Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009517.1 Kokia drynarioides strain JFW-HI SEQ_124228, 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: 34773
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:3330 original size:2 final size:2
Alignment explanation
Indices: 3323--3354 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3313 ATTCTAACTC
3323 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3355 ATTTTCGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3594 original size:3 final size:3
Alignment explanation
Indices: 3586--3618 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3576 TATGTTTTAT
*
3586 ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3619 TCAGGGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:6169 original size:21 final size:21
Alignment explanation
Indices: 6116--6192 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
6106 AGAGTTTTTA
*
6116 GTATCGGTAGAAGTATGACTT
1 GTATCGGTAGAAGTATCACTT
* **
6137 GTTTCGACAGAAGTATCACTT
1 GTATCGGTAGAAGTATCACTT
** * *
6158 GTATCGGTAGAACCATCCCTA
1 GTATCGGTAGAAGTATCACTT
6179 GTATCGGTAGAAGT
1 GTATCGGTAGAAGT
6193 TTGCTGCTGT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (21 bp):
GTATCGGTAGAAGTATCACTT
Found at i:7921 original size:24 final size:26
Alignment explanation
Indices: 7894--7941 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
7884 TTATATAAAA
7894 AAATTAATAAA-TAAAA-AATATATT
1 AAATTAATAAATTAAAATAATATATT
*
7918 AAATTATTAAATTAAAATAATATA
1 AAATTAATAAATTAAAATAATATA
7942 AATATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 5 0.24
26 6 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AAATTAATAAATTAAAATAATATATT
Found at i:14562 original size:17 final size:17
Alignment explanation
Indices: 14539--14631 Score: 116
Period size: 17 Copynumber: 5.4 Consensus size: 17
14529 CCAAACTCAT
14539 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
14557 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
14574 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
14591 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* * *
14609 TTTAAAATTCTTATAAA
1 TTTAAATTTATTTTAAA
14626 TTTAAA
1 TTTAAA
14632 ATAAATAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
17 39 0.58
18 28 0.42
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:14578 original size:35 final size:35
Alignment explanation
Indices: 14539--14631 Score: 125
Period size: 35 Copynumber: 2.7 Consensus size: 35
14529 CCAAACTCAT
*
14539 TTTAAATTTATTTTAAGA-TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTATTTTAAAA
*
14574 TTTAAATTTATTTTAAATTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAATTTAAATTTATTTTAAAA
* * *
14609 TTTAAAATTCTTATAAATTTAAA
1 TTTAAATTTATTTTAAATTTAAA
14632 ATAAATAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
34 1 0.02
35 51 0.98
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTTAAAA
Found at i:16489 original size:21 final size:22
Alignment explanation
