Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012602.1 Kokia drynarioides strain JFW-HI SEQ_127611, 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: 107664
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 320 characters in sequence are not A, C, G, or T
Found at i:6533 original size:22 final size:23
Alignment explanation
Indices: 6508--6550 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
6498 TGAATTTGCA
*
6508 ACTCGAATTAGTT-ATTTAAATG
1 ACTCGAATTAATTAATTTAAATG
*
6530 ACTCGATTTAATTAATTTAAA
1 ACTCGAATTAATTAATTTAAA
6551 ATTCAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (23 bp):
ACTCGAATTAATTAATTTAAATG
Found at i:8383 original size:2 final size:2
Alignment explanation
Indices: 8376--8406 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8366 CAAAATAATG
8376 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8407 AAACAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15101 original size:9 final size:9
Alignment explanation
Indices: 15066--15095 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
15056 TCTTTCGTGA
15066 TAATTAATG
1 TAATTAATG
15075 TAACTTAATG
1 TAA-TTAATG
15085 TAATTAATG
1 TAATTAATG
15094 TA
1 TA
15096 TATAATTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.43
Consensus pattern (9 bp):
TAATTAATG
Found at i:22047 original size:19 final size:18
Alignment explanation
Indices: 22019--22054 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
22009 AAGCTTTAAA
*
22019 ATGGAAGGTATATTTATG
1 ATGGAAGGTAGATTTATG
22037 ATGGTAAGGTAGATTTAT
1 ATGG-AAGGTAGATTTAT
22055 AAATCATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (18 bp):
ATGGAAGGTAGATTTATG
Found at i:23992 original size:30 final size:31
Alignment explanation
Indices: 23958--24015 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
23948 CTTATGGTAA
23958 AAATAAAA-ATTAATAAAA-TTTATTAAATCT
1 AAATAAAAGA-TAATAAAATTTTATTAAATCT
*
23988 AAATAAAAGATATTAAAATTTTATTAAA
1 AAATAAAAGATAATAAAATTTTATTAAA
24016 AATTAAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (31 bp):
AAATAAAAGATAATAAAATTTTATTAAATCT
Found at i:24402 original size:21 final size:21
Alignment explanation
Indices: 24368--24413 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
24358 TGAGTTTAAT
* * *
24368 TTTTTTTAATATTTTGTATAA
1 TTTTTTTAAGATTTTATAAAA
*
24389 TTTTTTTACGATTTTATAAAA
1 TTTTTTTAAGATTTTATAAAA
24410 TTTT
1 TTTT
24414 ATAATTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTTTTTAAGATTTTATAAAA
Found at i:24403 original size:29 final size:26
Alignment explanation
Indices: 24371--24457 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 26
24361 GTTTAATTTT
24371 TTTTAATATTTTGTATAATTTTTTTACGA
1 TTTTAA-ATTTT-TATAATTTTTTTAC-A
* *
24400 TTTTATAAAATTTTATAATTTTTTTATA
1 -TTT-TAAATTTTTATAATTTTTTTACA
*
24428 TTTTTAAATATTTATAA-TTTTTTACA
1 -TTTTAAATTTTTATAATTTTTTTACA
24454 TTTT
1 TTTT
24458 TATAAAATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
25 4 0.08
26 8 0.16
27 11 0.22
28 5 0.10
29 13 0.25
30 7 0.14
31 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTTAAATTTTTATAATTTTTTTACA
Found at i:24420 original size:18 final size:18
Alignment explanation
