Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010851.1 Kokia drynarioides strain JFW-HI SEQ_125818, 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: 60320
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:731 original size:17 final size:16
Alignment explanation
Indices: 709--795 Score: 59
Period size: 17 Copynumber: 5.2 Consensus size: 16
699 GGACATTTTT
709 TTTAAATGAATTTTAAA
1 TTTAAAT-AATTTTAAA
* **
726 TTTAAATTCATAATAAA
1 TTTAAA-TAATTTTAAA
*
743 TTTAAATAAATTTAAA
1 TTTAAATAATTTTAAA
* *
759 TTTAAGATACA-CTTAAT
1 TTTAA-ATA-ATTTTAAA
*
776 TTTAAAATAAATTTAAA
1 TTT-AAATAATTTTAAA
793 TTT
1 TTT
796 GTTGGGCCCA
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
16 12 0.22
17 38 0.70
18 4 0.07
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (16 bp):
TTTAAATAATTTTAAA
Found at i:1392 original size:206 final size:206
Alignment explanation
Indices: 1032--1580 Score: 825
Period size: 206 Copynumber: 2.7 Consensus size: 206
1022 TCTTGACCTT
* * * *
1032 CTTCTCAGTATCTCATCAGGACA-CTAACCG-TTCATTGCTTCGACCCGCTTCTCCGTGTCTCAT
1 CTTCTCAGTATCTCATCAGGA-AGCCAACCGTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCAT
** ** * *
1095 C-AGAAAGCTGGTATTCGAAGATTTGCTTATATCGAGCGTGGGTTTAATTTGGTCTTCTTCTCAG
65 CAAG-AAGCTGGGGTTCGAAGATTTGCTTACGTCGAGCGTGGATTTGATTTGGTCTTCTTCTCAG
* * * *
1159 AATCTCATCGAGAAGATGACTGCGTCGTTTGTTTCAATTTGTTTCTCTGTATCTCATCAGGAAGA
129 TATCTCATCGAGAAGATGACCGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGA
*
1224 TGAATTTGGTCCA
194 CGAATTTGGTCCA
* *
1237 CTTCTCAGTATCTCATCAGGAAGCCAACCGTTTTATTGCTTTGACCTGCTTCTCAGTTTCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCCAACCGTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATC
*
1302 AAGAAGCTGGGGTTCGAAGATTTACTTACGTCGAGCGTGGATTTGATTTGGTCTTCTTCTCAGTA
66 AAGAAGCTGGGGTTCGAAGATTTGCTTACGTCGAGCGTGGATTTGATTTGGTCTTCTTCTCAGTA
*
1367 TCTCATCGGGAAGATGACCGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACG
131 TCTCATCGAGAAGATGACCGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACG
1432 AATTTGGTCCA
196 AATTTGGTCCA
* * * * * *
1443 CTTTTCAGTATCTCATAAGGAAGCCAACTGTCTTATTACTTCGACCTGCTTCTTAGTGTCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCCAACCGTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATC
*
1508 AGGAAGCTGGGGTTCGAAGATTTGCTTACGTCGAGCGTGGATTTGATTTGGTCTTCTTCTCAGTA
66 AAGAAGCTGGGGTTCGAAGATTTGCTTACGTCGAGCGTGGATTTGATTTGGTCTTCTTCTCAGTA
1573 TCTCATCG
131 TCTCATCG
1581 NNNNNNNNNN
Statistics
Matches: 312, Mismatches: 29, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
204 1 0.00
205 27 0.09
206 282 0.90
207 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (206 bp):
CTTCTCAGTATCTCATCAGGAAGCCAACCGTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATC
AAGAAGCTGGGGTTCGAAGATTTGCTTACGTCGAGCGTGGATTTGATTTGGTCTTCTTCTCAGTA
TCTCATCGAGAAGATGACCGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACG
AATTTGGTCCA
Found at i:13301 original size:96 final size:95
Alignment explanation
Indices: 13128--13308 Score: 233
Period size: 96 Copynumber: 1.9 Consensus size: 95
13118 AAGATATTTA
* *
13128 ATTATCTCGATTTAAAGAAAAGTTGCACCTAGTAAGTTAAGGCGTAATATTTCAGAATCGAAGAT
