Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011128.1 Kokia drynarioides strain JFW-HI SEQ_126101, 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: 72536
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:9959 original size:58 final size:56
Alignment explanation
Indices: 9878--10029 Score: 153
Period size: 58 Copynumber: 2.6 Consensus size: 56
9868 TTTTAATTTT
* * *
9878 GTATTTAAATTTTTTTATTCAATTTGGTACGTAAACTTGACACTTTTTCTTAACTTG
1 GTATCTAAATTTTTTAATTCAATTTGGTACCTAAACTTGACACTTTTTC-TAACTTG
* * * * * *
9935 GTATCTAAATTTTTTGAATCCAATTTGGTACTTGAACTTGGCATTTTTTCTAATTTG
1 GTATCTAAATTTTTT-AATTCAATTTGGTACCTAAACTTGACACTTTTTCTAACTTG
*
9992 GCA-CTTAAACTTTTTTTAGATTCAATTTGGTACCTAAA
1 GTATC-TAAA--TTTTTTA-ATTCAATTTGGTACCTAAA
10030 TTTATTAAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
56 1 0.01
57 26 0.33
58 29 0.37
59 22 0.28
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (56 bp):
GTATCTAAATTTTTTAATTCAATTTGGTACCTAAACTTGACACTTTTTCTAACTTG
Found at i:12375 original size:27 final size:27
Alignment explanation
Indices: 12317--12375 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
12307 GATTCAATAC
* * *
12317 TTTAATTCGGTTAATTTTTTTAATTCG
1 TTTAATTCGGGTAATTTTTATAATTAG
* * *
12344 GTTAATTCGGGTAATTTTTATACTTAT
1 TTTAATTCGGGTAATTTTTATAATTAG
12371 TTTAA
1 TTTAA
12376 CCAAAAATAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.56
Consensus pattern (27 bp):
TTTAATTCGGGTAATTTTTATAATTAG
Found at i:23528 original size:7 final size:7
Alignment explanation
Indices: 23516--23560 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
23506 GACCCAACCT
23516 GTTGATC
1 GTTGATC
23523 GTTGATC
1 GTTGATC
23530 GTTGATC
1 GTTGATC
23537 GTTGA-C
1 GTTGATC
* *
23543 TTTGACC
1 GTTGATC
*
23550 GTTGACC
1 GTTGATC
23557 GTTG
1 GTTG
23561 GCTTTTTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 5 0.14
7 30 0.86
ACGTcount: A:0.13, C:0.18, G:0.29, T:0.40
Consensus pattern (7 bp):
GTTGATC
Found at i:23552 original size:20 final size:20
Alignment explanation
Indices: 23524--23565 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
23514 CTGTTGATCG
* *
23524 TTGATCGTTGATCGTTGACT
1 TTGACCGTTGACCGTTGACT
*
23544 TTGACCGTTGACCGTTGGCT
1 TTGACCGTTGACCGTTGACT
23564 TT
1 TT
23566 TTTCAAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.19, G:0.26, T:0.43
Consensus pattern (20 bp):
TTGACCGTTGACCGTTGACT
Found at i:25623 original size:25 final size:24
Alignment explanation
Indices: 25576--25624 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
25566 TTTTCGTTTC
* *
25576 TTTTTCTCTTCTTTTTCGTTTAGA
1 TTTTTCTCTTCTTTTTAGGTTAGA
*
25600 TTTTCTCTTTTCTTTTTAGGTTAGA
1 TTTT-TCTCTTCTTTTTAGGTTAGA
25625 CTTTAATCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.10, C:0.14, G:0.10, T:0.65
Consensus pattern (24 bp):
TTTTTCTCTTCTTTTTAGGTTAGA
Found at i:26058 original size:13 final size:13
Alignment explanation
Indices: 26007--26059 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 13
25997 ACGAAAAATT
26007 AATTATTTTTTTAA
1 AATTA-TTTTTTAA
26021 AATATAATTTTTTAA
1 AAT-T-ATTTTTTAA
26036 AA-TA--TTTTAA
1 AATTATTTTTTAA
26046 AATTATTTTTTAA
1 AATTATTTTTTAA
26059 A
1 A
26060 TATAAAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
10 8 0.24
11 2 0.06
12 1 0.03
13 8 0.24
14 3 0.09
15 11 0.32
16 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AATTATTTTTTAA
Found at i:26404 original size:44 final size:44
Alignment explanation
Indices: 26355--26441 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
26345 GTGAATAATT
26355 CTGATCTGGGTTTCTATCTTTCAAATCTCTAGAGTTGGTTCTAA
1 CTGATCTGGGTTTCTATCTTTCAAATCTCTAGAGTTGGTTCTAA