Indices: 24392--24476 Score: 73
Period size: 18 Copynumber: 4.7 Consensus size: 18
24382 TGTATAATTT
*
24392 TTTTACGATTTTATAAAA
1 TTTTACAATTTTATAAAA
* * * *
24410 TTTTATAATTTTTTTATAT
1 TTTTACAA-TTTTATAAAA
**
24429 TTTTA-AATATTTATAATT
1 TTTTACAAT-TTTATAAAA
*
24447 TTTTACATTTTTATAAAA
1 TTTTACAATTTTATAAAA
24465 TTTTACAATTTT
1 TTTTACAATTTT
24477 TAATAATAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
17 1 0.02
18 37 0.71
19 14 0.27
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (18 bp):
TTTTACAATTTTATAAAA
Found at i:24423 original size:10 final size:10
Alignment explanation
Indices: 24364--24505 Score: 59
Period size: 10 Copynumber: 14.7 Consensus size: 10
24354 ATTATGAGTT
*
24364 TAATTTTTTT
1 TAATTTTTTA
24374 TAATATTTTGTA
1 TAAT-TTTT-TA
24386 TAATTTTTT-
1 TAATTTTTTA
***
24395 TACGATTTTA
1 TAATTTTTTA
**
24405 TAAAATTTTA
1 TAATTTTTTA
24415 TAATTTTTT-
1 TAATTTTTTA
24424 T-ATATTTTTA
1 TAAT-TTTTTA
*
24434 -AA-TATTTA
1 TAATTTTTTA
24442 TAATTTTTTA
1 TAATTTTTTA
*
24452 -CA-TTTTTA
1 TAATTTTTTA
**
24460 TAAAATTTTA
1 TAATTTTTTA
* *
24470 CAATTTTTAA
1 TAATTTTTTA
**
24480 TAATAATTTA
1 TAATTTTTTA
24490 GT-ATTTTTTA
1 -TAATTTTTTA
24500 T-ATTTT
1 TAATTTT
24506 ATAAATTTAA
Statistics
Matches: 98, Mismatches: 23, Indels: 23
0.68 0.16 0.16
Matches are distributed among these distances:
8 13 0.13
9 22 0.22
10 49 0.50
11 9 0.09
12 5 0.05
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:26653 original size:13 final size:13
Alignment explanation
Indices: 26635--26660 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26625 TTTATATAGC
26635 TAATATTAAAATT
1 TAATATTAAAATT
26648 TAATATTAAAATT
1 TAATATTAAAATT
26661 ATAGAAAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATATTAAAATT
Found at i:28820 original size:31 final size:32
Alignment explanation
Indices: 28784--28846 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
28774 TTGATCATTG
* *
28784 AACTATTCGAAAG-TTTTTATTTAAGTTACTA
1 AACTATTCAAAAGTTTTTTATTTAAGTAACTA
28815 AACTATTCAAAAGTTTTTTATTTAAGTAACTA
1 AACTATTCAAAAGTTTTTTATTTAAGTAACTA
28847 GGCTGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 12 0.41
32 17 0.59
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (32 bp):
AACTATTCAAAAGTTTTTTATTTAAGTAACTA
Found at i:29123 original size:62 final size:62
Alignment explanation
Indices: 29026--29151 Score: 180
Period size: 62 Copynumber: 2.0 Consensus size: 62
29016 AATTGAATTG
* * * *
29026 TAGAAGAGAAGGGGAAAAAACACTTTTGATTGATGCACACAATGCAAATAGAGCAAGCCATA
1 TAGAAGAGAAGAGGAAAAAACACTGTTGATTGATGCACACAATACAAATAGAGAAAGCCATA
* * * *
29088 TAGAAGAGAAGAGGAAAGAGCGCTGTTGATTGATGCACACAATATAAATAGAGAAAGCCATA
1 TAGAAGAGAAGAGGAAAAAACACTGTTGATTGATGCACACAATACAAATAGAGAAAGCCATA
29150 TA
1 TA
29152 TCATCGATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.45, C:0.13, G:0.24, T:0.18
Consensus pattern (62 bp):
TAGAAGAGAAGAGGAAAAAACACTGTTGATTGATGCACACAATACAAATAGAGAAAGCCATA
Found at i:42574 original size:18 final size:18
Alignment explanation
Indices: 42551--42587 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
42541 AAACGTCAGC
42551 AACCATGGGAGAGGACAT
1 AACCATGGGAGAGGACAT
