Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010199.1 Kokia drynarioides strain JFW-HI SEQ_125014, 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: 18154
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Found at i:1470 original size:22 final size:23
Alignment explanation
Indices: 1422--1476 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
1412 ATCTTAGCGC
*
1422 GCTCTCCGTTTAGCACTTTGTGT
1 GCTCTCCGTTTAGCACGTTGTGT
1445 GCTCTCCGTTTAGCACGTT-TGT
1 GCTCTCCGTTTAGCACGTTGTGT
1467 GCTCTCCGTT
1 GCTCTCCGTT
1477 CATTTGTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.07, C:0.29, G:0.22, T:0.42
Consensus pattern (23 bp):
GCTCTCCGTTTAGCACGTTGTGT
Found at i:2920 original size:31 final size:30
Alignment explanation
Indices: 2882--3005 Score: 128
Period size: 31 Copynumber: 4.1 Consensus size: 30
2872 TTAAATGAAA
* *
2882 TTTTAGAAAAGTTTTAGGGTTAAAATGTGGT
1 TTTTAGAAAAG-TTTAGGGTCAAAATGTGAT
*
2913 TTTTAG-AAAGTTTGGGGTCAAAATGTG-T
1 TTTTAGAAAAGTTTAGGGTCAAAATGTGAT
** *
2941 TATTT-GAAAAACTTAGGAGTCAAAATGTAAT
1 T-TTTAGAAAAGTTTAGG-GTCAAAATGTGAT
*
2972 TTTTGGAAAAGTTTAGGGGTCAAAATGTGAT
1 TTTTAGAAAAGTTTA-GGGTCAAAATGTGAT
3003 TTT
1 TTT
3006 GGGAAATTAA
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
28 3 0.04
29 25 0.32
30 17 0.22
31 31 0.40
32 2 0.03
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.39
Consensus pattern (30 bp):
TTTTAGAAAAGTTTAGGGTCAAAATGTGAT
Found at i:4755 original size:37 final size:37
Alignment explanation
Indices: 4696--4769 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
4686 CGCTTCATTG
4696 ATTTAATCCACTTCTCTGTATCTCATCAGGAAGATGA
1 ATTTAATCCACTTCTCTGTATCTCATCAGGAAGATGA
* *
4733 ATTTGATCTACTTCTCTGTATCTCATCAGGAAGATGA
1 ATTTAATCCACTTCTCTGTATCTCATCAGGAAGATGA
4770 TCGCTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.36
Consensus pattern (37 bp):
ATTTAATCCACTTCTCTGTATCTCATCAGGAAGATGA
Found at i:4797 original size:85 final size:85
Alignment explanation
Indices: 4649--4816 Score: 248
Period size: 85 Copynumber: 2.0 Consensus size: 85
4639 CTTCATTTGG
* *
4649 TTTGTTCTACTTCTCTATATCTCATCAGGAAGACGACCGCTTCATTGATTTAATCCACTTCTCTG
1 TTTGATCTACTTCTCTATATCTCATCAGGAAGACGACCGCTTCATTGATTTAACCCACTTCTCTG
*
4714 TATCTCATCAGGAAGATGAA
66 TATCTCATCAAGAAGATGAA
* * * * *
4734 TTTGATCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTTATT-ACTTTGACCCACTTCTCT
1 TTTGATCTACTTCTCTATATCTCATCAGGAAGACGACCGCTTCATTGA-TTTAACCCACTTCTCT
4798 GTATCTCATCAAGAAGATG
65 GTATCTCATCAAGAAGATG
4817 GGGTTTATCC
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
84 1 0.01
85 73 0.99
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (85 bp):
TTTGATCTACTTCTCTATATCTCATCAGGAAGACGACCGCTTCATTGATTTAACCCACTTCTCTG
TATCTCATCAAGAAGATGAA
Found at i:4975 original size:37 final size:37
Alignment explanation
Indices: 4925--4995 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
4915 CACTTTATTG
* **
4925 ATTTAATCTACTTCTTTGTATCTCATCAGGAAGACAA