26399 CTGATCTGGGTTTCTATCTTTCAAATCTCTAGAGTTGGTTCTA
1 CTGATCTGGGTTTCTATCTTTCAAATCTCTAGAGTTGGTTCTA
26442 CTTTCATTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (44 bp):
CTGATCTGGGTTTCTATCTTTCAAATCTCTAGAGTTGGTTCTAA
Found at i:27296 original size:29 final size:30
Alignment explanation
Indices: 27234--27297 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
27224 TCAATTTGAC
** *
27234 CCAAAAAAAAAAGTTAAGGAACAAAGTGAG
1 CCAAAAAAAAAACATAAGAAACAAAGTGAG
*
27264 CCAAAAAAAAATCATAAGAAACAAAGTGA-
1 CCAAAAAAAAAACATAAGAAACAAAGTGAG
27293 CCAAA
1 CCAAA
27298 CACCCAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.62, C:0.14, G:0.14, T:0.09
Consensus pattern (30 bp):
CCAAAAAAAAAACATAAGAAACAAAGTGAG
Found at i:38547 original size:17 final size:18
Alignment explanation
Indices: 38525--38562 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
38515 ATTAAATGGG
38525 TATTTAAAATATTTTA-T
1 TATTTAAAATATTTTAGT
38542 TATTTAAAATATTTTAGT
1 TATTTAAAATATTTTAGT
38560 TAT
1 TAT
38563 AGAATTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TATTTAAAATATTTTAGT
Found at i:39025 original size:31 final size:31
Alignment explanation
Indices: 38990--39048 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
38980 GTGTAATTAA
38990 TATTCGAATTAAACCGAAAAACTTAATTTTT
1 TATTCGAATTAAACCGAAAAACTTAATTTTT
* * * *
39021 TATTCGAGTTTATCCGAATAACTTAATT
1 TATTCGAATTAAACCGAAAAACTTAATT
39049 AACTCAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (31 bp):
TATTCGAATTAAACCGAAAAACTTAATTTTT
Found at i:40899 original size:30 final size:30
Alignment explanation
Indices: 40863--41095 Score: 181
Period size: 30 Copynumber: 7.8 Consensus size: 30
40853 AAAATGATAT
* **
40863 TTTGACCTCCGAACTTTCCAAAGTTTTAAA
1 TTTGACCTCCAAACTTTCCAAAAATTTAAA
* * *
40893 TTTGACCTTCGAACTTTCCAAAAATTTGAA
1 TTTGACCTCCAAACTTTCCAAAAATTTAAA
* **
40923 TTTGACCCCTCAAAC-TTCC-AAAATTTCATT
1 TTTGACCTC-CAAACTTTCCAAAAATTT-AAA
** * *
40953 TTTGACC-CTTGAACTTTCCAAATATTTGAA
1 TTTGACCTC-CAAACTTTCCAAAAATTTAAA
* *
40983 TTTAACCTCCAAACTTTCCAAAAATTCAAA
1 TTTGACCTCCAAACTTTCCAAAAATTTAAA
*
41013 TTTGAACC-CTAAACTTTCCAAAAATTTAAA
1 TTTG-ACCTCCAAACTTTCCAAAAATTTAAA
* * *
41043 TTTGACC-CGTAAACTTTCAAAAAATTTGAA
1 TTTGACCTC-CAAACTTTCCAAAAATTTAAA
* *
41073 TTTGGCC-CTCGAACTTTCCAAAA
1 TTTGACCTC-CAAACTTTCCAAAA
41096 TTTCATTTTT
Statistics
Matches: 164, Mismatches: 32, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
29 16 0.10
30 134 0.82
31 14 0.09
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (30 bp):
TTTGACCTCCAAACTTTCCAAAAATTTAAA
Found at i:40957 original size:60 final size:59
Alignment explanation
Indices: 40874--41095 Score: 225
Period size: 60 Copynumber: 3.7 Consensus size: 59
40864 TTGACCTCCG
* * *
40874 AACTTTCCAAAGTTTTAAATTTGACCTTCGAACTTTCCAAAAATTTGAATTTGACCCCTCA
1 AACTTTCCAAA-ATTTCAATTTGACCCT-GAACTTTCCAAAAATTTGAATTTGACCCCTCA
* * * *
40935 AAC-TTCCAAAATTTCATTTTTGACCCTTGAACTTTCCAAATATTTGAATTTAACCTC-CA
1 AACTTTCCAAAATTTCA-ATTTGACCC-TGAACTTTCCAAAAATTTGAATTTGACCCCTCA
* * * *
40994 AACTTTCCAAAAATTCAAATTTGAACCCTAAACTTTCCAAAAATTTAAATTTGACCCGT-A
1 AACTTTCCAAAATTTC-AATTTG-ACCCTGAACTTTCCAAAAATTTGAATTTGACCCCTCA
* * *
41054 AACTTTCAAAAAATTTGAATTTGGCCCTCGAACTTTCCAAAA
1 AACTTTC-CAAAATTTCAATTTGACCCT-GAACTTTCCAAAA
41096 TTTCATTTTT
Statistics
Matches: 133, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
59 13 0.10
60 105 0.79
61 15 0.11
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.35
Consensus pattern (59 bp):
AACTTTCCAAAATTTCAATTTGACCCTGAACTTTCCAAAAATTTGAATTTGACCCCTCA
Found at i:41088 original size:90 final size:90
Alignment explanation
Indices: 40891--41100 Score: 246
Period size: 90 Copynumber: 2.3 Consensus size: 90