1 ATTATCTCGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCGAAATATTTCAGAATCGAAGAT
13193 AAGGAAACATTGCCTCGATTAAGGGTATTCG
66 AAGG-AACATTGCCTCGATTAAGGGTATTCG
* * * *
13224 ATTATTTCGATTTGAGGAAAAATTGCACCTAGTAAGTTAAGGCGCAAAT-TTTCGGAACTCGAA-
1 ATTATCTCGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCG-AAATATTTCAGAA-TCGAAG
*
13287 ATAAAAGG-ATATTGCCTCGATT
64 AT--AAGGAACATTGCCTCGATT
13309 TTAAAGTTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
96 62 0.84
97 8 0.11
98 4 0.05
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (95 bp):
ATTATCTCGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCGAAATATTTCAGAATCGAAGAT
AAGGAACATTGCCTCGATTAAGGGTATTCG
Found at i:13667 original size:59 final size:59
Alignment explanation
Indices: 13604--14091 Score: 533
Period size: 59 Copynumber: 8.3 Consensus size: 59
13594 AATTCAGGGT
* * *
13604 TAAAAATGGGATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAGTTCGGGGG
1 TAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
* * * * * *
13663 TAAAAATGAAATTTTTTGAAGTTTTAGGGTTAAAAATGGGATTTTTGGGAGTTCAGGGG
1 TAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
* * * * *
13722 TAAAAATGAAAATTTTTAGAACTTTAGGGGTCAAAAATGGGATTTTT-GAGAGTTTGGGGG
1 TAAAAATG-GAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGA-AGTTCGGGGG
* *
13782 T-AAAATGGTAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGG
1 TAAAAATGG-AATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
* * * * * **
13841 T-AAAATGGTAA-TTTTGGAAGGTTCGAGATCAAAAATGGGATTTTTGAAAGTTCAAGGG
1 TAAAAATGG-AATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
* * * * *
13899 TAAAAATGAAATATTTGGAAGTTTCGGGGTTAAAAATGGGATTTTTGGGAGTTCGGGGG
1 TAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
* * * *
13958 T-AAAATGGTAATTTTTAGAAGTTTTAGGGTCAAAAATGGGATTTTTGGAAGTTTGAGGG
1 TAAAAATGG-AATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
* * *
14017 T-AAAATGGTGATTTTTGGAAAG-TTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
1 TAAAAATGG-AATTTTTGG-AAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
14076 T-AAAATGGTAATTTTT
1 TAAAAATGG-AATTTTT
14092 AGACAATCTA
Statistics
Matches: 367, Mismatches: 54, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
58 47 0.13
59 273 0.74
60 47 0.13
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (59 bp):
TAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
Found at i:14091 original size:29 final size:29
Alignment explanation
Indices: 13604--14080 Score: 383
Period size: 30 Copynumber: 16.2 Consensus size: 29
13594 AATTCAGGGT
* *
13604 TAAAAATGGGATTTTTGGAAGTTTTGGGGT
1 TAAAAATGGGATTTTTGGAAG-TTCGGGGG
*
13634 TAAAAATGGGATTTTTAGAAGTTCGGGGG
1 TAAAAATGGGATTTTTGGAAGTTCGGGGG
** * ** *
13663 TAAAAATGAAATTTTTTGAAGTTTTAGGGT
1 TAAAAATGGGATTTTTGGAAG-TTCGGGGG
* *
13693 TAAAAATGGGATTTTTGGGAGTTCAGGGG
1 TAAAAATGGGATTTTTGGAAGTTCGGGGG
** * * **
13722 TAAAAATGAAAATTTTTAGAACTTTAGGGG
1 TAAAAATG-GGATTTTTGGAAGTTCGGGGG
*
13752 TCAAAAATGGGATTTTT-GAGAGTTTGGGGG
1 T-AAAAATGGGATTTTTGGA-AGTTCGGGGG
* * **
13782 T-AAAATGGTAATTTTTAGAAGTTTTGGGG