1 ATTTAATCTACTTCTCTGTATCAAATCAGGAAGACAA
*
4962 ATTTAGTCTACTTCTCTGTATCAAATCAGGAAGA
1 ATTTAATCTACTTCTCTGTATCAAATCAGGAAGA
4996 TGACTGCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (37 bp):
ATTTAATCTACTTCTCTGTATCAAATCAGGAAGACAA
Found at i:5146 original size:48 final size:48
Alignment explanation
Indices: 5075--5214 Score: 174
Period size: 48 Copynumber: 2.9 Consensus size: 48
5065 TATTGAGCTT
* * * *
5075 CGCTTCGTTGATTTGATCTACTTCTCTGCATCTCATCAAGAAGATGAC
1 CGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGAC
*
5123 CGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGATGAC
1 CGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGAC
* * * * * *
5171 AGTTTTATTG-CTTGACCCACTTCTCTATATCTCATCAGGAAGAT
1 CGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGAT
5215 AGGGTTTGAA
Statistics
Matches: 80, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
47 30 0.38
48 50 0.62
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (48 bp):
CGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGAC
Found at i:7328 original size:36 final size:36
Alignment explanation
Indices: 7276--7375 Score: 137
Period size: 36 Copynumber: 2.8 Consensus size: 36
7266 TGGTAACAGG
*
7276 CATGACCTTTGGGTCAATAGGGAGTGAAACGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
* * * *
7312 CATGACCTCTGCGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
* *
7348 CCTGACCTTTGGGTCAATAGAGAGTAAA
1 CATGACCTTTGGGTCAATAGGGAGTAAA
7376 TCGAATATTG
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (36 bp):
CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
Found at i:9071 original size:124 final size:123
Alignment explanation
Indices: 8847--9120 Score: 413
Period size: 124 Copynumber: 2.2 Consensus size: 123
8837 GCGAATTTGG
* ***
8847 TTCACTTCTCTATATCTCATCAGGAAGATGGAGTTTGAAGTCTCATTTGTATTGAGATTCGCTTC
1 TTCACTTCTCTATATCTCATCAGGAAGATGGAGTTTGAAGTCTCACTCACATTGAGATTCGCTTC
* * * *
8912 ATTGATTTGGTCTGCTTCTCTGTATCTCATCAGGAAGATGATCGCTTTATTGATTTAA
66 ATCGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATCTAA
* * * *
8970 TTCATTTCTCTATATCTCATAAGGAAGATGGGAGTTTGAAGTTTCACTCACATTGAGCTTCGCTT
1 TTCACTTCTCTATATCTCATCAGGAAGAT-GGAGTTTGAAGTCTCACTCACATTGAGATTCGCTT
*
9035 TATCGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATCTAA
65 CATCGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATCTAA
*
9094 TCCACTTCTCTATATCTCATCAGGAAG
1 TTCACTTCTCTATATCTCATCAGGAAG
9121 GCGGATTTGT
Statistics
Matches: 134, Mismatches: 16, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
123 27 0.20
124 107 0.80
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (123 bp):
TTCACTTCTCTATATCTCATCAGGAAGATGGAGTTTGAAGTCTCACTCACATTGAGATTCGCTTC
ATCGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATCTAA
Found at i:9186 original size:84 final size:85
Alignment explanation
Indices: 9039--9204 Score: 246
Period size: 84 Copynumber: 2.0 Consensus size: 85