40881 CAAAGTTTTA
* ** * **
40891 AATTTGACCTTCGAACTTTCCAAAAATTTGAATTTGACCCCTCAAACTTCCAAAATTTCATTTTT
1 AATTTGACCCTCGAACTTTCCAAAAATTCAAATTTGAACCCTCAAACTTCCAAAATTTCAAATTT
* * * *
40956 GACCCTTGAACTTTCCAAATATTTG
66 GACCCGTAAACTTTCAAAAAATTTG
* *
40981 AATTT-AACCTCCAAACTTTCCAAAAATTCAAATTTGAACCCT-AAACTTTCCAAAAATTT-AAA
1 AATTTGACCCT-CGAACTTTCCAAAAATTCAAATTTGAACCCTCAAAC-TTCC-AAAATTTCAAA
41043 TTTGACCCGTAAACTTTCAAAAAATTTG
63 TTTGACCCGTAAACTTTCAAAAAATTTG
* *
41071 AATTTGGCCCTCGAACTTTCCAAAATTTCA
1 AATTTGACCCTCGAACTTTCCAAAAATTCA
41101 TTTTTGACCC
Statistics
Matches: 100, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
89 7 0.07
90 83 0.83
91 10 0.10
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.35
Consensus pattern (90 bp):
AATTTGACCCTCGAACTTTCCAAAAATTCAAATTTGAACCCTCAAACTTCCAAAATTTCAAATTT
GACCCGTAAACTTTCAAAAAATTTG
Found at i:41410 original size:16 final size:15
Alignment explanation
Indices: 41379--41408 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41369 TTTTTAAAAA
41379 AATAAAAAATATTTT
1 AATAAAAAATATTTT
41394 AATAAAAAATATTTT
1 AATAAAAAATATTTT
41409 TATTTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAAAAAATATTTT
Found at i:41615 original size:104 final size:105
Alignment explanation
Indices: 41450--41749 Score: 277
Period size: 104 Copynumber: 2.8 Consensus size: 105
41440 AAATATTTTC
* * * * * * **
41450 AAAATCGAGGCAATGTT-TCTTTA-TTTAGGGAACTCGAGAAATTATGCTCAAATGTACTGGGTA
1 AAAATTGAAGCAATGTTCT-TTTATTTTAGGGAACTCGAGAAATTGTGCCCTAACGTGTTGGGTA
* * *
41513 CGATTTTTCTTTTAACCTAAGTAACTGAATATCCTATTC-A
65 TGATTTTTCTTTAAACCTAAGTAACTGAATATCCAATTCGA
*
41553 AAAATTGAAGCAATGTTCTTTTATTTTAGGGAAGTCGAGAAATTGTGCCCTAACGTGTTGGGTAT
1 AAAATTGAAGCAATGTTCTTTTATTTTAGGGAACTCGAGAAATTGTGCCCTAACGTGTTGGGTAT
* * * *
41618 GTTTTTTCTTTGAACCTAAATAATTGAATATCCAATTCGGA
66 GATTTTTCTTTAAACCTAAGTAACTGAATATCCAATTC-GA
* * * * * *
41659 ACTAAGT-AATGCTCAATATTCTGTTATTTTAAGGG-ACTCGAAAAATTGTGCCCTAACGTGTTA
1 A-AAATTGAA-G--CAATGTTCTTTTATTTT-AGGGAACTCGAGAAATTGTGCCCTAACGTGTTG
* * *
41722 AGTATGATTTTGCCTTAAACCTAAGTAA
61 GGTATGATTTTTCTTTAAACCTAAGTAA
41750 TTAAATATTT
Statistics
Matches: 160, Mismatches: 28, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
103 19 0.12
104 67 0.42
106 4 0.03
107 4 0.03
109 62 0.39
110 4 0.03
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (105 bp):
AAAATTGAAGCAATGTTCTTTTATTTTAGGGAACTCGAGAAATTGTGCCCTAACGTGTTGGGTAT
GATTTTTCTTTAAACCTAAGTAACTGAATATCCAATTCGA
Found at i:45449 original size:19 final size:17
Alignment explanation
Indices: 45414--45462 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 17
45404 GAGGAGATAA
*
45414 AAAAAAAAAAAAGAAAG
1 AAAAAAAGAAAAGAAAG
45431 AAGAAAAAGAAAAGAAAAG
1 AA-AAAAAGAAAAG-AAAG
45450 AAAAGAAAGAAAA
1 AAAA-AAAGAAAA
45463 AGTCAAGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 2 0.07
18 12 0.43
19 14 0.50
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAAAGAAAG
Found at i:45458 original size:14 final size:13
Alignment explanation
Indices: 45418--45463 Score: 65
Period size: 14 Copynumber: 3.4 Consensus size: 13
45408 AGATAAAAAA
45418 AAAAAAAAGAAAG
1 AAAAAAAAGAAAG
*
45431 AAGAAAAAGAAAAG
1 AAAAAAAAG-AAAG
45445 AAAAGAAAAGAAAG
1 AAAA-AAAAGAAAG
45459 AAAAA
1 AAAAA
45464 GTCAAGATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 9 0.31
14 15 0.52
15 5 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAG
Found at i:45463 original size:10 final size:10
Alignment explanation
Indices: 45412--45464 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
45402 AAGAGGAGAT
*
45412 AAAAA-AAAA
1 AAAAAGAAAG
45421 AAAAAGAAAG
1 AAAAAGAAAG
*
45431 AAGAA-AAAG
1 AAAAAGAAAG