Indices: 16463--16506 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
16453 CCTGAACTAT
16463 CAAAAAATTCCATTTTT-ACCC
1 CAAAAAATTCCATTTTTAACCC
*
16484 CAAAAACTTCCATTTTTAACCC
1 CAAAAAATTCCATTTTTAACCC
16506 C
1 C
16507 GAAACTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (22 bp):
CAAAAAATTCCATTTTTAACCC
Found at i:16511 original size:21 final size:21
Alignment explanation
Indices: 16463--16514 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
16453 CCTGAACTAT
*
16463 CAAAAAATTCCATTTTTACCC
1 CAAAAACTTCCATTTTTACCC
16484 CAAAAACTTCCATTTTTAACCC
1 CAAAAACTTCCATTTTT-ACCC
*
16506 C-GAAACTTC
1 CAAAAACTTC
16515 TCAAAATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.37, C:0.31, G:0.02, T:0.31
Consensus pattern (21 bp):
CAAAAACTTCCATTTTTACCC
Found at i:16559 original size:29 final size:30
Alignment explanation
Indices: 16483--16799 Score: 278
Period size: 30 Copynumber: 10.7 Consensus size: 30
16473 CATTTTTACC
* *
16483 CCAAAAACTTCCATTTTTAACCCCGAAACTT
1 CCAAAAA-TTCCATTTTTGACCCCTAAACTT
* *
16514 CTCAAAATTTCCCTTTTT-ACCCCTAAACTT
1 C-CAAAAATTCCATTTTTGACCCCTAAACTT
* * *
16544 CCAAAAATCCCATTTTTGACCCCAAAATTT
1 CCAAAAATTCCATTTTTGACCCCTAAACTT
* **
16574 CAAAAAATTCCATTTTT-ACCCCCGAACTT
1 CCAAAAATTCCATTTTTGACCCCTAAACTT
*
16603 CC-AAAA-TCCATTTTTGA-CCTTAAAACTT
1 CCAAAAATTCCATTTTTGACCCCT-AAACTT
* *
16631 CCAAAAATTCTATTTTTGA-CTCTAAAACTT
1 CCAAAAATTCCATTTTTGACCCCT-AAACTT
* **
16661 CCAAACATTTGATTTTTGA-CCCTAAAACTT
1 CCAAAAATTCCATTTTTGACCCCT-AAACTT
* * *
16691 CCAAACATTCCATTTTTAACCCCAAAACTT
1 CCAAAAATTCCATTTTTGACCCCTAAACTT
*
16721 CCAAAAATAT--AATTTTGACCCCTAAACTT
1 CCAAAAAT-TCCATTTTTGACCCCTAAACTT
* * *
16750 CCAAAAATCCCATTTTT-ACCCTTAAACCT
1 CCAAAAATTCCATTTTTGACCCCTAAACTT
*
16779 CC-AAAATCTCCATTTTCGACC
1 CCAAAAAT-TCCATTTTTGACC
16800 TCGAAACTCT
Statistics
Matches: 236, Mismatches: 38, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
27 11 0.05
28 17 0.07
29 70 0.30
30 119 0.50
31 14 0.06
32 5 0.02
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (30 bp):
CCAAAAATTCCATTTTTGACCCCTAAACTT
Found at i:16814 original size:88 final size:88
Alignment explanation
Indices: 16483--16807 Score: 289
Period size: 88 Copynumber: 3.6 Consensus size: 88
16473 CATTTTTACC
** * * *
16483 CCAAAAACTTCCATTTTTAACCCCGAAACTTCTCAAAATTTCCCTTTTT-ACCCCTAAACTTCCA
1 CCAAAAA-TTCCATTTTT-ACCCTAAAACTTC-CAAAA-TTCCATTTTTGACCTCAAAACTTCCA
*** * * *
16547 AAAATCCCATTTTTGACCCCAAAATTT
62 AAAATTATAATTTTGACCCCTAAACTT
* *** *
16574 CAAAAAATTCCATTTTTACCCCCGAACTTCCAAAA-TCCATTTTTGACCTTAAAACTTCCAAAAA
1 CCAAAAATTCCATTTTTACCCTAAAACTTCCAAAATTCCATTTTTGACCTCAAAACTTCCAAAAA
* * *
16638 TTCTATTTTTGA-CTCTAAAACTT
66 TTATAATTTTGACCCCT-AAACTT
* ** * *
16661 CCAAACATTTGATTTTTGACCCTAAAACTTCCAAACATTCCATTTTTAACCCCAAAACTTCCAAA
1 CCAAAAATTCCATTTTT-ACCCTAAAACTTCCAAA-ATTCCATTTTTGACCTCAAAACTTCCAAA
16726 AA-TATAATTTTGACCCCTAAACTT
64 AATTATAATTTTGACCCCTAAACTT
* * * * *
16750 CCAAAAATCCCATTTTTACCCTTAAACCTCCAAAATCTCCATTTTCGACCTCGAAACT