9029 TCGCTTTATC
* * *
9039 GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATCTAATCCACTTCTC
1 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCACTTCATTGATCTAACCCACTTCTC
9104 TATATCTCATCAGGAAGGCG
66 TATATCTCATCAGGAAGGCG
* * *
9124 GATTT-GTCTACTTCTCTGTATCTCATCAAGAAGATGATCACTTTATT-ACTTTGACCCACTTCT
1 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCACTTCATTGA-TCTAACCCACTTCT
*
9187 CTATATCTCATTAGGAAG
65 CTATATCTCATCAGGAAG
9205 ATAGGGTTTA
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
83 1 0.01
84 67 0.92
85 5 0.07
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (85 bp):
GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCACTTCATTGATCTAACCCACTTCTC
TATATCTCATCAGGAAGGCG
Found at i:9317 original size:207 final size:209
Alignment explanation
Indices: 8915--9322 Score: 563
Period size: 207 Copynumber: 2.0 Consensus size: 209
8905 TCGCTTCATT
* * * ** *
8915 GATTTGGTCTGCTTCTCTGTATCTCATCAGGAAGATGATCGCTTTATTGATTTAATTCATTTCTC
1 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCACTTTATTGATTTAACCCACTTCTC
* * * *
8980 TATATCTCATAAGGAAGATGGGAGTTTGAAGTTTCACTCACATTGAGCTTCGCTTTATCGATTTG
66 TATATCTCATAAGGAAGATAGGAGTTTAAAGTCTCACTCACATTGAGCTTCACTTTATCGATTTG
* * *
9045 GTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATCTAATCCACTTCTCTATATC
131 GTCTACTTCTCTGTATCCCATCAAGAAAATGATCGCTTCATTGATCTAATCCACTTCTCTATATC
9110 TCATCAGGAAGGCG
196 TCATCAGGAAGGCG
*
9124 GATTT-GTCTACTTCTCTGTATCTCATCAAGAAGATGATCACTTTATT-ACTTTGACCCACTTCT
1 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCACTTTATTGA-TTTAACCCACTTCT
* * ** * *
9187 CTATATCTCATTAGGAAGATAGG-GTTTAAAGTCTCATTCGTATTGAGCTTCACTTTGTTGATTT
65 CTATATCTCATAAGGAAGATAGGAGTTTAAAGTCTCACTCACATTGAGCTTCACTTTATCGATTT
* * *
9251 GGTCTACTTCTCTGTATCCCATCAAGAAAATGA-CTGCTTCATTGATTTAATCCACTTTTTTATA
130 GGTCTACTTCTCTGTATCCCATCAAGAAAATGATC-GCTTCATTGATCTAATCCACTTCTCTATA
9315 TCTCATCA
194 TCTCATCA
9323 TAAGATAATC
Statistics
Matches: 174, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
206 1 0.01
207 98 0.56
208 70 0.40
209 5 0.03
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (209 bp):
GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCACTTTATTGATTTAACCCACTTCTC
TATATCTCATAAGGAAGATAGGAGTTTAAAGTCTCACTCACATTGAGCTTCACTTTATCGATTTG
GTCTACTTCTCTGTATCCCATCAAGAAAATGATCGCTTCATTGATCTAATCCACTTCTCTATATC
TCATCAGGAAGGCG
Found at i:9446 original size:170 final size:171
Alignment explanation
Indices: 9142--9477 Score: 478
Period size: 170 Copynumber: 2.0 Consensus size: 171
9132 TACTTCTCTG
* *
9142 TATCTCATCAAGAAGATGATCACTTTATTACTTTGACCCACTTCTCTATATCTCATTAGGAAGAT
1 TATCTCATCAAGAAGATAATCACTTTATTACTTTGACCCACTTCTCTATATCTCATCAGGAAGAT
* * *
9207 AGGGTTTAAAGTCTCATTCGTATTGAGCTTCACTTTGTTGATTTGGTCTACTTCTCTGTATCCCA
66 AGGGTTTAAAGTCTCATTCGTATTGAGCATCACTTTATTGATTTGGTCTACTTCTCTATATCCCA
* *
9272 TCAAGAAAATGACTGCTTCATTGATTTAATCCACTTTTTTA
131 TCAAGAAAATGACCGATTCATTGATTTAATCCACTTTTTTA
