Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014930.1 Kokia drynarioides strain JFW-HI SEQ_129973, 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: 29256
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:10692 original size:36 final size:33
Alignment explanation
Indices: 10652--10721 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 33
10642 AATTTTTATT
10652 AAATAAATAATTTTTAAATATTATTTATATCAAATA
1 AAATAAAT-ATTTTT-AATATTATTT-TATCAAATA
* *
10688 AAATAAATATTTTTTATATTATTTTATTAAATA
1 AAATAAATATTTTTAATATTATTTTATCAAATA
10721 A
1 A
10722 CCTTGACAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 9 0.28
34 9 0.28
35 6 0.19
36 8 0.25
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (33 bp):
AAATAAATATTTTTAATATTATTTTATCAAATA
Found at i:11355 original size:9 final size:9
Alignment explanation
Indices: 11343--11389 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
11333 AAAATATATA
11343 TTTATAATT
1 TTTATAATT
*
11352 TTTATAGTT
1 TTTATAATT
11361 TTTAATAA-T
1 TTT-ATAATT
11370 TTT-TAATT
1 TTTATAATT
*
11378 TTTACAATT
1 TTTATAATT
11387 TTT
1 TTT
11390 GAAATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
7 3 0.09
8 4 0.12
9 22 0.69
10 3 0.09
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTATAATT
Found at i:11402 original size:16 final size:16
Alignment explanation
Indices: 11367--11404 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
11357 AGTTTTTAAT
*
11367 AATTTTTAATTTTTAC
1 AATTTTTAAATTTTAC
11383 AATTTTTGAAATTTTA-
1 AATTTTT-AAATTTTAC
11399 AATTTT
1 AATTTT
11405 AAAAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (16 bp):
AATTTTTAAATTTTAC
Found at i:14618 original size:15 final size:15
Alignment explanation
Indices: 14600--14670 Score: 97
Period size: 15 Copynumber: 4.7 Consensus size: 15
14590 TTTTGGGTAG
14600 TTTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
*
14615 TTTGTATTTGGGCCA
1 TTTGTAATTGGGCCA
* *
14630 TCTGTAATTAGGCCA
1 TTTGTAATTGGGCCA
* *
14645 TTTTTTATTGGGCCA
1 TTTGTAATTGGGCCA
14660 TTTGTAATTGG
1 TTTGTAATTGG
14671 ACTTTGTTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.18, C:0.13, G:0.24, T:0.45
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:14724 original size:17 final size:16
Alignment explanation
Indices: 14702--14763 Score: 79
Period size: 16 Copynumber: 3.8 Consensus size: 16
14692 TTGGACTTTC
14702 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
14719 TAAATTTAAATTTTAAA
1 TAAATTT-AATTTTAAA
* *
14736 TAAACTTAAATTTAAA
1 TAAATTTAATTTTAAA
*
14752 TAAATTCAATTT
1 TAAATTTAATTT
14764 CCAATAAGTC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
16 17 0.44
17 15 0.38
18 7 0.18
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:16204 original size:123 final size:124
Alignment explanation
Indices: 15921--16247 Score: 412
Period size: 123 Copynumber: 2.6 Consensus size: 124
15911 ACTTCATCTC
* * * * *