45440 -AAAAGAAA-
1 AAAAAGAAAG
45448 AGAAAAGAAAG
1 A-AAAAGAAAG
45459 AAAAAG
1 AAAAAG
45465 TCAAGATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
8 3 0.08
9 12 0.33
10 20 0.56
11 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:45476 original size:28 final size:23
Alignment explanation
Indices: 45412--45464 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
45402 AAGAGGAGAT
*
45412 AAAAA-AAAAAAAAAGAAAGAAG
1 AAAAAGAAAAGAAAAGAAAGAAG
45434 AAAAAGAAAAGAAAAGAAAAGAAAG
1 AAAAAGAAAAGAAAAG-AAAG-AAG
45459 AAAAAG
1 AAAAAG
45465 TCAAGATGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 5 0.19
23 9 0.33
24 4 0.15
25 9 0.33
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAGAAAAGAAAGAAG
Found at i:45512 original size:7 final size:7
Alignment explanation
Indices: 45497--45550 Score: 56
Period size: 7 Copynumber: 7.3 Consensus size: 7
45487 GCATCTTTTT
*
45497 AAAAGGA
1 AAAAAGA
45504 AAAAAGA
1 AAAAAGA
45511 AAAAAGAA
1 AAAAAG-A
45519 AAGATAAGA
1 AA-A-AAGA
45528 AGAAAA-A
1 A-AAAAGA
45535 AAAAAGA
1 AAAAAGA
45542 AAAAAGA
1 AAAAAGA
45549 AA
1 AA
45551 GTTAAGATGA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
6 4 0.10
7 24 0.59
8 5 0.12
9 4 0.10
10 4 0.10
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:45541 original size:31 final size:30
Alignment explanation
Indices: 45503--45563 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
45493 TTTTAAAAGG
45503 AAAAAAGAAAAAAGAAAAGATAAGAAGAAAA
1 AAAAAAGAAAAAAG-AAAGATAAGAAGAAAA
* *
45534 AAAAAAGAAAAAAGAAAGTTAAGATGAAAA
1 AAAAAAGAAAAAAGAAAGATAAGAAGAAAA
45564 CCCGCAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (30 bp):
AAAAAAGAAAAAAGAAAGATAAGAAGAAAA
Found at i:45583 original size:87 final size:83
Alignment explanation
Indices: 45420--45584 Score: 204
Period size: 87 Copynumber: 1.9 Consensus size: 83
45410 ATAAAAAAAA
* * *
45420 AAAAAAGAAAGAAGAAAAAGAAAAGAAAAGAAAAGAAAGAAAAAGTCAAGATGAAAACCAACAAA
1 AAAAAAGAAAAAAGAAAAAGAAAAGAAAAAAAAAGAAAAAAAAAGTCAAGATGAAAACCAACAAA
*
45485 AGGCATCTTTTTAAAAGG
66 AGGCATATTTTTAAAAGG
* * **
45503 AAAAAAGAAAAAAGAAAAGATAAGAAGAAAAAAAAAAGAAAAAAGAAAGTTAAGATGAAAACCCG
1 AAAAAAGAAAAAAGAAAA-AGAA-AAG-AAAAAAAAAGAAAAAA-AAAGTCAAGATGAAAACCAA
* *
45568 CAAATGGCTTATTTTTA
62 CAAAAGGCATATTTTTA
45585 TGTGAGACAT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
83 17 0.25
84 3 0.04
85 3 0.04
86 14 0.21
87 31 0.46
ACGTcount: A:0.64, C:0.07, G:0.17, T:0.12
Consensus pattern (83 bp):
AAAAAAGAAAAAAGAAAAAGAAAAGAAAAAAAAAGAAAAAAAAAGTCAAGATGAAAACCAACAAA
AGGCATATTTTTAAAAGG
Found at i:46385 original size:14 final size:13
Alignment explanation
Indices: 46365--46409 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
46355 AATTTCACCC
*
46365 AAAAAAATAAAA-
1 AAAAAAAAAAAAG
*
46377 AAGAAAAAAAAAG
1 AAAAAAAAAAAAG
46390 AAAAAAAAAAGAAG
1 AAAAAAAAAA-AAG
46404 AAAAAA
1 AAAAAA
46410 GAAGGAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 10 0.36
13 9 0.32
14 9 0.32
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.02
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:46387 original size:17 final size:16
Alignment explanation
Indices: 46365--46412 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
46355 AATTTCACCC
*
46365 AAAAAAATAAAAAAGA
1 AAAAAAAAAAAAAAGA
*
46381 AAAAAAAAGAAAAA-A
1 AAAAAAAAAAAAAAGA
* *
46396 AAAAGAAGAAAAAAGA
1 AAAAAAAAAAAAAAGA
46412 A
1 A
46413 GGAAAAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGA
Found at i:46394 original size:11 final size:11
Alignment explanation
Indices: 46368--46419 Score: 61
Period size: 11 Copynumber: 4.5 Consensus size: 11
46358 TTCACCCAAA
46368 AAAATAAAAAAG
1 AAAA-AAAAAAG
46380 -AAAAAAAAAG