1 TAAAAATGG-GATTTTTGGAAGTTCGGGGG
*
13811 TCAAAAATGGGATTTTTGGAAGTTTGGGGG
1 T-AAAAATGGGATTTTTGGAAGTTCGGGGG
* * * *
13841 T-AAAATGGTAATTTTGGAAGGTTC-GAGA
1 TAAAAATGGGATTTTTGGAA-GTTCGGGGG
* **
13869 TCAAAAATGGGATTTTTGAAAGTTCAAGGG
1 T-AAAAATGGGATTTTTGGAAGTTCGGGGG
** * *
13899 TAAAAATGAAATATTTGGAAGTTTCGGGGT
1 TAAAAATGGGATTTTTGGAAG-TTCGGGGG
*
13929 TAAAAATGGGATTTTTGGGAGTTCGGGGG
1 TAAAAATGGGATTTTTGGAAGTTCGGGGG
* * ***
13958 T-AAAATGGTAATTTTTAGAAGTTTTAGGG
1 TAAAAATGG-GATTTTTGGAAGTTCGGGGG
* *
13987 TCAAAAATGGGATTTTTGGAAGTTTGAGGG
1 T-AAAAATGGGATTTTTGGAAGTTCGGGGG
*
14017 T-AAAATGGTGATTTTTGGAAAGTTC-GAGG
1 TAAAAATGG-GATTTTTGG-AAGTTCGGGGG
14046 TCAAAAATGGGATTTTTGGAAGTTCGGGGG
1 T-AAAAATGGGATTTTTGGAAGTTCGGGGG
14076 TAAAA
1 TAAAA
14081 TGGTAATTTT
Statistics
Matches: 360, Mismatches: 66, Indels: 43
0.77 0.14 0.09
Matches are distributed among these distances:
28 40 0.11
29 124 0.34
30 168 0.47
31 28 0.08
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (29 bp):
TAAAAATGGGATTTTTGGAAGTTCGGGGG
Found at i:15788 original size:17 final size:16
Alignment explanation
Indices: 15768--15851 Score: 51
Period size: 17 Copynumber: 5.0 Consensus size: 16
15758 TTTTTTTTAA
15768 AAATGAATTTTAAATTT
1 AAAT-AATTTTAAATTT
* ** *
15785 AAATTCATAATAAATTC
1 AAA-TAATTTTAAATTT
*
15802 AAATAAATTTAAATTT
1 AAATAATTTTAAATTT
** *
15818 AAGATAAACTTAATTTT
1 AA-ATAATTTTAAATTT
*
15835 AAAATAAATTTAAATTT
1 -AAATAATTTTAAATTT
15852 GTTGGGCCCA
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
16 10 0.20
17 38 0.75
18 3 0.06
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (16 bp):
AAATAATTTTAAATTT
Found at i:22230 original size:58 final size:58
Alignment explanation
Indices: 22140--22257 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
22130 CTATAATGTT
22140 ATTCGTAATGCTTCTCTCAGGAACAAAACAAGATTGGTTCGGATGTACCCATTTTATC
1 ATTCGTAATGCTTCTCTCAGGAACAAAACAAGATTGGTTCGGATGTACCCATTTTATC
22198 ATTCGTAATGCTTCTCTCAGGAACAAAACAAGATTGGTTCGGATGTACCCATTTTATC
1 ATTCGTAATGCTTCTCTCAGGAACAAAACAAGATTGGTTCGGATGTACCCATTTTATC
22256 AT
1 AT
22258 CAAGGGCCGC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (58 bp):
ATTCGTAATGCTTCTCTCAGGAACAAAACAAGATTGGTTCGGATGTACCCATTTTATC
Found at i:26351 original size:11 final size:11
Alignment explanation
Indices: 26335--26402 Score: 50
Period size: 11 Copynumber: 6.0 Consensus size: 11
26325 ATCAAACCTT
26335 TTTTAAATTTA
1 TTTTAAATTTA
26346 TTTTAAATTTTAA
1 TTTTAAA-TTT-A
*
26359 TTTT--TTTTAA
1 TTTTAAATTT-A
* *
26369 ATTTAAATTAA
1 TTTTAAATTTA
*
26380 ATTTAAATTTA
1 TTTTAAATTTA
26391 CTTTTAAATTTA
1 -TTTTAAATTTA
26403 AAATTATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
10 8 0.17
11 18 0.39
12 15 0.33
13 5 0.11
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:26371 original size:28 final size:28
Alignment explanation
Indices: 26333--26404 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
26323 AAATCAAACC
** *
26333 TTTTTTAAATTTATTTTAAATTTTAATT
1 TTTTTTAAATTTAAATTAAATTTAAATT
26361 TTTTTTAAATTTAAATTAAATTTAAATT
1 TTTTTTAAATTTAAATTAAATTTAAATT
*
26389 TACTTTTAAATTTAAA
1 T-TTTTTAAATTTAAA