15921 TTGGTCTACTTCTCTGTGTCTCATCAGGAAGATGACCGCTTTATTGCTTCGACGCGCTTCTCTGT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTTATTGCTTCGACTCACTTCTCTTT
* * * *
15986 ATCTCATCAGGAAGATAGGGGTTTGAAGTTTCACTCGCTTTGAACTTTGCTTCATTGAT
66 ATCTCATCAGGAAGATAGGGGTTTGAAATCTCACTCGCTTTGAACTTTACTTCATAGAT
**
16045 TCAGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTTATTGCTTCGACTCACTTCTCTTT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTTATTGCTTCGACTCACTTCTCTTT
* *
16110 ATCTCATCAGGAAGAT-GGGGTTTGAAATCTCATTCG-TATT-AAGTTTCACTTCATAGAT
66 ATCTCATCAGGAAGATAGGGGTTTGAAATCTCACTCGCT-TTGAACTTT-ACTTCATAGAT
* * * * * *
16168 TTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACTGCCTCATTGTTTC-AATCCACTT-TTTT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTTATTGCTTCGACT-CACTTCTCTT
16231 ATATCTCATCAGGAAGA
65 -TATCTCATCAGGAAGA
16248 CGGCCTTGGT
Statistics
Matches: 178, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
122 11 0.06
123 93 0.52
124 74 0.42
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (124 bp):
TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTTATTGCTTCGACTCACTTCTCTTT
ATCTCATCAGGAAGATAGGGGTTTGAAATCTCACTCGCTTTGAACTTTACTTCATAGAT
Found at i:16311 original size:85 final size:85
Alignment explanation
Indices: 16168--16332 Score: 199
Period size: 85 Copynumber: 1.9 Consensus size: 85
16158 CTTCATAGAT
* ** *
16168 TTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACTGCCTCATTGTTTCAATCCACTTTTTTAT
1 TTGGTCCACTTCTCAGTATCTCATCAGGAAGATGACCACCTCATTGTTTCAACCCACTTTTTTAT
* *
16233 ATCTCATCAGGAAGACGGCC
66 ATCTAATCAGAAAGACGGCC
* * * *
16253 TTGGTCCACTTCTCTA-TATCTCATTAGGAAGATGACCACTTTATTGCTTT-GACCCACTTTTTT
1 TTGGTCCACTTCTC-AGTATCTCATCAGGAAGATGACCACCTCATTG-TTTCAACCCACTTTTTT
*
16316 GTATCTAATCAGAAAGA
64 ATATCTAATCAGAAAGA
16333 TGGGGTTTGA
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
85 63 0.94
86 4 0.06
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (85 bp):
TTGGTCCACTTCTCAGTATCTCATCAGGAAGATGACCACCTCATTGTTTCAACCCACTTTTTTAT
ATCTAATCAGAAAGACGGCC
Found at i:16335 original size:208 final size:208
Alignment explanation
Indices: 16052--16911 Score: 1116
Period size: 208 Copynumber: 4.1 Consensus size: 208
16042 GATTCAGTCT
* * * *
16052 ACTTCTCTGTATCTCATCAGGAAGATGACTGCTTTATTGCTTCGACTCACTTCTCTTTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTATATCTCAT
* * * * * *
16117 CAGGAAGATGGGGTTTGAAATCTCATTCGTATTAAGTTTCACTTCATAGATTTGGTCTACTTCTC
66 CAGAAAGATGGGGTTTGAAGTCTCATTCGTATTAAGCTTCGCTTCATTGATTTGATCTACTTCTC
* * * * *
16182 AGTATCTCATCAGGAAGATGA-CTGCCTCATTGTTTCAATCCACTTTTTTATATCTCATCAGGAA
131 TGTATCTCATCAGGAAGATGATC-GCCTCATTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAA
**
16246 GACGGCCTTGGTCC
195 GACGGATTTGGTCC
* * * * * * *
16260 ACTTCTCTATATCTCATTAGGAAGATGACCACTTTATTGCTTTGACCCACTTTTTTGTATCTAAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTATATCTCAT
* * *
16325 CAGAAAGATGGGGTTTGAAGTCTCATTTGTATTGAGCTTCGCTTCATTGATTTGATATACTTCTC
66 CAGAAAGATGGGGTTTGAAGTCTCATTCGTATTAAGCTTCGCTTCATTGATTTGATCTACTTCTC
* * * *
16390 TGTATCTCATCAGGAAGATGATCGCTTCAATGTTTCAACCCGCTTCTCTGTATCTCATTAGGAAG
131 TGTATCTCATCAGGAAGATGATCGCCTCATTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAG
*
16455 ACGGATTTGGTTC
196 ACGGATTTGGTCC
* *
16468 ACTTCTCTGTATCTCATCAGGAAGATGATCGCTTTATTACTTTGACCCACTTCTCTATATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTATATCTCAT
* * *
16533 CAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGATCTACTTCTC
66 CAGAAAGATGGGGTTTGAAGTCTCATTCGTATTAAGCTTCGCTTCATTGATTTGATCTACTTCTC
* * ** * *
16598 TGTATCTCATTAGGAAGATGATCGCCACATTGTTTCAATTTGCTTATCTGTATCTCATCGGGAAG
131 TGTATCTCATCAGGAAGATGATCGCCTCATTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAG
* *
16663 AGGGATTTGATCC
196 ACGGATTTGGTCC
* * * *
16676 ACTTCTCTGTATCTTATTAAGAAGAT-AGCCGCTTTATTGCTTTGGCCCACTTCTCTATATCTCA
1 ACTTCTCTGTATCTCATCAGGAAGATGA-CCGCTTTATTGCTTTGACCCACTTCTCTATATCTCA
* * * *
16740 TCA-AGAAGATGGGGTTCGAAGTCTCATTCGTATTAAGTTTCGCTTCATTGATTTGGTCTAATTC
65 TCAGA-AAGATGGGGTTTGAAGTCTCATTCGTATTAAGCTTCGCTTCATTGATTTGATCTACTTC
* * * *
16804 TCTGTATCTCATAAGGAAGATGA-CTGCCTCATTGTTTTAATCCGCTTCTTTGTATCTCATCTGG
129 TCTGTATCTCATCAGGAAGATGATC-GCCTCATTGTTTCAATCCGCTTCTCTGTATCTCATCAGG
* *
16868 AATACAGATTTGGTCC
193 AAGACGGATTTGGTCC
*
16884 ACTTCTCTGTATCTCATCAAGAAGATGA
1 ACTTCTCTGTATCTCATCAGGAAGATGA
16912 GGTTTGATGT
Statistics
Matches: 563, Mismatches: 84, Indels: 9
0.86 0.13 0.01
Matches are distributed among these distances:
207 2 0.00
208 559 0.99
209 2 0.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (208 bp):
ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTATATCTCAT
CAGAAAGATGGGGTTTGAAGTCTCATTCGTATTAAGCTTCGCTTCATTGATTTGATCTACTTCTC
TGTATCTCATCAGGAAGATGATCGCCTCATTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAG
ACGGATTTGGTCC
Found at i:16521 original size:85 final size:85
Alignment explanation
Indices: 16383--16540 Score: 237
Period size: 85 Copynumber: 1.9 Consensus size: 85
16373 GATTTGATAT
* * *
16383 ACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCAATGTTTCAACCCGCTTCTCTGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCAATCTTTCAACCCACTTCTCTATATCTCAT
*
16448 TAGGAAGACGGATTTGGTTC
66 CAGGAAGACGGATTTGGTTC
* * *
16468 ACTTCTCTGTATCTCATCAGGAAGATGATCGCTTTATTACTTT-GACCCACTTCTCTATATCTCA
1 ACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCAAT-CTTTCAACCCACTTCTCTATATCTCA
16532 TCAGGAAGA
65 TCAGGAAGA
16541 TGAGGTTTGA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
85 62 0.95
86 3 0.05
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (85 bp):
ACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCAATCTTTCAACCCACTTCTCTATATCTCAT
CAGGAAGACGGATTTGGTTC
Found at i:17228 original size:49 final size:49
Alignment explanation