42569 AACCATGGGAGAGGACAT
1 AACCATGGGAGAGGACAT
42587 A
1 A
42588 CTCTCCTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.32, T:0.11
Consensus pattern (18 bp):
AACCATGGGAGAGGACAT
Found at i:42899 original size:15 final size:15
Alignment explanation
Indices: 42861--42901 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
42851 TTACGAAAAA
42861 TATTATTTTTATAAT
1 TATTATTTTTATAAT
*
42876 TATT-GTTTT-TAAT
1 TATTATTTTTATAAT
42889 TACTTATTTTTAT
1 TA-TTATTTTTAT
42902 TATTGATAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
13 6 0.29
14 6 0.29
15 8 0.38
16 1 0.05
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (15 bp):
TATTATTTTTATAAT
Found at i:59199 original size:18 final size:18
Alignment explanation
Indices: 59176--59210 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59166 TGGGGTAATC
59176 TAAATAACCTAAACATAA
1 TAAATAACCTAAACATAA
* *
59194 TAAATAGCTTAAACATA
1 TAAATAACCTAAACATA
59211 TTTAAGAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.26
Consensus pattern (18 bp):
TAAATAACCTAAACATAA
Found at i:61320 original size:4 final size:4
Alignment explanation
Indices: 61313--61337 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
61303 GAAACCTCTC
61313 TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
61338 TGCAAGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:62801 original size:14 final size:14
Alignment explanation
Indices: 62765--62802 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
62755 TATTATGTTT
62765 ATATAA-TTTTTTA
1 ATATAATTTTTTTA
62778 ATA-AAGTTTTTTTA
1 ATATAA-TTTTTTTA
62792 ATATAATTTTT
1 ATATAATTTTT
62803 AAATAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 2 0.09
13 3 0.14
14 15 0.68
15 2 0.09
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (14 bp):
ATATAATTTTTTTA
Found at i:62811 original size:12 final size:12
Alignment explanation
Indices: 62769--62811 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 12
62759 ATGTTTATAT
62769 AATTTTTTAATA
1 AATTTTTTAATA
62781 AAGTTTTTTTAATA
1 AA--TTTTTTAATA
*
62795 TAATTTTTAAATA
1 -AATTTTTTAATA
62808 AATT
1 AATT
62812 AATATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 6 0.22
13 9 0.33
14 10 0.37
15 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
AATTTTTTAATA
Found at i:66254 original size:93 final size:93
Alignment explanation
Indices: 66105--66456 Score: 420
Period size: 93 Copynumber: 3.8 Consensus size: 93
66095 GGTGGTGGTG
* * * * * * * * *
66105 CATGGGGACCTGACCCTAGAGGAGGAGCGTGGCCTGGATGAGGATGACCAGCATGTGATGCACCC
1 CATGGGGACCTGGCCCTGGAGGAGGAGCATGGCTTGGATGAAGATGATCATCATGTGGTGCACCT
*
66170 GGAGAATGTCCAGGTCTTGGTGGTGACA
66 GGAGGATGTCCAGGTCTTGGTGGTGACA
* * * * *
66198 CATGAGGACCTGGTCCTGGAGGAGGAGCATGGCTTGGATGAAGATGATCATTATGTGGTGGACTT
1 CATGGGGACCTGGCCCTGGAGGAGGAGCATGGCTTGGATGAAGATGATCATCATGTGGTGCACCT
* * * *
66263 GGAGGATGACCTGGT-TCTAGTGGTGACG
66 GGAGGATGTCCAGGTCT-TGGTGGTGACA
* * *
66291 CATGGGGACCTGGCCCTGGAGGAGGAGCATGGCTTGGATGAGGATGCTCAACATGTGGTGCACCT
1 CATGGGGACCTGGCCCTGGAGGAGGAGCATGGCTTGGATGAAGATGATCATCATGTGGTGCACCT
*
66356 GGAGGATGTCTAGGTCTTGGTGGTGACA
66 GGAGGATGTCCAGGTCTTGGTGGTGACA
* * * * *