26405 ATTATTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 26 0.67
29 13 0.33
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTTTAAATTTAAATTAAATTTAAATT
Found at i:26399 original size:18 final size:17
Alignment explanation
Indices: 26336--26422 Score: 69
Period size: 17 Copynumber: 5.4 Consensus size: 17
26326 TCAAACCTTT
*
26336 TTTAAATTTATTTTAAA
1 TTTAAAATTATTTTAAA
* * *
26353 TTTTAATTTTTTTTAAA
1 TTTAAAATTATTTTAAA
26370 TTT--AA--A--TTAAA
1 TTTAAAATTATTTTAAA
*
26381 TTTAAATTTACTTTTAAA
1 TTTAAAATTA-TTTTAAA
*
26399 TTTAAAATTATTTTATA
1 TTTAAAATTATTTTAAA
26416 TTTAAAA
1 TTTAAAA
26423 AAAAGTTCAA
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
11 8 0.14
13 1 0.02
15 2 0.04
17 31 0.55
18 14 0.25
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAAATTATTTTAAA
Found at i:26404 original size:6 final size:6
Alignment explanation
Indices: 26336--26404 Score: 63
Period size: 6 Copynumber: 12.0 Consensus size: 6
26326 TCAAACCTTT
* * **
26336 TTTAAA TTT-AT TTTAAA TTTTAA TTT-TT TTTAAA TTTAAA -TTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
26381 TTTAAA TTTACT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
26405 ATTATTTTAT
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
5 12 0.24
6 37 0.76
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:26418 original size:17 final size:18
Alignment explanation
Indices: 26376--26422 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
26366 TAAATTTAAA
*
26376 TTAAATTTAAATTTACTT
1 TTAAATTTAAAATTACTT
26394 TTAAATTTAAAATTA-TT
1 TTAAATTTAAAATTACTT
*
26411 TTATATTTAAAA
1 TTAAATTTAAAA
26423 AAAAGTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAAATTTAAAATTACTT
Found at i:26419 original size:23 final size:22
Alignment explanation
Indices: 26342--26421 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
26332 CTTTTTTAAA
* *
26342 TTTATTTTAAATTTTAATTTTT
1 TTTATTTTAAATTTAAATTTAT
* *
26364 TTTAAATTTAAA-TTAAATTTAAA
1 TTT-ATTTTAAATTTAAATTT-AT
*
26387 TTTACTTTTAAATTTAAAATTAT
1 TTTA-TTTTAAATTTAAATTTAT
26410 TTTATATTTAAA
1 TTTAT-TTTAAA
26422 AAAAAGTTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
22 12 0.26
23 27 0.59
24 7 0.15
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTATTTTAAATTTAAATTTAT
Found at i:28058 original size:29 final size:29
Alignment explanation
Indices: 27973--28456 Score: 304
Period size: 29 Copynumber: 16.6 Consensus size: 29
27963 CCCATAAGAT
*
27973 CCCTAAACTATTCAAAAA-T-CATGTTTTGAC
1 CCCTAAACT-TCCAAAAATTACAT-TTTT-AC
* * *
28003 CCCCAAACTTTCCAAAAATTATATTTTGAC
1 CCCTAAAC-TTCCAAAAATTACATTTTTAC
*
28033 CCCTAATCTT-CAAAAATTACATTTTTAC
1 CCCTAAACTTCCAAAAATTACATTTTTAC
* * *
28061 CCTTAAACTTTCAAAAAATTGCATTTTTA-
1 CCCTAAAC-TTCCAAAAATTACATTTTTAC
* ** *
28090 CCATCGACTTCCAAAAATTACCA-TTTT-G
1 CCCTAAACTTCCAAAAATTA-CATTTTTAC
*
28118 CCCTCAAACTTCCAAAAATTGCATTTTTA-
1 CCCT-AAACTTCCAAAAATTACATTTTTAC
* *
28147 CCCTCAAATTTCCAAAAATTATCA-TTTTGC
1 CCCT-AAACTTCCAAAAATTA-CATTTTTAC
* *
28177 CCCCAAACTTTCCAAAAATCACATTTTTAC
1 CCCTAAAC-TTCCAAAAATTACATTTTTAC
*
28207 CCCTAAACTTACAAAAATTACCA-TTTTAC
1 CCCTAAACTTCCAAAAATTA-CATTTTTAC
*
28236 CCCTAAACTTCCAAAAAATCACATTTTT-C