1 AAAAAAAAAAG
46390 AAAAAAAAAAG
1 AAAAAAAAAAG
46401 AAGAAAAAAGAAG
1 AA-AAAAAA-AAG
*
46414 GAAAAA
1 AAAAAA
46420 GGAAAAGAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
10 7 0.19
11 15 0.42
12 10 0.28
13 4 0.11
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:46399 original size:21 final size:22
Alignment explanation
Indices: 46368--46412 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
46358 TTCACCCAAA
46368 AAAATAAAAAAGAAAAAAAAAG
1 AAAATAAAAAAGAAAAAAAAAG
*
46390 AAAA-AAAAAAGAAGAAAAAAG
1 AAAATAAAAAAGAAAAAAAAAG
46411 AA
1 AA
46413 GGAAAAAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (22 bp):
AAAATAAAAAAGAAAAAAAAAG
Found at i:46413 original size:10 final size:10
Alignment explanation
Indices: 46373--46412 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
46363 CCAAAAAAAT
46373 AAAAAAGAAA
1 AAAAAAGAAA
46383 AAAAAAGAAAA
1 AAAAAAG-AAA
*
46394 AAAAAAGAAG
1 AAAAAAGAAA
46404 AAAAAAGAA
1 AAAAAAGAA
46413 GGAAAAAGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:46418 original size:10 final size:10
Alignment explanation
Indices: 46373--46420 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
46363 CCAAAAAAAT
*
46373 AAAAAAGAAA
1 AAAAAAGAAG
*
46383 AAAAAAGAAAA
1 AAAAAAG-AAG
46394 AAAAAAGAAG
1 AAAAAAGAAG
46404 AAAAAAGAAG
1 AAAAAAGAAG
*
46414 GAAAAAG
1 AAAAAAG
46421 GAAAAGAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
10 25 0.71
11 10 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:46876 original size:113 final size:115
Alignment explanation
Indices: 46741--46954 Score: 326
Period size: 113 Copynumber: 1.9 Consensus size: 115
46731 TTGTCATTTT
* * *
46741 TAATCTTTTCATTCATATGAGCTTTGCCTCTAATAAAATTCAATTTTATCTACCTTTA-AACCTT
1 TAATCTTTTCATTCATACGAGCTTTGCCTCTAATAAAACTCAATTTTATCCACC-TTACAACCTT
*
46805 G-TTCAAGCATTTTTTTCA-TTGAAATAACGGTTAGTAGACCAATGATTCG
65 GATTCAAGCATTTTTTGCATTTGAAATAACGGTTAGTAGACCAATGATTCG
* * *
46854 TAATCTTTTTATTCATACGAGCTTTGTCTCTAATAAAACTCAATTTTATCCATCTTACAACCTTG
1 TAATCTTTTCATTCATACGAGCTTTGCCTCTAATAAAACTCAATTTTATCCACCTTACAACCTTG
*
46919 ATTTAAGCATTTTTTGCATTTGAAATAACGGTTAGT
66 ATTCAAGCATTTTTTGCATTTGAAATAACGGTTAGT
46955 GGTCTAACGA
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
112 3 0.03
113 55 0.61
114 15 0.17
115 17 0.19
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (115 bp):
TAATCTTTTCATTCATACGAGCTTTGCCTCTAATAAAACTCAATTTTATCCACCTTACAACCTTG
ATTCAAGCATTTTTTGCATTTGAAATAACGGTTAGTAGACCAATGATTCG
Found at i:47283 original size:24 final size:24
Alignment explanation
Indices: 47248--47299 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
47238 TTGCATTAAT
47248 CATTCATACCCATCTAGTTAGGAG
1 CATTCATACCCATCTAGTTAGGAG
*
47272 CATTCATTCCCATCTAGTTAGGAG
1 CATTCATACCCATCTAGTTAGGAG
47296 CATT
1 CATT
47300 TGTCTCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (24 bp):
CATTCATACCCATCTAGTTAGGAG
Found at i:47975 original size:87 final size:85
Alignment explanation
Indices: 47833--48307 Score: 289
Period size: 87 Copynumber: 5.4 Consensus size: 85
47823 AGATTGATTA
* * * *
47833 CCATCAAATCTTTTACCCCCAAGTCAAGAGGGGAAGATTGAAGTTATCATTCAATCTTTTACCCC
1 CCATCAAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAG--ATAATCCAATCTTTTACCCC
*
47898 TAATCCAA-ATAGAAAAATTAAAG
63 TAAT-CAAGAGAGAAAAATTAAAG
* *
47921 CCATCTAATCTTTTACCCCTAATCCAA-AGGGGCAGATTGAAGCCATAACCCAATCTTTTACCCC
1 CCATCAAATCTTTTACCCCTAAT-CAAGAGGGGCAGATTGAAG--ATAATCCAATCTTTTACCCC
* ** * *
47985 TAATCAAGAGGGGCATATTGAAG
63 TAATCAAGAGAGAAAAATTAAAG
* * *
48008 CCACCGTCCAATCTTTTACCCCTAATTAAGAGGGGCAGATTGAAG-TAATCTAATCTTTTACCCC
1 CCA---TCAAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGATAATCCAATCTTTTACCCC
** ** *
48072 TAAGTCAAGA-AGGGCAGCTTGAAG
63 TAA-TCAAGAGA-GAAAAATTAAAG
* * ** * ***
48096 CCACCATACAATCTTTTACCCCTAATTAAGAAAGGTAGATTGAAGCCACCGTCCAATCTTTTA-C
1 CCATC--A-AATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAG--ATAATCCAATCTTTTACC
** * *
48160 CCT--TCAAGAGAGGCAGATTAAAA
61 CCTAATCAAGAGAGAAAAATTAAAG
* * * **
48183 CCATGGTCCAATCTTTTACCCCTAGTCAAGAGGGGCATATTGAAGCCACCATCCAATCTTTTACC
1 CCA---TCAAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAG--ATAATCCAATCTTTTACC
* * * * *
48248 CTTAATCAAGAGGGACAGATTGAAG
61 CCTAATCAAGAGAGAAAAATTAAAG
*
48273 CCACCATCCAATCTTTTACCCCTAATCAAGAGGGG
1 ---CCATCAAATCTTTTACCCCTAATCAAGAGGGG
48308 TAAATTGACG
Statistics
Matches: 315, Mismatches: 48, Indels: 46
0.77 0.12 0.11
Matches are distributed among these distances:
85 1 0.00
86 3 0.01
87 133 0.42
88 79 0.25
89 2 0.01
90 83 0.26
91 11 0.03
93 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (85 bp):
CCATCAAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGATAATCCAATCTTTTACCCCTAA
TCAAGAGAGAAAAATTAAAG
Found at i:48026 original size:132 final size:132
Alignment explanation
Indices: 47790--48304 Score: 542
Period size: 132 Copynumber: 3.9 Consensus size: 132
47780 AGTTACATCA
* * * ** *
47790 CCATCCAATTTTTTA-CCCTAAGTCAAGAGGGACAGATTG-A-TTACCATCAAATCTTTTACCCC
1 CCATCTAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCC
* * ** * * * ** *
47852 CAAGTCAAGAGGGGAAGATTGAAGTTATCATTCAATCTTTTACCCCTAATCCAA-ATAGAAAAAT
65 TAA-TCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAAT-CAAGAGAGGCAGAT
47916 TAAAG
128 TAAAG
** *
47921 CCATCTAATCTTTTACCCCTAATCCAA-AGGGGCAGATTGAAGCCATAACCCAATCTTTTACCCC
1 CCATCTAATCTTTTACCCCTAAT-CAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCC
* * * * *
47985 TAATCAAGAGGGGCATATTGAAGCCACCGTCCAATCTTTTACCCCTAATTAAGAGGGGCAGATTG
65 TAATCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCAAGAGAGGCAGATTA
48050 AAG
130 AAG
** * * *
48053 TAATCTAATCTTTTACCCCTAAGTCAAGAAGGGCAGCTTGAAGCCACCATACAATCTTTTACCCC
1 CCATCTAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCC
* ** * *
48118 TAATTAAGAAAGGTAGATTGAAGCCACCGTCCAATCTTTTA-CCCT--TCAAGAGAGGCAGATTA
65 TAATCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCAAGAGAGGCAGATTA
*
48180 AAA
130 AAG
* * *
48183 CCATGGTCCAATCTTTTACCCCTAGTCAAGAGGGGCATATTGAAGCCACCATCCAATCTTTTACC
1 CCA---TCTAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACC
* *
48248 CTTAATCAAGAGGGACAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCAAGAG
63 CCTAATCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCAAGAG
48305 GGGTAAATTG
Statistics
Matches: 315, Mismatches: 56, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
130 17 0.05
131 27 0.09
132 157 0.50
133 107 0.34
135 7 0.02
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (132 bp):
CCATCTAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCT
AATCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCAAGAGAGGCAGATTAA
AG
Found at i:48196 original size:220 final size:220
Alignment explanation
Indices: 47788--48303 Score: 607
Period size: 220 Copynumber: 2.3 Consensus size: 220
47778 GAAGTTACAT
* *
47788 CACCATCCAATTTTTTA-CCCTAAGTCAAGAGGGACAGATTG-ATTACCATCAAATCTTTTACCC
1 CACCATCCAATCTTTTACCCCTAA-TCAAGAGGGACAGATTGAAGTA-CATCAAATCTTTTACCC
* * ** * * *
47851 CCAAGTCAAGAGGGGAAGATTGAAGTTATCATTCAATCTTTTACCCCTAATCCAAATAGAAAAAT
64 CTAAGTCAAGAAGGGAAGATTGAAGCCACCATACAATCTTTTACCCCTAATCCAAAAAGAAAAAT
* * * *
47916 TAAAGCCATCTAATCTTTTACCCCTAATCCAAAGGGGCAGATTGAAGCCATAACCCAATCTTTTA
129 TAAAGCCATCCAATCTTTTACCCCT-ATCCAAAGAGGCAGATTAAAACCATAACCCAATCTTTTA
47981 CCCCTAATCAAGAGGGGCATATTGAAGC
193 CCCCTAATCAAGAGGGGCATATTGAAGC