* * * * * * **
9313 TATCTCATC-ATAAGATAATCGCTTTATTGCTTTGGCCTACTTCTCTGTATCTTGTCAGGAAGAT
1 TATCTCATCAAGAAGATAATCACTTTATTACTTTGACCCACTTCTCTATATCTCATCAGGAAGAT
** * *
9377 AGGGTTTGCAGTCTCATTCGTATTGAGCATC-GTTTCATTGATTTGGTCTACTTCTCTATATCTC
66 AGGGTTTAAAGTCTCATTCGTATTGAGCATCACTTT-ATTGATTTGGTCTACTTCTCTATATCCC
9441 ATCAAGAAAATGACCGATTCATTGATTTAATCCACTT
130 ATCAAGAAAATGACCGATTCATTGATTTAATCCACTT
9478 CTCTGTATCT
Statistics
Matches: 145, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
169 3 0.02
170 133 0.92
171 9 0.06
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (171 bp):
TATCTCATCAAGAAGATAATCACTTTATTACTTTGACCCACTTCTCTATATCTCATCAGGAAGAT
AGGGTTTAAAGTCTCATTCGTATTGAGCATCACTTTATTGATTTGGTCTACTTCTCTATATCCCA
TCAAGAAAATGACCGATTCATTGATTTAATCCACTTTTTTA
Found at i:9581 original size:208 final size:208
Alignment explanation
Indices: 9301--10873 Score: 1873
Period size: 208 Copynumber: 7.6 Consensus size: 208
9291 ATTGATTTAA
* * * * * * *
9301 TCCACTTTTTTATATCTCATCA-TAAGATAATCGCTTTATTGCTTTGGCCTACTTCTCTGTATCT
1 TCCACTTCTTTGTATCTCATCAGGAAGATGATCGCTTTATTGCTTTGACCCACTTCTTTGTATCT
** * * * *
9365 TGTCAGGAAGATAGGGTTTGCAGTCTCATTCGTATTGAGCATCGTTTCATTGATTTGGTCTACTT
66 CATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTT
* * * * * *
9430 CTCTATATCTCATCAAGAAAATGACCGATTCATTGATTTAATCCACTTCTCTGTATCTTATTAGG
131 CTCTATATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGG
9495 AAGGAGGATTTGG
196 AAGGAGGATTTGG
* * * *
9508 TCCACTTTTTTGTATCTCATCAGGAAGATGATTGCTTTATTGCTTTGACCTACTTCTGTGTATCT
1 TCCACTTCTTTGTATCTCATCAGGAAGATGATCGCTTTATTGCTTTGACCCACTTCTTTGTATCT
* ** * *
9573 TATCAGGAAGATATGGTTTGAAGTCTCATTCGTATTGAGCTTCGTTTCATTTATTTGGTCTACTT
66 CATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTT
* * * * *
9638 CTCTATATCTCATCAGGAAGACGACCACTTTATTGATTTAATCCACTTCTCTGTATCTCATCAAG
131 CTCTATATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGG
*
9703 AAGGCA-GATCTGG
196 AAGG-AGGATTTGG
* * * * *
9716 TTCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGATCCACTT-TTCTATATC
1 TCCACTTCTTTGTATCTCATCAGGAAGATGATCGCTTTATTGCTTTGACCCACTTCTT-TGTATC
* * * * * *
9780 TCATCAGTAATATAGGGTCTAAAGTCTCATTTGTATTGAGCTTCGCTTCATT-ACTTTGGTCTAC
65 TCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGA-TTTGGTCTAC
* * * * * *
9844 TTCTCTGTATCTCATCAGGAAGATGACCACTTCATTTATTTAATTCACTTCTCTGTATCTCATCG
129 TTCTCTATATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCA
*
9909 GGAATGCA-GATTTGG
194 GGAA-GGAGGATTTGG
* * * * * * * *
9924 TCCACTTCTCTATATCTCATCAGGAAGATGGTTGTTTTATTTCTTTAACCCATTTCTTTGTATCT
1 TCCACTTCTTTGTATCTCATCAGGAAGATGATCGCTTTATTGCTTTGACCCACTTCTTTGTATCT
* ** *
9989 CATTAGGAAGATGGGGTTTGAAGTCTCATTCAAATTGAGCTTCACTTCATTGATTTGGTCTACTT
66 CATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTT
* * * * * *
10054 CTATATATCTCATTAGGAAGATGATCTCTTCATTGATTTAATCTACTTCTTTGTATCTCATAAGG
131 CTCTATATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGG
*
10119 AAGGCGGATTTGG
196 AAGGAGGATTTGG
* * * * *
10132 TCCACTTCTTTGTATCTCATTAGGAAGATGGTTGCTATATTGCTTTGACCTACTTCTTTGTATCT
1 TCCACTTCTTTGTATCTCATCAGGAAGATGATCGCTTTATTGCTTTGACCCACTTCTTTGTATCT
* * * *
10197 CATCAGAAATATGGGGTTTGAAGTCTCATTCGTATTGAGCTTTGCTTTATTGATTTGGTCTACTT
66 CATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTT
* * * *
10262 CTCTATATCTCATCAAGAAGATGATCGCTTCATTAATTTAATTCACTTCTCTATATCTCATCAGG
131 CTCTATATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGG
* * * *
10327 AATGCGGCTTTGA
196 AAGGAGGATTTGG
* * * * *
10340 TCTACTTCTTTGTATCTCATCAGGAAGGTGGTCGCTTTATTGCTTTGACCCATTTCTTTATATCT
1 TCCACTTCTTTGTATCTCATCAGGAAGATGATCGCTTTATTGCTTTGACCCACTTCTTTGTATCT
* *
10405 CATCAGGAAGATGGGGTTTGAAGTCTCATCCGTATTGAGCTTCGCTTCATTGAGTTGGTCTACTT
66 CATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTT
* * * *
10470 TTCTGTATCTCATTAGGAAGATGATCGCTTAATTGATTTAATCCACTTCTCTGTATCTCATCAGG
131 CTCTATATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGG
*
10535 AAGGTGGATTTGG
196 AAGGAGGATTTGG
* * * * *
10548 TCCACTTCTTTGTATCTCATTAGGAAGATGGTTGCTTTATTTCTTTGACCCACTTCTTTATATCT
1 TCCACTTCTTTGTATCTCATCAGGAAGATGATCGCTTTATTGCTTTGACCCACTTCTTTGTATCT
* * * * *
10613 CATTAGGAAGATGGGGTTTGAAGTCTCATTCATATTGAGCTTCGCTTCATTAATGTGTTCTACTT
66 CATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTT
* * * * * *
10678 CTCTGTATCTCATTAGGAAGATGTTTGCTTCATTGATTTAATCCTCTTCTCTGTATCTCCTCAAG
131 CTCTATATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATC-AG
* *
10743 CAAGCA-GATTTGG
195 GAAGGAGGATTTGG
* * * * * *
10756 TCTACTTCTCTGTATCTCATCATGAAGATGATCACTTTATTGCTTTGATCCACTTCTCTGTATCT
1 TCCACTTCTTTGTATCTCATCAGGAAGATGATCGCTTTATTGCTTTGACCCACTTCTTTGTATCT
** * * *
10821 CATCAGGAAGATGAAAGTTTGAAGTTTCACTC-TCATTGAGCTTTGCTTCATTG
66 CATCAGGAAGATG-GGGTTTGAAGTCTCATTCGT-ATTGAGCTTCGCTTCATTG
10874 CTTTAATCTG
Statistics
Matches: 1178, Mismatches: 177, Indels: 20
0.86 0.13 0.01
Matches are distributed among these distances:
207 24 0.02
208 1113 0.94
209 41 0.03
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (208 bp):
TCCACTTCTTTGTATCTCATCAGGAAGATGATCGCTTTATTGCTTTGACCCACTTCTTTGTATCT
CATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTT
CTCTATATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGG
AAGGAGGATTTGG
Found at i:9675 original size:378 final size:377
Alignment explanation
Indices: 9021--9700 Score: 959
Period size: 378 Copynumber: 1.8 Consensus size: 377
9011 TTTCACTCAC
* * * * * *
9021 ATTGAGCTTCGCTTTATCGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCAT
1 ATTGAGCATCGCTTTATCGATTTGGTCTACTTCTCTATATCTCATCAAGAAAATGACCGATTCAT
* *
9086 TGATCTAATCCACTTCTCTATATCTCATCAGGAAGGCGGATTTGTCTACTTCTCTGTATCTCATC
66 TGATCTAATCCACTTCTCTATATCTCATCAGGAAGGAGGATTTGTCCACTTCTCTGTATCTCATC
*
9151 AAGAAGATGATCACTTTATTACTTTGACCCACTTCTCTATATCTCATTAGGAAGATAGGGTTTAA
131 AAGAAGATGATCACTTTATTACTTTGACCCACTTCTCTATATCTCATCAGGAAGATAGGGTTTAA
* *