66384 CATGGGGACCTGGTCCTGGAGGAAGAGCATGG-TGTGGATGAAGATGATCATTATGTGGTGGACT
1 CATGGGGACCTGGCCCTGGAGGAGGAGCATGGCT-TGGATGAAGATGATCATCATGTGGTGCACC
66448 TGGAGGATG
65 TGGAGGATG
66457 ACTTGATCCT
Statistics
Matches: 216, Mismatches: 40, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
92 2 0.01
93 213 0.99
94 1 0.00
ACGTcount: A:0.22, C:0.16, G:0.39, T:0.23
Consensus pattern (93 bp):
CATGGGGACCTGGCCCTGGAGGAGGAGCATGGCTTGGATGAAGATGATCATCATGTGGTGCACCT
GGAGGATGTCCAGGTCTTGGTGGTGACA
Found at i:66395 original size:186 final size:186
Alignment explanation
Indices: 66078--66502 Score: 629
Period size: 186 Copynumber: 2.3 Consensus size: 186
66068 TGTGGCTCAA
* * * *
66078 GAGGATGACCTGATCCTGGTGGTGGTGCATGGGGACCTGACCCTAGAGGAGGAGCGTGGCCTGGA
1 GAGGATGACCTGATCCTAGTGGTGGTGCATGGGGACCTGGCCCTGGAGGAGGAGCATGGCCTGGA
*
66143 TGAGGATGACCAGCATGTGATGCACCCGGAGAATGTCCAGGTCTTGGTGGTGACACATGAGGACC
66 TGAGGATGACCAACATGTGATGCACCCGGAGAATGTCCAGGTCTTGGTGGTGACACATGAGGACC
*
66208 TGGTCCTGGAGGAGGAGCATGGCT-TGGATGAAGATGATCATTATGTGGTGGACTTG
131 TGGTCCTGGAGGAAGAGCATGG-TGTGGATGAAGATGATCATTATGTGGTGGACTTG
* * ** *
66264 GAGGATGACCTGGTTCTAGTGGTGACGCATGGGGACCTGGCCCTGGAGGAGGAGCATGGCTTGGA
1 GAGGATGACCTGATCCTAGTGGTGGTGCATGGGGACCTGGCCCTGGAGGAGGAGCATGGCCTGGA
* * * * *
66329 TGAGGATG-CTCAACATGTGGTGCACCTGGAGGATGTCTAGGTCTTGGTGGTGACACATGGGGAC
66 TGAGGATGAC-CAACATGTGATGCACCCGGAGAATGTCCAGGTCTTGGTGGTGACACATGAGGAC
66393 CTGGTCCTGGAGGAAGAGCATGGTGTGGATGAAGATGATCATTATGTGGTGGACTTG
130 CTGGTCCTGGAGGAAGAGCATGGTGTGGATGAAGATGATCATTATGTGGTGGACTTG
* ** * *
66450 GAGGATGACTTGATCCTAACGGTGGTGCATGGGGACCTAGTCCTGGAGGAGGA
1 GAGGATGACCTGATCCTAGTGGTGGTGCATGGGGACCTGGCCCTGGAGGAGGA
66503 CGCTTAACAT
Statistics
Matches: 212, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
185 2 0.01
186 210 0.99
ACGTcount: A:0.21, C:0.17, G:0.39, T:0.23
Consensus pattern (186 bp):
GAGGATGACCTGATCCTAGTGGTGGTGCATGGGGACCTGGCCCTGGAGGAGGAGCATGGCCTGGA
TGAGGATGACCAACATGTGATGCACCCGGAGAATGTCCAGGTCTTGGTGGTGACACATGAGGACC
TGGTCCTGGAGGAAGAGCATGGTGTGGATGAAGATGATCATTATGTGGTGGACTTG
Found at i:66481 original size:93 final size:91
Alignment explanation
Indices: 66097--66502 Score: 386
Period size: 93 Copynumber: 4.4 Consensus size: 91
66087 CTGATCCTGG
** * * * * * **
66097 TGGTGGTGCATGGGGACCTGACCCTAGAGGAGGAGCGTGGCCTGGATGAGGATGACCAGCATGTG
1 TGGTGGTGCATGGGGACCTGGTCCTGGAGGAGGAGCATGGCTTGGATGAAGATGATCATTATGTG
* * ** * * **
66162 ATGCACCCGGAGAATGTCCAGGTCT-
66 GTGGACTTGGAGGATGACTTGGTCTA
*
66187 TGGTGGTGACACATGAGGACCTGGTCCTGGAGGAGGAGCATGGCTTGGATGAAGATGATCATTAT
1 TGGTGGTG---CATGGGGACCTGGTCCTGGAGGAGGAGCATGGCTTGGATGAAGATGATCATTAT
*
66252 GTGGTGGACTTGGAGGATGACCTGGTTCTA
63 GTGGTGGACTTGGAGGATGACTTGG-TCTA
** * * * **
66282 GTGGTGACGCATGGGGACCTGGCCCTGGAGGAGGAGCATGGCTTGGATGAGGATGCTCAACATGT
1 -TGGTGGTGCATGGGGACCTGGTCCTGGAGGAGGAGCATGGCTTGGATGAAGATGATCATTATGT
* * * *
66347 GGTGCACCTGGAGGATGTCTAGGTCT-
65 GGTGGACTTGGAGGATGACTTGGTCTA
*
66373 TGGTGGTGACACATGGGGACCTGGTCCTGGAGGAAGAGCATGG-TGTGGATGAAGATGATCATTA
1 TGGTGGTG---CATGGGGACCTGGTCCTGGAGGAGGAGCATGGCT-TGGATGAAGATGATCATTA
*
66437 TGTGGTGGACTTGGAGGATGACTTGATCCTAA
62 TGTGGTGGACTTGGAGGATGACTTGGT-CT-A
* *
66469 CGGTGGTGCATGGGGACCTAGTCCTGGAGGAGGA