1 CCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAT-TCCATTTTTGACCTCAAAACT
16808 CTCAAAATTA
Statistics
Matches: 192, Mismatches: 35, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
86 10 0.05
87 46 0.24
88 51 0.27
89 40 0.21
90 39 0.20
91 6 0.03
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (88 bp):
CCAAAAATTCCATTTTTACCCTAAAACTTCCAAAATTCCATTTTTGACCTCAAAACTTCCAAAAA
TTATAATTTTGACCCCTAAACTT
Found at i:28683 original size:206 final size:205
Alignment explanation
Indices: 28229--29280 Score: 1347
Period size: 206 Copynumber: 5.2 Consensus size: 205
28219 AAACAACAAT
* * *
28229 GCGGTCATCTTCCTGATGAAATACTGAGAAGAAGATCAAATCAAACCCACGCTC-------G---
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATGTGAGCAA
* *
28284 ATCTTCGAACCCCAGCTTCTTGATGAGACGCTGAGAAGCAGGTCGAAGCAATCAAAGGTTAGCTT
66 ATCTTCGAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTT
*
28349 CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAG-AGATGAATTG
131 CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG-CGAATTG
28413 AAACAAACGAC
195 AAACAAACGAC
* * *
28424 GCGGTCATCTCCCTGATGAGGTACTGAGAAGAAGACCAAATCAAACTCACGCTCGATGTGAACAA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATGTGAGCAA
* * * ** * * * *
28489 ATATTCGAACCCCAACTTTTTGATGAGACGTTAAGAAGTAGGTCGAAGTAATCAAAGGTTAGCTT
66 ATCTTCGAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTT
* * *
28554 CCTGATGAGATACTGAGAAGTGGACCAAAATTCTTCTTCCTGATGAGATACAGAGAGGTGAATTG
131 CCTGATGAGATACTGAGAAGTGGACC-AAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTG
28619 AAACAAACGAC
195 AAACAAACGAC
* * * * * *
28630 GCGGTCATCTTCTTGATAAGGTACTGAGAAAAATACCAAATCAAA-TCCACGCTCGAAGTGAGCA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACT-CACGCTCGATGTGAGCA
* * *
28694 AATCTTCGAACCTCAGCTTCTTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAATGGTCAGC
65 AATCTTCGAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA-GGTTAGC
* * * * *
28759 TTCCTGATGAGTTATTGAAAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGGATT
129 TTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATT
* *
28824 GAAACAAACAAT
194 GAAACAAACGAC
* * * *
28836 TCGGTTATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACACTTGATGTGAGCAA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATGTGAGCAA
* * * *
28901 ATCTTCGGATCCCAGCTTCCT-ATTGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCT
66 ATCTTCGAACCCCAGCTTCTTGA-TGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCT
* * *
28965 TCCTGATGAGGTACTGAGAAGTGGACCAAAATCGTCTTCCTGATGAGGTACAGAGAAGCGAATTG
130 TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTG
* *
29030 AAGCGAACGAC
195 AAACAAACGAC
* * * * *
29041 GCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCAAAATCAAACCCACGTTCGATGTGGGTA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACC-AAATCAAACTCACGCTCGATGTGAGCA
* * * * *
29106 AATCTTCGAATCCCAGCTTCTTGATGAGATACTGAGAAGCAGTTTGAAGAAATAAAAGGTTAGCT
65 AATCTTCGAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCT
* * * * *
29171 TCCCGATGAGATACTGAGAAGTGGATCAAATTCGTCTTCCTGATGAGGTACAGAGAAACGGATTG
130 TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTG
* *
29236 AAGCGAACGAC
195 AAACAAACGAC
*
29247 GCGGTCATCTTCCTGATGAGATATTGAGAAGAAG
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAG
29281 GTCAAGTTAA
Statistics
Matches: 745, Mismatches: 94, Indels: 25
0.86 0.11 0.03
Matches are distributed among these distances:
195 49 0.07
205 192 0.26
206 470 0.63
207 34 0.05
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (205 bp):
GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATGTGAGCAA
ATCTTCGAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTT
CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGA
AACAAACGAC
Found at i:29624 original size:11 final size:11
Alignment explanation
Indices: 29610--29712 Score: 59
Period size: 11 Copynumber: 9.0 Consensus size: 11
29600 CCAAACTCAT
*
29610 TTTAAATTTAT
1 TTTAAATTTAA
*
29621 TTTAAGATTAAA
1 TTTAA-ATTTAA
*
29633 TTT-GATTTAAAA
1 TTTAAATTT--AA
*
29645 TTTAAATTTAT
1 TTTAAATTTAA
29656 TTTAAATTTAA
1 TTTAAATTTAA
*
29667 TTTAAGTTTGAA
1 TTTAAATTT-AA
*
29679 TTT-ATTTTCAAA
1 TTTAAATTT--AA
*
29691 TTTAAAATT-A
1 TTTAAATTTAA
29701 TTATAAATTTAA
1 TT-TAAATTTAA
29713 AATAAATAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
10 6 0.09
11 34 0.49
12 23 0.33
13 7 0.10
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:29633 original size:17 final size:16
Alignment explanation
Indices: 29611--29670 Score: 75
Period size: 17 Copynumber: 3.6 Consensus size: 16
29601 CAAACTCATT
29611 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAA-A
*
29628 TTAAATTTGATTTAAAA
1 TTAAATTT-ATTTTAAA
29645 TTTAAATTTATTTTAAA
1 -TTAAATTTATTTTAAA
*
29662 TTTAATTTA
1 TTAAATTTA
29671 AGTTTGAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
16 8 0.21
17 16 0.42
18 14 0.37
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTAAATTTATTTTAAA
Found at i:29658 original size:46 final size:46
Alignment explanation
Indices: 29608--29712 Score: 140
Period size: 46 Copynumber: 2.3 Consensus size: 46
29598 CCCCAAACTC
* *
29608 ATTTTAAATTTATTTTAAGATTAAATTTGA-TTTAAAATTTAAATTT
1 ATTTTAAATTTAATTTAAGATTAAATTT-ATTTTAAAATTTAAAATT
* * *
29654 ATTTTAAATTTAATTTAAGTTTGAATTTATTTTCAAATTTAAAATT
1 ATTTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATT
*
29700 ATTATAAATTTAA
1 ATTTTAAATTTAA
29713 AATAAATAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 1 0.02
46 51 0.98
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (46 bp):
ATTTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATT
Found at i:29660 original size:29 final size:28
Alignment explanation
Indices: 29628--29695 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 28
29618 TATTTTAAGA
*
29628 TTAAATTTGATTTAAAATTTAAATTTATT
1 TTAAATTTAATTT-AAATTTAAATTTATT
* *
29657 TTAAATTTAATTTAAGTTTGAATTTATT
1 TTAAATTTAATTTAAATTTAAATTTATT
29685 TTCAAATTTAA
1 TT-AAATTTAA