* * * *
48009 CACCGTCCAATCTTTTACCCCTAATTAAGAGGGGCAGATTGAAGTA-ATCTAATCTTTTACCCCT
1 CACCATCCAATCTTTTACCCCTAATCAAGAGGGACAGATTGAAGTACATCAAATCTTTTACCCCT
* * * ** *
48073 AAGTCAAGAAGGGCAGCTTGAAGCCACCATACAATCTTTTACCCCTAAT-TAAGAAAGGTAGATT
66 AAGTCAAGAAGGGAAGATTGAAGCCACCATACAATCTTTTACCCCTAATCCAA-AAAGAAAAATT
* ***
48137 GAAGCCACCGTCCAATCTTTTA-CCCT-T-CAAGAGAGGCAGATTAAAACCATGGTCCAATCTTT
130 AAAGCCA---TCCAATCTTTTACCCCTATCCAA-AGAGGCAGATTAAAACCATAACCCAATCTTT
*
48199 TACCCCTAGTCAAGAGGGGCATATTGAAGC
191 TACCCCTAATCAAGAGGGGCATATTGAAGC
* * *
48229 CACCATCCAATCTTTTACCCTTAATCAAGAGGGACAGATTGAAGCCACCATCCAATCTTTTACCC
1 CACCATCCAATCTTTTACCCCTAATCAAGAGGGACAGATTGAAG-TA-CATCAAATCTTTTACCC
48294 CTAA-TCAAGA
64 CTAAGTCAAGA
48304 GGGGTAAATT
Statistics
Matches: 251, Mismatches: 34, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
219 5 0.02
220 166 0.66
221 31 0.12
222 19 0.08
223 30 0.12
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.26
Consensus pattern (220 bp):
CACCATCCAATCTTTTACCCCTAATCAAGAGGGACAGATTGAAGTACATCAAATCTTTTACCCCT
AAGTCAAGAAGGGAAGATTGAAGCCACCATACAATCTTTTACCCCTAATCCAAAAAGAAAAATTA
AAGCCATCCAATCTTTTACCCCTATCCAAAGAGGCAGATTAAAACCATAACCCAATCTTTTACCC
CTAATCAAGAGGGGCATATTGAAGC
Found at i:48315 original size:45 final size:45
Alignment explanation
Indices: 47788--48307 Score: 501
Period size: 45 Copynumber: 11.8 Consensus size: 45
47778 GAAGTTACAT
* * *
47788 CACCATCCAATTTTTTA-CCCTAAGTCAAGAGGGACAGATTG-A-T
1 CACCATCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGC
* * * * *
47831 TACCATCAAATCTTTTACCCCCAAGTCAAGAGGGGAAGATTGAAGT
1 CACCATCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGC
* * * ** ** * *
47877 TATCATTCAATCTTTTACCCCTAATCCAA-ATAGAAAAATTAAAG-
1 CACCATCCAATCTTTTACCCCTAAT-CAAGAGGGGCAGATTGAAGC
*
47921 --CCATCTAATCTTTTACCCCTAATCCAA-AGGGGCAGATTGAAGC
1 CACCATCCAATCTTTTACCCCTAAT-CAAGAGGGGCAGATTGAAGC
** * *
47964 CATAACCCAATCTTTTACCCCTAATCAAGAGGGGCATATTGAAGC
1 CACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGC
* *
48009 CACCGTCCAATCTTTTACCCCTAATTAAGAGGGGCAGATTGAAG-
1 CACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGC
* * * *
48053 TA--ATCTAATCTTTTACCCCTAAGTCAAGAAGGGCAGCTTGAAGC
1 CACCATCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGC
* * ** *
48097 CACCATACAATCTTTTACCCCTAATTAAGAAAGGTAGATTGAAGC
1 CACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGC
* * * *
48142 CACCGTCCAATCTTTTA-CCCT--TCAAGAGAGGCAGATTAAAAC
1 CACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGC
*** * *
48184 CATGGTCCAATCTTTTACCCCTAGTCAAGAGGGGCATATTGAAGC
1 CACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGC
* *
48229 CACCATCCAATCTTTTACCCTTAATCAAGAGGGACAGATTGAAGC
1 CACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGC
48274 CACCATCCAATCTTTTACCCCTAATCAAGAGGGG
1 CACCATCCAATCTTTTACCCCTAATCAAGAGGGG
48308 TAAATTGACG
Statistics
Matches: 392, Mismatches: 70, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
42 82 0.21
43 35 0.09
44 30 0.08
45 203 0.52
46 42 0.11
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (45 bp):
CACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGC
Found at i:49787 original size:19 final size:19
Alignment explanation
Indices: 49763--49799 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
49753 GCTTAAAAGC
49763 CCCAAAACGACATCGTTTA
1 CCCAAAACGACATCGTTTA
49782 CCCAAAACGACATCGTTT
1 CCCAAAACGACATCGTTT
49800 TGGCTCAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.32, G:0.11, T:0.22
Consensus pattern (19 bp):
CCCAAAACGACATCGTTTA
Found at i:50081 original size:29 final size:30
Alignment explanation
Indices: 50048--50105 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