1 TGGTGGTGCATGGGGACCTGGTCCTGGAGGAGGA
66503 CGCTTAACAT
Statistics
Matches: 257, Mismatches: 46, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
90 14 0.05
92 4 0.02
93 221 0.86
94 5 0.02
96 13 0.05
ACGTcount: A:0.21, C:0.17, G:0.39, T:0.23
Consensus pattern (91 bp):
TGGTGGTGCATGGGGACCTGGTCCTGGAGGAGGAGCATGGCTTGGATGAAGATGATCATTATGTG
GTGGACTTGGAGGATGACTTGGTCTA
Found at i:76496 original size:15 final size:16
Alignment explanation
Indices: 76460--76495 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
76450 ATACAAATTT
76460 AAAAATTAAAAAAACG
1 AAAAATTAAAAAAACG
* *
76476 AAAAATTAAATAAACT
1 AAAAATTAAAAAAACG
76492 AAAA
1 AAAA
76496 TGATTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.75, C:0.06, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAAATTAAAAAAACG
Found at i:78051 original size:24 final size:25
Alignment explanation
Indices: 78024--78076 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
78014 TTGGATGGGC
* *
78024 TATTGTGTTTTCTTG-TGTTGAATT
1 TATTGTGTTTTATTGTTGTTAAATT
78048 TATTGTGTTTTATTGTTGTTAAATT
1 TATTGTGTTTTATTGTTGTTAAATT
78073 TATT
1 TATT
78077 TCTATATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.64
Consensus pattern (25 bp):
TATTGTGTTTTATTGTTGTTAAATT
Found at i:78276 original size:31 final size:31
Alignment explanation
Indices: 78167--78276 Score: 82
Period size: 31 Copynumber: 3.5 Consensus size: 31
78157 ATATTTTTCT
*
78167 ATTATGATATATTGATTATTTTAAAACTCAA
1 ATTATGATTTATTGATTATTTTAAAACTCAA
* * * * *** *
78198 ATTATAATTTATTGATAAATATCAGGGCTTAA
1 ATTATGATTTATTGAT-TATTTTAAAACTCAA
78230 A-TAT--TTGTACTTTGATTATTTTAAAACTCAA
1 ATTATGATT-TA--TTGATTATTTTAAAACTCAA
78261 ATTATGATTTATTGAT
1 ATTATGATTTATTGAT
78277 AAAAAAATAT
Statistics
Matches: 56, Mismatches: 16, Indels: 14
0.65 0.19 0.16
Matches are distributed among these distances:
29 2 0.04
30 2 0.04
31 31 0.55
32 17 0.30
33 2 0.04
34 2 0.04
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.46
Consensus pattern (31 bp):
ATTATGATTTATTGATTATTTTAAAACTCAA
Found at i:79154 original size:20 final size:21
Alignment explanation
Indices: 79125--79166 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
79115 TTTCATTACA
79125 TTTTAGTTTATTATAT-ACTT
1 TTTTAGTTTATTATATAACTT
* *
79145 TTTTATTTTATTTTATAACTT
1 TTTTAGTTTATTATATAACTT
79166 T
1 T
79167 AGTCTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTAGTTTATTATATAACTT
Found at i:92712 original size:15 final size:14
Alignment explanation
Indices: 92692--92743 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
92682 AAATTGAAAA
92692 TTTAATTTTTTATAT
1 TTTAA-TTTTTATAT
*
92707 TTTAATTTTTAAAT
1 TTTAATTTTTATAT
*
92721 ATTTAATTCTTATAT
1 -TTTAATTTTTATAT
*
92736 TTTTATTT
1 TTTAATTT
92744 AAAATTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 14 0.45
15 17 0.55
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:105920 original size:2 final size:2
Alignment explanation
Indices: 105913--105944 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
105903 ATGTTTGATG
105913 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
105945 GTATGTAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.