29696 AATTATTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 15 0.43
29 20 0.57
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (28 bp):
TTAAATTTAATTTAAATTTAAATTTATT
Found at i:30992 original size:6 final size:6
Alignment explanation
Indices: 30981--31044 Score: 64
Period size: 6 Copynumber: 11.0 Consensus size: 6
30971 TTTAATTTAT
* *
30981 TTTAAA TTTAAA -TT-AA TCTAAA TTTAAA TTT-AA TTTAAA TGTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
31026 TTT-AA TTTCAAAA TTTAAA
1 TTTAAA TTT--AAA TTTAAA
31045 AAAAAGTCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
4 2 0.04
5 13 0.27
6 28 0.58
8 5 0.10
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:30996 original size:11 final size:11
Alignment explanation
Indices: 30982--31033 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
30972 TTAATTTATT
30982 TTAAATTTAAA
1 TTAAATTTAAA
*
30993 TT-AATCTAAA
1 TTAAATTTAAA
*
31003 TTTAAATTTAAT
1 -TTAAATTTAAA
*
31015 TTAAATGTAAA
1 TTAAATTTAAA
*
31026 TTTAATTT
1 TTAAATTT
31034 CAAAATTTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
10 7 0.22
11 19 0.59
12 6 0.19
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:31032 original size:17 final size:17
Alignment explanation
Indices: 30974--31044 Score: 90
Period size: 17 Copynumber: 4.1 Consensus size: 17
30964 CCCTCTTTTT
*
30974 AATTTATTTTAAATTTA
1 AATTTAATTTAAATTTA
*
30991 AA-TTAATCTAAATTTA
1 AATTTAATTTAAATTTA
*
31007 AATTTAATTTAAATGTA
1 AATTTAATTTAAATTTA
31024 AATTTAATTTCAAAATTTA
1 AATTTAATTT--AAATTTA
31043 AA
1 AA
31045 AAAAAGTCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
16 14 0.30
17 24 0.52
19 8 0.17
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (17 bp):
AATTTAATTTAAATTTA
Found at i:31150 original size:26 final size:26
Alignment explanation
Indices: 31071--31150 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 26
31061 AACAATGTCC
31071 AATTACAAATGGCCCAAGTCAGCCCA
1 AATTACAAATGGCCCAAGTCAGCCCA
** * ** *
31097 AA-TAC--ATTACCCAAATGCCATACTA
1 AATTACAAATGGCCC-AA-GTCAGCCCA
31122 AATTACAAATGGCCCAAGTCAGCCCA
1 AATTACAAATGGCCCAAGTCAGCCCA
31148 AAT
1 AAT
31151 ACCCAAAGCC
Statistics
Matches: 37, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
23 5 0.14
24 2 0.05
25 10 0.27
26 13 0.35
27 2 0.05
28 5 0.14
ACGTcount: A:0.41, C:0.29, G:0.11, T:0.19
Consensus pattern (26 bp):
AATTACAAATGGCCCAAGTCAGCCCA
Found at i:31525 original size:3 final size:3
Alignment explanation
Indices: 31519--31557 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
31509 AATAGCTGTT
31519 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
31558 GCATTAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:31565 original size:15 final size:15
Alignment explanation
Indices: 31493--31565 Score: 58
Period size: 15 Copynumber: 4.8 Consensus size: 15
31483 AACGTTTTTA
31493 AATAGTCATTAATAAT
1 AATAG-CATTAATAAT
*
31509 AATAGC-TGTTATAAT
1 AATAGCAT-TAATAAT
** *
31524 AATAATAATAATAAT
1 AATAGCATTAATAAT
** *
31539 AATAATAATAATAAT
1 AATAGCATTAATAAT
