17 final size:17
Alignment explanation
Indices: 156871--156924 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
156861 CATGCATTTT
*
156871 TTTTAATTGTCAT-TGCA
1 TTTTATTTGTC-TCTGCA
156888 TTTT-TATTGTCTCTGCA
1 TTTTAT-TTGTCTCTGCA
156905 TTTTATTTGT-TCTAGCA
1 TTTTATTTGTCTCT-GCA
156922 TTT
1 TTT
156925 GCATTGTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
16 4 0.12
17 27 0.84
18 1 0.03
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (17 bp):
TTTTATTTGTCTCTGCA
Found at i:160475 original size:34 final size:34
Alignment explanation
Indices: 160432--160500 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
160422 ATCTCATTCT
*
160432 GACTGAAATGGATGGTATAGAGCTATACAACCCC
1 GACTGAAATGGATGGTAAAGAGCTATACAACCCC
160466 GACTGAAATGGATGGTAAAGAGCTATACAACCCC
1 GACTGAAATGGATGGTAAAGAGCTATACAACCCC
160500 G
1 G
160501 TGAATTTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (34 bp):
GACTGAAATGGATGGTAAAGAGCTATACAACCCC
Found at i:162462 original size:39 final size:39
Alignment explanation
Indices: 161560--162456 Score: 888
Period size: 39 Copynumber: 22.6 Consensus size: 39
161550 GCAAAACTAC
*
161560 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGATAT
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAG---T
*
161602 CATCCAATCTCTTACCCTC-ACCATGGGGCAAATTGAAGT
1 CATCCAATCTCTTACCC-CGACCATGGGGCAGATTGAAGT
* ** * **
161641 CATCCAATCTCTTACCCCGATCATAAGGTAGATTGAAAACAC
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTG--AA-GT
** *
161683 CATCCAATCTCTTACCCCGATTATGAGGCAGATTGAAGAT
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAG-T
* * * *
161723 ACCATCCAATCTCTTACCCCTATCATGAGGCAGATTGAAGC
1 --CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGT
* * *
161764 CATCTAATCTCTTACTCCGACCATGGGGCAAATTGAAGACAT
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAG---T
* * * * * *
161806 CATCTAATCTCTTATCCAGACCATGGGCCAGACTGAAGC
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGT
* * * *
161845 CATCCAATCTATTACCCCAACCATGGGGCATATTGAAGC
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGT
** * *
161884 CA-CACAATCTCTTACCATGACTATAGGGCAGATTGAAGT
1 CATC-CAATCTCTTACCCCGACCATGGGGCAGATTGAAGT
* *
161923 CATCCAATCTCTTACCTCGACCATGGGGCAGATTGAAGC
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGT
* *
161962 CATCCAATCTCTTACCCCGACCATGGGGTAGATTTAAGT
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGT
** * *
162001 TTTCCAATCTCTTACCCCGACCATGGGGTAGATTGAAGC
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGT
*
162040 CA-CCTAATCTCTTACCCCGACCATGGGGCAAATT-AGAGT
1 CATCC-AATCTCTTACCCCGACCATGGGGCAGATTGA-AGT
* *
162079 CATCCAATCTCTTACTCCGACCATGGGGCAGATTGAAGC
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGT
* *
162118 CATCCAATCTCTTACCCCAACCATAGGGCAGATTGAAGACAT
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAG---T
*
162160 CATCCAATCTCTTACCCCGACCATGGGGTAGATTGAAGT
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGT
* * * * *
162199 CATTCAATCTCTTACCCTGACCATGGGGTAAATTGTAGT
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGT
* ** * * *
162238 CA-CTCAATCTCTTAACTTGACCATAGGGAAAATTGAAG-
1 CATC-CAATCTCTTACCCCGACCATGGGGCAGATTGAAGT
* * * *
162276 CTATTCAATCTCTTACCCCGACGATGGGGCAAATTGAAGC
1 C-ATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGT
* * *
162316 CATCCAATCTCTTACCCTGACCATGTGGCAGATTGAAGA
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGT
* * ** * * * *
162355 CATTCAATCTCTTATCTTGACCATGAGGCATATTAAAGC
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGT
* * *
162394 CATCCAATCTCTTACCCCGACCATGAGGCAAATTAAAGT
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGT
162433 CATCCAATCTCTTACCCCGACCAT
1 CATCCAATCTCTTACCCCGACCAT
162457 TAGGCACATT
Statistics
Matches: 720, Mismatches: 111, Indels: 51
0.82 0.13 0.06
Matches are distributed among these distances:
38 6 0.01
39 535 0.74
40 7 0.01
41 2 0.00
42 169 0.23
43 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (39 bp):
CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGT
Found at i:162707 original size:14 final size:14
Alignment explanation
Indices: 162688--162715 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
162678 AACCAAAACC
162688 AATAAATAATAATA
1 AATAAATAATAATA
162702 AATAAATAATAATA
1 AATAAATAATAATA
162716 GTGTGTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAAATAATAATA
Found at i:163701 original size:14 final size:14
Alignment explanation
Indices: 163684--163713 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
163674 TTTAAACTCT
*
163684 AAAAGATAAATATA
1 AAAAGATAAACATA
163698 AAAAGATAAACATA
1 AAAAGATAAACATA
163712 AA
1 AA