Indices: 17155--17973 Score: 670
Period size: 49 Copynumber: 16.7 Consensus size: 49
17145 CTTCTAAGGT
* * * **
17155 GCCTCAATCTTTCCTTTCAAATCTTCATGGTACCAGGTTTACCGTTGCG
1 GCCTCAACCTTTCCCTTCACATCTTCATGGTACCAGGTTCGCCGTTGCG
* * * **
17204 GCCTCAACCTTTCCCATCACATCTTCTAAGGTATC-GAGTTCGCCGTTATG
1 GCCTCAACCTTTCCCTTCACATCTTC-ATGGTACCAG-GTTCGCCGTTGCG
** * * * *
17254 GCCTCAACCTTTCCCTTCTTATTTTCATGGTACCAGATTCACCATTGCG
1 GCCTCAACCTTTCCCTTCACATCTTCATGGTACCAGGTTCGCCGTTGCG
* * * * *
17303 GCCTTAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTACG
1 GCCTCAACCTTTCCCTTCACATCTTC-ATGGTACCAGGTTCGCCGTTGCG
* ** ***
17353 GCCTCAACCTTTCCCTTCATATCTTCATGGTACTGGGTTTATCGTTGCG
1 GCCTCAACCTTTCCCTTCACATCTTCATGGTACCAGGTTCGCCGTTGCG
* * * * ** * *
17402 ACCTCAACCTTTCCCATCACAT-TACA-GGTATCATATTCGTCATTGCG
1 GCCTCAACCTTTCCCTTCACATCTTCATGGTACCAGGTTCGCCGTTGCG
* * * * * *
17449 GCCTCAATCTTTCCCATCACATCTTCTAAGGTATCAGGTTCACCGTTGTG
1 GCCTCAACCTTTCCCTTCACATCTTC-ATGGTACCAGGTTCGCCGTTGCG
* * *
17499 ACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTCGCCGTTGCG
1 GCCTCAACCTTTCCCTTCACATCTTCATGGTACCAGGTTCGCCGTTGCG
** * * * *
17548 GCCTCAACCTTTCCCTTCGTATCTT-ATGATACTAGGTTCGTCGTTGTG
1 GCCTCAACCTTTCCCTTCACATCTTCATGGTACCAGGTTCGCCGTTGCG
* **
17596 GCCTCAACCTTTCCCTTCATATCTTCATGGTACTGGGTTCGCCGTTGCG
1 GCCTCAACCTTTCCCTTCACATCTTCATGGTACCAGGTTCGCCGTTGCG
* **
17645 GCCTCAACCTTTCCCATCACAT-TTCATGGTACC-GGATTCGCTATTGCG
1 GCCTCAACCTTTCCCTTCACATCTTCATGGTACCAGG-TTCGCCGTTGCG
* * * * * * *
17693 GCCTCAATCTTTCTCATCACATCTTTTAAGGTACCAGGTTCACCGTTACG
1 GCCTCAACCTTTCCCTTCACATC-TTCATGGTACCAGGTTCGCCGTTGCG
** * *
17743 GCCTCAACCTTTCCCTTCGTATCTTCATGGTACCAGGTTCGCTGTTACG
1 GCCTCAACCTTTCCCTTCACATCTTCATGGTACCAGGTTCGCCGTTGCG
* * * * *
17792 GCCTCAA-CTTTTCCATCACATCTTCTAAGGTATC-GTGTTCGCCGTTACG
1 GCCTCAACCTTTCCCTTCACATCTTC-ATGGTACCAG-GTTCGCCGTTGCG
* * * * * * *
17841 GCCTCAACCTTTCCCTTCATATCTTTAGGGTATC-GAGTTTGCCATTACG
1 GCCTCAACCTTTCCCTTCACATCTTCATGGTACCAG-GTTCGCCGTTGCG
* * * * * * *
17890 GTCTTAACCTTT-CCTGTCACATCTTTTAAGATACC-GAGTTCTCTGTTGCG
1 GCCTCAACCTTTCCCT-TCACATC-TTCATGGTACCAG-GTTCGCCGTTGCG
*
17940 GCCTCAACCTTTCCCTTCATATCTTCATGGTACC
1 GCCTCAACCTTTCCCTTCACATCTTCATGGTACC
17974 TCGGTTCATA
Statistics
Matches: 614, Mismatches: 138, Indels: 36
0.78 0.18 0.05
Matches are distributed among these distances:
47 35 0.06
48 105 0.17
49 271 0.44
50 198 0.32
51 5 0.01
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (49 bp):
GCCTCAACCTTTCCCTTCACATCTTCATGGTACCAGGTTCGCCGTTGCG
Found at i:17326 original size:99 final size:99
Alignment explanation
Indices: 17155--17973 Score: 798
Period size: 99 Copynumber: 8.3 Consensus size: 99
17145 CTTCTAAGGT
* * * *
17155 GCCTCAATCTTTCCTTTCAAATCTTCATGGTACCAGGTTTACCGTTGCGGCCTCAACCTTTCCCA
1 GCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGGTTCACCGTTGCGGCCTCAACCTTTCCCA
* *
17220 TCACATCTTCTAAGGTATCGAGTTCGCCGTTATG