31554 AATAGCATTAAT
1 AATAGCATTAAT
31566 GACATTAACA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
14 1 0.02
15 41 0.87
16 5 0.11
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (15 bp):
AATAGCATTAATAAT
Found at i:32254 original size:12 final size:12
Alignment explanation
Indices: 32232--32260 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
32222 CTGAGCTATT
32232 ACCCG-AATCCG
1 ACCCGAAATCCG
32243 ACCCGAAATCCG
1 ACCCGAAATCCG
32255 ACCCGA
1 ACCCGA
32261 CTTGACTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.31, C:0.45, G:0.17, T:0.07
Consensus pattern (12 bp):
ACCCGAAATCCG
Found at i:32807 original size:59 final size:59
Alignment explanation
Indices: 32633--32953 Score: 394
Period size: 59 Copynumber: 5.4 Consensus size: 59
32623 CCCTGGAGGT
* * * *
32633 CCCCGAACTTCCAAATATCCCATTTTTTACCCCGAAAACTTCCAAAAATT-TCGTTTTTAC
1 CCCCAAACTTCCAAAAATCCCATTTTTAACCCC-AAAACTTCCAAAAATTCT-ATTTTTAC
* * * * * *
32693 CCCCGAACTTTCGAAAATCCCATTTTT-ACCTCGAAACTTCCAAAAATTCTATTTTTAA
1 CCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCTATTTTTAC
* *
32751 CCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCTATTTTTAC
1 CCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCTATTTTTAC
* * * *
32810 CCCCGAACTTCCAAAAATCTCATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTTAC
1 CCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCTATTTTTAC
* * * *
32869 CCCCAAACTGCCCAAAATCCCATTTTTAACCCAAAAACTTCCAAAAATTCCATTTTTAC
1 CCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCTATTTTTAC
** * *
32928 CCTTAAATTTCGAAAAATCCCATTTT
1 CCCCAAACTTCCAAAAATCCCATTTT
32954 CGACACTCTC
Statistics
Matches: 228, Mismatches: 31, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
58 44 0.19
59 160 0.70
60 24 0.11
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.32
Consensus pattern (59 bp):
CCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCTATTTTTAC
Found at i:32943 original size:29 final size:30
Alignment explanation
Indices: 32638--32953 Score: 295
Period size: 29 Copynumber: 10.7 Consensus size: 30
32628 GAGGTCCCCG
* * *
32638 AACTTCCAAATATCCCATTTTTTACCCCGAA
1 AACTTCCAAAAATTCCATTTTTAACCCC-AA
* * **
32669 AACTTCCAAAAATTTCGTTTTT-ACCCCCG
1 AACTTCCAAAAATTCCATTTTTAACCCCAA
* * * * *
32698 AACTTTCGAAAATCCCATTTTT-ACCTCGA
1 AACTTCCAAAAATTCCATTTTTAACCCCAA
* *
32727 AACTTCCAAAAATTCTATTTTTAA-CCCTA
1 AACTTCCAAAAATTCCATTTTTAACCCCAA
* *
32756 AACTTCCAAAAATCCCATTTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTTAACCCCAA
* **
32786 AACTTCCAAAAATTCTATTTTT-ACCCCCG
1 AACTTCCAAAAATTCCATTTTTAACCCCAA
*
32815 AACTTCCAAAAA-TCTCATTTTTAACCCTAA
1 AACTTCCAAAAATTC-CATTTTTAACCCCAA
*
32845 AACTTCCAAAAATTCCATTTTT-ACCCCCA
1 AACTTCCAAAAATTCCATTTTTAACCCCAA
* * * *
32874 AACTGCCCAAAATCCCATTTTTAACCCAAA
1 AACTTCCAAAAATTCCATTTTTAACCCCAA
**
32904 AACTTCCAAAAATTCCATTTTT-ACCCTTA
1 AACTTCCAAAAATTCCATTTTTAACCCCAA
* * *
32933 AATTTCGAAAAATCCCATTTT
1 AACTTCCAAAAATTCCATTTT
32954 CGACACTCTC
Statistics