1 CCCTAAACTTCC-AAAAATTACATTTTTAC
** * *
28265 CCCCGAACTTCTAAAAACTAC-TATTTTA-
1 CCCTAAACTTCCAAAAATTACAT-TTTTAC
* *
28293 CCCTCGAACTTCC-AAAATTGCATTTTTAC
1 CCCT-AAACTTCCAAAAATTACATTTTTAC
* * *
28322 CCTTGAACTTTCTAAAAATTACCA-TTTTAC
1 CCCTAAAC-TTCCAAAAATTA-CATTTTTAC
* *
28352 CCTTGAACTTCCAAAAA-TATCATTTTTGAC
1 CCCTAAACTTCCAAAAATTA-CATTTTT-AC
* * * *
28382 CCC-AAATTTTTCGAAAATTAC-TGTTTTGC
1 CCCTAAA-CTTCCAAAAATTACAT-TTTTAC
* *
28411 TTCC-AAGCTTCCAAAAATTACCA-TTTTAC
1 -CCCTAAACTTCCAAAAATTA-CATTTTTAC
28440 CCCTTAAACTTCCAAAA
1 CCC-TAAACTTCCAAAA
28457 GTCGCATTTT
Statistics
Matches: 358, Mismatches: 61, Indels: 70
0.73 0.12 0.14
Matches are distributed among these distances:
27 1 0.00
28 76 0.21
29 140 0.39
30 130 0.36
31 9 0.03
32 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTACATTTTTAC
Found at i:28401 original size:175 final size:176
Alignment explanation
Indices: 27996--28402 Score: 472
Period size: 175 Copynumber: 2.3 Consensus size: 176
27986 AAAAATCATG
* *
27996 TTTTGACCCCCAAACTTTCCAAAAAT-T-ATATTTTGACCCCTAATCTTCAAAAATTA-CATTTT
1 TTTT-ACCCCCAAACTTTCCAAAAATATCAT-TTTTGACCCCAAATTTTCAAAAATTACCATTTT
* * ** * * *
28058 TACCCTTAAACTTTCAAAAAATTGCATTTTTACCATCGACTTCCAAAAATTACCATTTTGCCCTC
64 TACCCCTAAACTTCCAAAAAATCACATTTTTACCACCGACTTCCAAAAACTACCATTTTACCCTC
*
28123 AAACTTCCAAAAATTGCATTTTTACCCTCAAATTTCCAAAAATTATCA
129 AAACTTCCAAAAATTGCATTTTTACCCTCAAATTTCCAAAAATTACCA
* * *
28171 TTTTGCCCCCAAACTTTCCAAAAATCA-CATTTTT-ACCCCTAAACTTACAAAAATTACCA-TTT
1 TTTTACCCCCAAACTTTCCAAAAAT-ATCATTTTTGACCCC-AAATTTTCAAAAATTACCATTTT
* * *
28233 TACCCCTAAACTTCCAAAAAATCACATTTTT-CCCCCGAACTTCTAAAAACTACTATTTTACCCT
64 TACCCCTAAACTTCCAAAAAATCACATTTTTACCACCG-ACTTCCAAAAACTACCATTTTACCCT
* * * *
28297 CGAACTTCC-AAAATTGCATTTTTACCCTTGAACTTTCTAAAAATTACCA
128 CAAACTTCCAAAAATTGCATTTTTACCC-TCAAATTTCCAAAAATTACCA
*** *
28346 TTTTACCCTTGAAC-TTCCAAAAATATCATTTTTGACCCCAAATTTTTCGAAAATTAC
1 TTTTACCCCCAAACTTTCCAAAAATATCATTTTTGACCCCAAA-TTTTCAAAAATTAC
28403 TGTTTTGCTT
Statistics
Matches: 195, Mismatches: 27, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
173 1 0.01
174 67 0.34
175 123 0.63
176 4 0.02
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (176 bp):
TTTTACCCCCAAACTTTCCAAAAATATCATTTTTGACCCCAAATTTTCAAAAATTACCATTTTTA
CCCCTAAACTTCCAAAAAATCACATTTTTACCACCGACTTCCAAAAACTACCATTTTACCCTCAA
ACTTCCAAAAATTGCATTTTTACCCTCAAATTTCCAAAAATTACCA
Found at i:32520 original size:16 final size:16
Alignment explanation
Indices: 32478--32525 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
32468 TTTTTTTTAC
* *
32478 TATTTTGATGCTGTTA
1 TATTTTGATGTTGTTT
*
32494 T-TTTTGTTGTTGTTT
1 TATTTTGATGTTGTTT
*
32509 TATTTTGATGTTATTT
1 TATTTTGATGTTGTTT
32525 T
1 T
32526 TGTTACTGTT
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:0.12, C:0.02, G:0.17, T:0.69
Consensus pattern (16 bp):
TATTTTGATGTTGTTT
Found at i:39358 original size:30 final size:31
Alignment explanation
Indices: 39292--39367 Score: 111
Period size: 30 Copynumber: 2.5 Consensus size: 31
39282 AGCAAATGAT
39292 TATAAAATTATTAAAATTATTTTTTTAAAAA
1 TATAAAATTATTAAAATTATTTTTTTAAAAA
*