66 TCACATCTTCTAAGGTACCGAGTTCGCCGTTACG
* * * * *
17254 GCCTCAACCTTTCCCTTCTTATTTTCATGGTACCAGATTCACCATTGCGGCCTTAACCTTTCCCA
1 GCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGGTTCACCGTTGCGGCCTCAACCTTTCCCA
*
17319 TCACATCTTCTAAGGTACCGGGTTCGCCGTTACG
66 TCACATCTTCTAAGGTACCGAGTTCGCCGTTACG
** * * *
17353 GCCTCAACCTTTCCCTTCATATCTTCATGGTACTGGGTTTATCGTTGCGACCTCAACCTTTCCCA
1 GCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGGTTCACCGTTGCGGCCTCAACCTTTCCCA
* * * * * *
17418 TCACAT-TAC--AGGTATC-ATATTCGTCATTGCG
66 TCACATCTTCTAAGGTACCGA-GTTCGCCGTTACG
* * * * * * *
17449 GCCTCAATCTTTCCCATCACATCTTCTAAGGTATCAGGTTCACCGTTGTGACCTCAACCTTTCCC
1 GCCTCAACCTTTCCCTTCATATCTTC-ATGGTACCAGGTTCACCGTTGCGGCCTCAACCTTTCCC
* * * * *
17514 TTCAAATCTTC-ATGGTACCGGGTTCGCCGTTGCG
65 ATCACATCTTCTAAGGTACCGAGTTCGCCGTTACG
* * * ** * *
17548 GCCTCAACCTTTCCCTTCGTATCTT-ATGATACTAGGTTCGTCGTTGTGGCCTCAACCTTTCCCT
1 GCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGGTTCACCGTTGCGGCCTCAACCTTTCCCA
* * * * *
17612 TCATATCTTC-ATGGTACTGGGTTCGCCGTTGCG
66 TCACATCTTCTAAGGTACCGAGTTCGCCGTTACG
* * * ** * *
17645 GCCTCAACCTTTCCCATCACAT-TTCATGGTACC-GGATTCGCTATTGCGGCCTCAATCTTTCTC
1 GCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGG-TTCACCGTTGCGGCCTCAACCTTTCCC
* *
17708 ATCACATCTTTTAAGGTACC-AGGTTCACCGTTACG
65 ATCACATCTTCTAAGGTACCGA-GTTCGCCGTTACG
* * * * *
17743 GCCTCAACCTTTCCCTTCGTATCTTCATGGTACCAGGTTCGCTGTTACGGCCTCAA-CTTTTCCA
1 GCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGGTTCACCGTTGCGGCCTCAACCTTTCCCA
* *
17807 TCACATCTTCTAAGGTATCGTGTTCGCCGTTACG
66 TCACATCTTCTAAGGTACCGAGTTCGCCGTTACG
* * * ** * * * * *
17841 GCCTCAACCTTTCCCTTCATATCTTTAGGGTATC-GAGTTTGCCATTACGGTCTTAACCTTTCCT
1 GCCTCAACCTTTCCCTTCATATCTTCATGGTACCAG-GTTCACCGTTGCGGCCTCAACCTTTCCC
* * * * * *
17905 GTCACATCTTTTAAGATACCGAGTTCTCTGTTGCG
65 ATCACATCTTCTAAGGTACCGAGTTCGCCGTTACG
17940 GCCTCAACCTTTCCCTTCATATCTTCATGGTACC
1 GCCTCAACCTTTCCCTTCATATCTTCATGGTACC
17974 TCGGTTCATA
Statistics
Matches: 593, Mismatches: 113, Indels: 28
0.81 0.15 0.04
Matches are distributed among these distances:
96 42 0.07
97 154 0.26
98 120 0.20
99 275 0.46
100 2 0.00
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (99 bp):
GCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGGTTCACCGTTGCGGCCTCAACCTTTCCCA
TCACATCTTCTAAGGTACCGAGTTCGCCGTTACG
Found at i:17479 original size:146 final size:145
Alignment explanation
Indices: 17155--17972 Score: 589
Period size: 146 Copynumber: 5.6 Consensus size: 145
17145 CTTCTAAGGT
* ** * * * **
17155 GCCTCAATCTTTCCTTTCAAATCTTC-ATGGTACCAGGTTTACCGTTGCGGCCTCAACCTTTCCC
1 GCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCC
* * * ** * ** *
17219 ATCACATCTTCTAAGGTA-TCGAGTTCGCCGTTATGGCCTCAACCTTTCCCTTCTTATTTTCATG
66 TTCACATCTTC-ATGGTACT-GGGTTCGCCGTTGCGGCCTCAACCTTTCCCATC--ACATT-AAG
* * *
17283 GTACCAGATTCACCATTGCG
126 GTATCATATTCGCCATTGCG
* *