163714 TTAAATACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAAGATAAACATA
Found at i:163782 original size:16 final size:16
Alignment explanation
Indices: 163761--163808 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
163751 ATCAAATCCT
163761 AATAAAATAATATTTA
1 AATAAAATAATATTTA
* *
163777 AATAAAATAA-AATAA
1 AATAAAATAATATTTA
163792 AATAAAACTAAGTATTT
1 AATAAAA-TAA-TATTT
163809 TTGTCCTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 10 0.40
16 13 0.52
18 2 0.08
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (16 bp):
AATAAAATAATATTTA
Found at i:166475 original size:12 final size:13
Alignment explanation
Indices: 166436--166477 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
166426 TTTCCTGGAC
166436 ATAAAATA-AATAA
1 ATAAAATAGAA-AA
166449 ATAAAATAGAAAA
1 ATAAAATAGAAAA
*
166462 ATAAAA-ATAAAA
1 ATAAAATAGAAAA
166474 ATAA
1 ATAA
166478 TTGGGTTGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 9 0.33
13 16 0.59
14 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (13 bp):
ATAAAATAGAAAA
Found at i:172126 original size:20 final size:22
Alignment explanation
Indices: 172073--172131 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
172063 CGATCTAGGG
*
172073 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
172094 AAAAATAAAAGAAAATAGAA-T
1 AAAAATAAAAGAAAATAGAATT
*
172115 AAAAA-AATAGAAAATAG
1 AAAAATAAAAGAAAATAG
172132 GGAAGTTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 11 0.31
21 17 0.49
22 7 0.20
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.14
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:172955 original size:19 final size:19
Alignment explanation
Indices: 172931--172973 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
172921 AAACATAAAT
172931 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
172950 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
172969 TAAAT
1 TAAAT
172974 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:174590 original size:7 final size:7
Alignment explanation
Indices: 174578--174602 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
174568 TCAGCAGTGT
174578 TTTTCAA
1 TTTTCAA
174585 TTTTCAA
1 TTTTCAA
174592 TTTTCAA
1 TTTTCAA
174599 TTTT
1 TTTT
174603 GCCCTATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTCAA
Found at i:176989 original size:27 final size:27
Alignment explanation
Indices: 176951--177005 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
176941 GCGCAAGTAC
176951 AGGTAATTCTCAAAGTTCGAGAGGTGA
1 AGGTAATTCTCAAAGTTCGAGAGGTGA
176978 AGGTAATTCTCAAAGTTCGAGAGGTGA
1 AGGTAATTCTCAAAGTTCGAGAGGTGA
177005 A
1 A
177006 CCTAGCATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.25
Consensus pattern (27 bp):
AGGTAATTCTCAAAGTTCGAGAGGTGA
Found at i:180884 original size:36 final size:38
Alignment explanation
Indices: 180820--180891 Score: 96
Period size: 36 Copynumber: 1.9 Consensus size: 38
180810 TTTTTTTGTT
*
180820 TATATTTAACTTTAATTTGTAATTATTATTT-TTTAATA
1 TATATTTAACTTT-ATTTGTAATAATTATTTCTTTAATA
180858 TATATTTAA-TTT-TTTGATAATAATTATTTCTTTA
1 TATATTTAACTTTATTTG-TAATAATTATTTCTTTA
180892 CATTTTTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
35 4 0.13
36 11 0.35
37 7 0.23
38 9 0.29
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (38 bp):
TATATTTAACTTTATTTGTAATAATTATTTCTTTAATA
Found at i:182745 original size:2 final size:2
Alignment explanation
Indices: 182738--182762 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
182728 ATTCGTCATT
182738 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
182763 TTATTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:186702 original size:18 final size:20
Alignment explanation
Indices: 186661--186710 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
186651 TTTCTTAATA
186661 AAAATTACAAAATAATTTTC
1 AAAATTACAAAATAATTTTC
186681 AAAATT-CAAAAT-ATTTAT-
1 AAAATTACAAAATAATTT-TC
*
186699 AAAATTATAAAA
1 AAAATTACAAAA
186711 ATTTCAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 10 0.37
19 11 0.41
20 6 0.22
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATTACAAAATAATTTTC
Found at i:186710 original size:19 final size:19
Alignment explanation
Indices: 186661--186719 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
186651 TTTCTTAATA
186661 AAAATTACAAAATAATTTTC
1 AAAATTACAAAAT-ATTTTC
186681 AAAATT-CAAAATATTTAT-
1 AAAATTACAAAATATTT-TC
*
186699 AAAATTATAAAA-A-TTTC
1 AAAATTACAAAATATTTTC
186716 AAAA
1 AAAA
186720 AATAATAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
16 1 0.03
17 6 0.17
18 11 0.31
19 11 0.31
20 6 0.17
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTACAAAATATTTTC
Done.