39323 TATAAAATT-TTAAAATTATTTTTTT-GAAA
1 TATAAAATTATTAAAATTATTTTTTTAAAAA
*
39352 TAATAAATTTATTAAA
1 T-ATAAAATTATTAAA
39368 TAATTTTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 23 0.56
31 14 0.34
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
TATAAAATTATTAAAATTATTTTTTTAAAAA
Found at i:39374 original size:29 final size:30
Alignment explanation
Indices: 39292--39374 Score: 71
Period size: 31 Copynumber: 2.7 Consensus size: 30
39282 AGCAAATGAT
* * *
39292 TATAAAATTATTAAAATTATTTTTTTAAAAA
1 TATAAATTTATT-AAATAATTTTTTGAAAAA
* * *
39323 TATAAAATTT-TAAAATTATTTTTTTGAAATA
1 TAT-AAATTTATTAAA-TAATTTTTTGAAAAA
39354 -ATAAATTTATTAAATAATTTT
1 TATAAATTTATTAAATAATTTT
39375 AATTTTCAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
29 12 0.29
30 9 0.22
31 15 0.37
32 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
TATAAATTTATTAAATAATTTTTTGAAAAA
Found at i:40540 original size:21 final size:22
Alignment explanation
Indices: 40510--40551 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
40500 AAATTTTTTT
*
40510 AATAAATTT-ATATTTTTAAAA
1 AATAAATTTAATAATTTTAAAA
*
40531 AATAATTTTAATAATTTTAAA
1 AATAAATTTAATAATTTTAAA
40552 GTTATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAAATTTAATAATTTTAAAA
Found at i:44048 original size:57 final size:60
Alignment explanation
Indices: 43943--44061 Score: 154
Period size: 58 Copynumber: 2.0 Consensus size: 60
43933 TTTTACTAAT
* * *
43943 TTATATTTTAATAATAACTATATTAAAAATGTTATTAAATTATATATTA-TTTCATTAAA
1 TTATATTTTAATAATAACTATAGTAAAAATATAATTAAATTATATATTATTTTCATTAAA
* * * *
44002 TTATA-TTTAATAATAATTATGGT-AAAATATAATTAAATTATTTATTATTTTTATTAAA
1 TTATATTTTAATAATAACTATAGTAAAAATATAATTAAATTATATATTATTTTCATTAAA
44060 TT
1 TT
44062 TAATTGTCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 21 0.40
58 26 0.50
59 5 0.10
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (60 bp):
TTATATTTTAATAATAACTATAGTAAAAATATAATTAAATTATATATTATTTTCATTAAA
Found at i:44270 original size:16 final size:16
Alignment explanation
Indices: 44249--44288 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
44239 TGAATTTCTA
44249 ATTACAG-TCCTATTCC
1 ATTACAGCT-CTATTCC
44265 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
44281 ATTACAGC
1 ATTACAGC
44289 AAACCAAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 22 0.96
17 1 0.04
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:47488 original size:70 final size:67
Alignment explanation
Indices: 47395--47527 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 67
47385 ATCCAAATAA
* ** *
47395 AAAAGATAAAACTACGTCGTTTTGATAAATGTTTATCCTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAGATAAAACTACGTCATTTTGATAAATGTTTA-CCCAT-T-AAGTTAAAAGGCAAAACCATT
47460 AAGTT
63 AAGTT
* * *
47465 AAAAGGTAAAATTATGTCATTTTGATAAATGTTTACCCATTAAGTTAAAAGGCAAAACCATTA
1 AAAAGATAAAACTACGTCATTTTGATAAATGTTTACCCATTAAGTTAAAAGGCAAAACCATTA
47528 TATTGTTTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 21 0.38
68 1 0.02
69 3 0.05
70 31 0.55
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (67 bp):
AAAAGATAAAACTACGTCATTTTGATAAATGTTTACCCATTAAGTTAAAAGGCAAAACCATTAAG
TT
Done.