17303 GCCTTAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTACGGCCTCAACCTTTCCC
1 GCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCC
* *** *
17368 TTCATATCTTCATGGTACTGGGTTTATCGTTGCGACCTCAACCTTTCCCATCACATTACAGGTAT
66 TTCACATCTTCATGGTACTGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATTA-AGGTAT
*
17433 CATATTCGTCATTGCG
130 CATATTCGCCATTGCG
* * * * * *
17449 GCCTCAATCTTTCCCATCACATCTTCTAAGGTATCAGGTTCACCGTTGTGACCTCAACCTTTCCC
1 GCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCC
* * * * *
17514 TTCAAATCTTCATGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCGTATC-TTATGAT
66 TTCACATCTTCATGGTACTGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATC--A-CATTAAGGT
* * *
17578 A-C-TAGGTTCGTCGTTGTG
128 ATCATA--TTCGCCATTGCG
* * * *
17596 GCCTCAACCTTTCCCTTCATATCTTC-ATGGTACTGGGTTCGCCGTTGCGGCCTCAACCTTTCCC
1 GCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCC
* * * ** * *
17660 ATCACAT-TTCATGGTACCGGATTCGCTATTGCGGCCTCAATCTTTCTCATCACATCTTTTAAGG
66 TTCACATCTTCATGGTACTGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACA----TTAAGG
* ** * * *
17724 TACCAGGTTCACCGTTACG
127 TATCATATTCGCCATTGCG
* ** * * * * *
17743 GCCTCAACCTTTCCCTTCGTATCTTC-ATGGTACCAGGTTCGCTGTTACGGCCTCAA-CTTTTCC
1 GCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCC
* * * * * * *
17806 ATCACATCTTCTAAGGTA-TCGTGTTCGCCGTTACGGCCTCAACCTTTCCCTTCATATCTTTAGG
66 TTCACATCTTC-ATGGTACT-GGGTTCGCCGTTGCGGCCTCAACCTTTCCCATC--A-CATTAAG
*
17870 GTATCGAGT-TT-GCCATTACG
126 GTATC-A-TATTCGCCATTGCG
* * ** * * * * *
17890 GTCTTAACCTTTCCTGTCACATCTTTTAAGATACCGAGTTCTCTGTTGCGGCCTCAACCTTTCCC
1 GCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCC
*
17955 TTCATATCTTCATGGTAC
66 TTCACATCTTCATGGTAC
17973 CTCGGTTCAT
Statistics
Matches: 532, Mismatches: 112, Indels: 51
0.77 0.16 0.07
Matches are distributed among these distances:
142 1 0.00
143 1 0.00
145 41 0.08
146 172 0.32
147 138 0.26
148 118 0.22
149 59 0.11
150 1 0.00
151 1 0.00
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (145 bp):
GCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCC
TTCACATCTTCATGGTACTGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATTAAGGTATC
ATATTCGCCATTGCG
Found at i:18937 original size:15 final size:15
Alignment explanation
Indices: 18890--18959 Score: 70
Period size: 16 Copynumber: 4.5 Consensus size: 15
18880 CGACCTCTCA
18890 TTTTCTTTTTCCTTTT
1 TTTTCTTTTT-CTTTT
* *
18906 TTCTCTTTTT-TAATT
1 TTTTCTTTTTCT-TTT
18921 TTTTCTTTTTCTTTT
1 TTTTCTTTTTCTTTT
*
18936 TTTTCTTTTTTATTTAT
1 TTTTC-TTTTTCTTT-T
18953 TTTTCTT
1 TTTTCTT
18960 CATCGAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
14 1 0.02
15 18 0.40
16 20 0.44
17 6 0.13
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTCTTTTTCTTTT
Found at i:18937 original size:30 final size:31
Alignment explanation
Indices: 18890--18947 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