Matches: 232, Mismatches: 47, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
28 2 0.01
29 133 0.57
30 77 0.33
31 20 0.09
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (30 bp):
AACTTCCAAAAATTCCATTTTTAACCCCAA
Found at i:34055 original size:29 final size:29
Alignment explanation
Indices: 34000--34189 Score: 170
Period size: 29 Copynumber: 6.4 Consensus size: 29
33990 CCCTAGAGGT
* * *
34000 CCCTGAACTATCCAAAATTTTCATTTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAC
* *
34030 CTCTAAACTTCTAAAAATTCCATTTTTGAC
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* *
34060 CTC-GAACTTCCAAAAATTCCATTTTTTAC
1 CCCTAAACTTCCAAAAATTCCA-TTTTTAC
* *
34089 CCCCAAACTTCC-AAAATCCCATTTTTGAC
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* * * *
34118 CCCAAAATTTCCAAAAGTTTCATTTTTA-
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
*
34146 CCCTCGAACTTCCAAAAATTCCATTTTTAAC
1 CCCT-AAACTTCCAAAAATTCCATTTTT-AC
*
34177 CCCGAAACTTCCA
1 CCCTAAACTTCCA
34190 TTTTTTACCC
Statistics
Matches: 130, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
28 8 0.06
29 75 0.58
30 44 0.34
31 3 0.02
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAC
Found at i:34076 original size:59 final size:55
Alignment explanation
Indices: 34004--34189 Score: 183
Period size: 59 Copynumber: 3.2 Consensus size: 55
33994 AGAGGTCCCT
*
34004 GAACTATCCAAAATTTTCATTTTTACCTCTAAACTTCTAAAAATTCCATTTTTGACCTC
1 GAACT-TCCAAAA-TTTCATTTTTACC-CTAAACTTC-AAAAATTCCATTTTTGACCCC
* * * *
34063 GAACTTCCAAAAATTCCATTTTTTACCCCCAAACTTCCAAAATCCCATTTTTGACCCC
1 GAACTTCC-AAAATTTCA-TTTTTA-CCCTAAACTTCAAAAATTCCATTTTTGACCCC
* * * *
34121 AAAATTTCCAAAAGTTTCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCC
1 -GAACTTCCAAAA-TTTCATTTTTACCCT-AAACTT-CAAAAATTCCATTTTTGACCCC
34180 GAAACTTCCA
1 G-AACTTCCA
34190 TTTTTTACCC
Statistics
Matches: 104, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
57 3 0.03
58 40 0.38
59 59 0.57
60 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (55 bp):
GAACTTCCAAAATTTCATTTTTACCCTAAACTTCAAAAATTCCATTTTTGACCCC
Found at i:34190 original size:21 final size:21
Alignment explanation
Indices: 34164--34230 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
34154 CTTCCAAAAA
34164 TTCCATTTTTAACCCCGAAAC
1 TTCCATTTTTAACCCCGAAAC
* * *
34185 TTCCATTTTTTACCCCAAAAA
1 TTCCATTTTTAACCCCGAAAC
*
34206 TTCCATTTTTATCCCCG-AAC
1 TTCCATTTTTAACCCCGAAAC
34226 TTCCA
1 TTCCA
34231 AAAATGCCAT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 7 0.18
21 32 0.82
ACGTcount: A:0.27, C:0.33, G:0.03, T:0.37
Consensus pattern (21 bp):
TTCCATTTTTAACCCCGAAAC
Found at i:34216 original size:71 final size:72
Alignment explanation
Indices: 34128--34261 Score: 200
Period size: 71 Copynumber: 1.9 Consensus size: 72
34118 CCCAAAATTT
* * * *
34128 CCAAAAGTTTCATTTTTA-CCCTCGAACTTCCAAAAATTCCA-TTTTTAACCCCGAAACTTCCAT
1 CCAAAAATTCCATTTTTATCCC-CGAACTTCCAAAAATGCCATTTTTTAACCCCAAAACTTCCAT
34191 TTTTTACC
65 TTTTTACC
*