50038 GTTTTATTTA
50048 AAAATGAT-ATTTTGACCCTTGAACTTTCT
1 AAAATGATGATTTTGACCCTTGAACTTTCT
** *
50077 AAAATTTTGTTTTTGACCCTTGAACTTTC
1 AAAATGATGATTTTGACCCTTGAACTTTC
50106 CAAATATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (30 bp):
AAAATGATGATTTTGACCCTTGAACTTTCT
Found at i:50091 original size:30 final size:31
Alignment explanation
Indices: 50057--50114 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
50047 AAAAATGATA
*
50057 TTTTGACCCTTGAACTTTCTAAA-ATTTTGT
1 TTTTGACCCTTGAACTTTCCAAATATTTTGT
50087 TTTTGACCCTTGAACTTTCCAAATATTT
1 TTTTGACCCTTGAACTTTCCAAATATTT
50115 GAATTATACC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.48
Consensus pattern (31 bp):
TTTTGACCCTTGAACTTTCCAAATATTTTGT
Found at i:50148 original size:29 final size:29
Alignment explanation
Indices: 50122--50234 Score: 84
Period size: 30 Copynumber: 3.8 Consensus size: 29
50112 TTTGAATTAT
*
50122 ACCCCAAACTTTCTAGAAATTCAAATTTGA
1 ACCCCAAACTTTCTAAAAATTCAAATTT-A
* * *
50152 ACCCTAAACTTTCTAAAAATTTAAACTTA
1 ACCCCAAACTTTCTAAAAATTCAAATTTA
* * * *
50181 ACCCGTAAACTTT-TCGAAAATTCGAATTTG
1 ACCC-CAAACTTTCT-AAAAATTCAAATTTA
* * *
50211 GCCACCAAACTTTCCAAAATTTCA
1 ACC-CCAAACTTTCTAAAAATTCA
50235 TTTTGACCCC
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
29 6 0.09
30 57 0.89
31 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (29 bp):
ACCCCAAACTTTCTAAAAATTCAAATTTA
Found at i:50163 original size:30 final size:30
Alignment explanation
Indices: 50122--50210 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
50112 TTTGAATTAT
*
50122 ACCCCAAACTTTCTAGAAATTCAAATTTGA
1 ACCCTAAACTTTCTAGAAATTCAAATTTGA
* * *
50152 ACCCTAAACTTTCTAAAAATTTAAACTT-A
1 ACCCTAAACTTTCTAGAAATTCAAATTTGA
* *
50181 ACCCGTAAACTTT-TCGAAAATTCGAATTTG
1 ACCC-TAAACTTTCTAG-AAATTCAAATTTG
50211 GCCACCAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 6 0.13
30 41 0.87
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (30 bp):
ACCCTAAACTTTCTAGAAATTCAAATTTGA
Found at i:55141 original size:19 final size:19
Alignment explanation
Indices: 55119--55161 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
55109 AGTTTTAATT
55119 TTCATTCTTCAATTTT-TTG
1 TTCATTCTTC-ATTTTATTG
* *
55138 TTCATTTTTCTTTTTATTG
1 TTCATTCTTCATTTTATTG
55157 TTCAT
1 TTCAT
55162 CGATGAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.67
Consensus pattern (19 bp):
TTCATTCTTCATTTTATTG
Found at i:55565 original size:9 final size:9
Alignment explanation
Indices: 55553--55579 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
55543 ATGTCAAAGG
55553 TCAAACAAA
1 TCAAACAAA
55562 TCAAACAAA
1 TCAAACAAA
55571 TCAAACAAA
1 TCAAACAAA
55580 AATTCGATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.22, G:0.00, T:0.11
Consensus pattern (9 bp):
TCAAACAAA
Found at i:58778 original size:22 final size:24
Alignment explanation
Indices: 58737--58783 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
58727 GTTTTTTTCT
*
58737 TTCTTTGTTTCTTTTGAGTGGTAG
1 TTCTTCGTTTCTTTTGAGTGGTAG
*
58761 TTCTTCGTTT-TTTT-AGTGTTAG
1 TTCTTCGTTTCTTTTGAGTGGTAG
58783 T
1 T
58784 CAAACTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.38
23 4 0.19
24 9 0.43
ACGTcount: A:0.09, C:0.09, G:0.21, T:0.62
Consensus pattern (24 bp):
TTCTTCGTTTCTTTTGAGTGGTAG
Found at i:67849 original size:17 final size:17
Alignment explanation
Indices: 67817--67860 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
67807 AAATCGTATG
*
67817 AAATTATTATTTTTTTCT
1 AAATTTTTATTTTTTT-T
*
67835 TAATTTTTATTTTTTTT
1 AAATTTTTATTTTTTTT
67852 AAATTTTTA
1 AAATTTTTA
67861 AATTTAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
AAATTTTTATTTTTTTT
Done.