18880 CGACCTCTCA
18890 TTTTCTTTTTCCTTTTTTCTCTTTTTTAATT
1 TTTTCTTTTTCCTTTTTTCTCTTTTTTAATT
*
18921 TTTTCTTTTT-CTTTTTTTTCTTTTTTA
1 TTTTCTTTTTCCTTTTTTCTCTTTTTTA
18948 TTTATTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (31 bp):
TTTTCTTTTTCCTTTTTTCTCTTTTTTAATT
Found at i:24500 original size:59 final size:57
Alignment explanation
Indices: 24409--24621 Score: 214
Period size: 59 Copynumber: 3.6 Consensus size: 57
24399 GAGAATTCGA
** *
24409 GGTTAAAACATAATTTTGGAAAAATTTAGGGTCAAAATGTGATTTTAAAGAAGTTT-G
1 GGTTAAAATGTAATTTTGGAAAATTTTAGGGTCAAAATGTGATTTT-AAGAAGTTTAG
* * **
24466 TGGTCAAAATGTAACTTTGGAAAAGTTTTAGGGTCAAAATGTGATTTTGGGAAGTTTAG
1 -GGTTAAAATGTAATTTTGGAAAA-TTTTAGGGTCAAAATGTGATTTTAAGAAGTTTAG
* * *** *
24525 GTGTTAAAATGTGATTTTGGAAAAATTTTAGGGTGAAAATCAAATTTTGGAA-AATTTTAGG
1 G-GTTAAAATGTAATTTTGG-AAAATTTTAGGGTCAAAATGTGATTTT--AAGAAGTTTA-G
24586 GGTTAAAATGTAATTTTGGAAAATTTTAGGGGTCAA
1 GGTTAAAATGTAATTTTGGAAAATTTTA-GGGTCAA
24622 GTGATTTTTG
Statistics
Matches: 128, Mismatches: 19, Indels: 14
0.80 0.12 0.09
Matches are distributed among these distances:
58 27 0.21
59 66 0.52
60 33 0.26
61 2 0.02
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (57 bp):
GGTTAAAATGTAATTTTGGAAAATTTTAGGGTCAAAATGTGATTTTAAGAAGTTTAG
Found at i:24503 original size:30 final size:29
Alignment explanation
Indices: 24419--24621 Score: 196
Period size: 30 Copynumber: 6.9 Consensus size: 29
24409 GGTTAAAACA
*
24419 TAATTTTGGAAAAATTTAGGGTCAAAATG
1 TAATTTTGGAAAATTTTAGGGTCAAAATG
* * *
24448 TGATTTT-AAAGAAGTTT-GTGGTCAAAATG
1 TAATTTTGGAA-AATTTTAG-GGTCAAAATG
*
24477 TAACTTTGGAAAAGTTTTAGGGTCAAAATG
1 TAATTTTGGAAAA-TTTTAGGGTCAAAATG
* * * *
24507 TGATTTTGG-GAAGTTTAGGTGTTAAAATG
1 TAATTTTGGAAAATTTTAGG-GTCAAAATG
* * *
24536 TGATTTTGGAAAAATTTTAGGGTGAAAATC
1 TAATTTTGG-AAAATTTTAGGGTCAAAATG
* *
24566 AAATTTTGGAAAATTTTAGGGGTTAAAATG
1 TAATTTTGGAAAATTTTA-GGGTCAAAATG
24596 TAATTTTGGAAAATTTTAGGGGTCAA
1 TAATTTTGGAAAATTTTA-GGGTCAA
24622 GTGATTTTTG
Statistics
Matches: 143, Mismatches: 22, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
28 9 0.06
29 56 0.39
30 69 0.48
31 9 0.06
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (29 bp):
TAATTTTGGAAAATTTTAGGGTCAAAATG
Found at i:24546 original size:28 final size:28
Alignment explanation
Indices: 24433--24544 Score: 118
Period size: 29 Copynumber: 3.9 Consensus size: 28
24423 TTTGGAAAAA
**
24433 TTTAGGGTCAAAATGTGATTTTAAAGAAG
1 TTTAGGGTCAAAATGTGATTTT-GGGAAG
* * *
24462 TTT-GTGGTCAAAATGTAACTTTGGAAAAG
1 TTTAG-GGTCAAAATGTGATTTTGG-GAAG
24491 TTTTAGGGTCAAAATGTGATTTTGGGAAG
1 -TTTAGGGTCAAAATGTGATTTTGGGAAG
*
24520 TTTAGGTGTTAAAATGTGATTTTGG
1 TTTAGG-GTCAAAATGTGATTTTGG
24545 AAAAATTTTA
Statistics
Matches: 69, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
28 7 0.10
29 41 0.59
30 20 0.29
31 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (28 bp):
TTTAGGGTCAAAATGTGATTTTGGGAAG
Done.