34199 CCAAAAATTCCATTTTTATCCCCGAACTTCCAAAAATGCCATTTTTTACCCCCAAAACTTCCA
1 CCAAAAATTCCATTTTTATCCCCGAACTTCCAAAAATGCCATTTTTTAACCCCAAAACTTCCA
34262 AAAATCCCAT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
71 34 0.61
72 22 0.39
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.34
Consensus pattern (72 bp):
CCAAAAATTCCATTTTTATCCCCGAACTTCCAAAAATGCCATTTTTTAACCCCAAAACTTCCATT
TTTTACC
Found at i:34261 original size:31 final size:29
Alignment explanation
Indices: 34199--34293 Score: 109
Period size: 29 Copynumber: 3.2 Consensus size: 29
34189 ATTTTTTACC
* * *
34199 CCAAAAATTCCATTTTTATCCCCGAACTT
1 CCAAAAATCCCATTTTTACCCCCAAACTT
*
34228 CCAAAAATGCCATTTTTTACCCCCAAAACTT
1 CCAAAAATCCCA-TTTTTACCCCC-AAACTT
* * *
34259 CCAAAAATCCCATTTTTACCCTCGAACCT
1 CCAAAAATCCCATTTTTACCCCCAAACTT
34288 CCAAAA
1 CCAAAA
34294 TCTCCAATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
29 21 0.37
30 20 0.35
31 16 0.28
ACGTcount: A:0.35, C:0.34, G:0.03, T:0.28
Consensus pattern (29 bp):
CCAAAAATCCCATTTTTACCCCCAAACTT
Found at i:34316 original size:131 final size:130
Alignment explanation
Indices: 34069--34316 Score: 338
Period size: 131 Copynumber: 1.9 Consensus size: 130
34059 CCTCGAACTT
*
34069 CCAAAAATTCCATTTTTTACCCCCAAACTTCCAAAATCCCATTTTTGACCCCAAAATTTCCAAAA
1 CCAAAAATTCCATTTTTTACCCCCAAACTTCCAAAATCCCATTTTTGACCCCAAAACTTCCAAAA
* ** * * * *
34134 GTTTCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCGAAACTTCCATTTTTTACC
66 ATCCCATTTTTACCCTCGAACCTCCAAAAATTCCAATTTCAACCCCAAAACTTCCATTTTTTACC
* * * *
34199 CCAAAAATTCCA-TTTTTATCCCCGAACTTCCAAAAATGCCATTTTTTACCCCCAAAACTTCCAA
1 CCAAAAATTCCATTTTTTACCCCCAAACTTCC-AAAATCCCATTTTTGA-CCCCAAAACTTCCAA
*
34263 AAATCCCATTTTTACCCTCGAACCTCC-AAAATCTCCAATTTCAACCTCAAAACT
64 AAATCCCATTTTTACCCTCGAACCTCCAAAAAT-TCCAATTTCAACCCCAAAACT
34317 CTCAAAATTA
Statistics
Matches: 102, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
129 17 0.17
130 31 0.30
131 54 0.53
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (130 bp):
CCAAAAATTCCATTTTTTACCCCCAAACTTCCAAAATCCCATTTTTGACCCCAAAACTTCCAAAA
ATCCCATTTTTACCCTCGAACCTCCAAAAATTCCAATTTCAACCCCAAAACTTCCATTTTTTACC
Found at i:34362 original size:29 final size:28
Alignment explanation
Indices: 34199--34362 Score: 93
Period size: 29 Copynumber: 5.6 Consensus size: 28
34189 ATTTTTTACC
34199 CCAAAAATTCCATTTTTATCCC-CGAACTT
1 CCAAAAATTCCATTTTTA-CCCTCGAA-TT
* * *
34228 CCAAAAATGCCATTTTTTACCCCCAAAACTT
1 CCAAAAATTCCA-TTTTTACCCTC-GAA-TT
* *
34259 CCAAAAATCCCATTTTTACCCTCGAACCT
1 CCAAAAATTCCATTTTTACCCTCGAA-TT
* * * * *
34288 CC-AAAATCTCCAATTTCAACCTCAAAACT
1 CCAAAAAT-TCCATTTTTACCCTC-GAATT
*
34317 CTC-AAAATTACC-CTTTTACCCTCGAATGT
1 C-CAAAAATT-CCATTTTTACCCTCGAAT-T
*
34346 CTAAAAATTCCATTTTT
1 CCAAAAATTCCATTTTT
34363 TTAACCTCAA
Statistics
Matches: 107, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
28 9 0.08
29 55 0.51
30 27 0.25
31 16 0.15
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.32
Consensus pattern (28 bp):
CCAAAAATTCCATTTTTACCCTCGAATT
Done.