9216 AGTCTCATTCGTATTGAGCTTCACTTTGTTGATTTGGTCTACTTCTCTGTATCCCATCAAGAAAA
196 AGTCTCATTCGTATTGAGCTTCACTTTATTGATTTGGTCTACTTCTCTATATCCCATCAAGAAAA
* ** * *
9281 TGACTGCTTCATTGATTTAATCCACTTTTTTATATCTCATCATAAGATAATCGCTTTATTGCTTT
261 CGACCACTTCATTGATTTAATCCACTTCTCTATATCTCATCATAAGATAATCGCTTTATTGCTTT
9346 GGCCTACTTCTCTGTATCTTGTCAGGAAGATAGGGTTTGCAGTCTCATTCGT
326 GGCCTACTTCTCTGTATCTTGTCAGGAAGATAGGGTTTGCAGTCTCATTCGT
*
9398 ATTGAGCATCG-TTTCATTGATTTGGTCTACTTCTCTATATCTCATCAAGAAAATGACCGATTCA
1 ATTGAGCATCGCTTT-ATCGATTTGGTCTACTTCTCTATATCTCATCAAGAAAATGACCGATTCA
* * * * * *
9462 TTGATTTAATCCACTTCTCTGTATCTTATTAGGAAGGAGGATTTGGTCCACTTTTTTGTATCTCA
65 TTGATCTAATCCACTTCTCTATATCTCATCAGGAAGGAGGATTT-GTCCACTTCTCTGTATCTCA
* ** * * * * * *
9527 TCAGGAAGATGATTGCTTTATTGCTTTGACCTACTTCTGTGTATCTTATCAGGAAGATATGGTTT
129 TCAAGAAGATGATCACTTTATTACTTTGACCCACTTCTCTATATCTCATCAGGAAGATAGGGTTT
* * * * *
9592 GAAGTCTCATTCGTATTGAGCTTC-GTTTCATTTATTTGGTCTACTTCTCTATATCTCATCAGGA
194 AAAGTCTCATTCGTATTGAGCTTCACTTT-ATTGATTTGGTCTACTTCTCTATATCCCATCAAGA
* * *
9656 AGACGACCACTTTATTGATTTAATCCACTTCTCTGTATCTCATCA
258 AAACGACCACTTCATTGATTTAATCCACTTCTCTATATCTCATCA
9701 AGAAGGCAGA
Statistics
Matches: 260, Mismatches: 40, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
376 3 0.01
377 95 0.37
378 162 0.62
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (377 bp):
ATTGAGCATCGCTTTATCGATTTGGTCTACTTCTCTATATCTCATCAAGAAAATGACCGATTCAT
TGATCTAATCCACTTCTCTATATCTCATCAGGAAGGAGGATTTGTCCACTTCTCTGTATCTCATC
AAGAAGATGATCACTTTATTACTTTGACCCACTTCTCTATATCTCATCAGGAAGATAGGGTTTAA
AGTCTCATTCGTATTGAGCTTCACTTTATTGATTTGGTCTACTTCTCTATATCCCATCAAGAAAA
CGACCACTTCATTGATTTAATCCACTTCTCTATATCTCATCATAAGATAATCGCTTTATTGCTTT
GGCCTACTTCTCTGTATCTTGTCAGGAAGATAGGGTTTGCAGTCTCATTCGT
Found at i:10185 original size:85 final size:85
Alignment explanation
Indices: 10040--10199 Score: 225
Period size: 85 Copynumber: 1.9 Consensus size: 85
10030 TCACTTCATT
* *
10040 GATTTGGTCTACTTCTATATATCTCATTAGGAAGATGATCTCTTCATTGATTTAATCTACTTCTT
1 GATTTGGTCCACTTCTATATATCTCATTAGGAAGATGATCTCTTCATTGATTTAACCTACTTCTT
10105 TGTATCTCATAAGGAAGGCG
66 TGTATCTCATAAGGAAGGCG
* * * * *
10125 GATTTGGTCCACTTCTTTGTATCTCATTAGGAAGATGGT-TGCTAT-ATTGCTTTGACCTACTTC
1 GATTTGGTCCACTTCTATATATCTCATTAGGAAGATGATCT-CT-TCATTGATTTAACCTACTTC
10188 TTTGTATCTCAT
64 TTTGTATCTCAT
10200 CAGAAATATG
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
84 1 0.02
85 64 0.97
86 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (85 bp):
GATTTGGTCCACTTCTATATATCTCATTAGGAAGATGATCTCTTCATTGATTTAACCTACTTCTT
TGTATCTCATAAGGAAGGCG
Found at i:10505 original size:48 final size:48
Alignment explanation
Indices: 10446--10537 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
10436 GTATTGAGCT
* ** * * *
10446 TCGCTTCATTGAGTTGGTCTACTTTTCTGTATCTCATTAGGAAGATGA
1 TCGCTTAATTGAGTTAATCCACTTCTCTGTATCTCATCAGGAAGATGA
*
10494 TCGCTTAATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAG
1 TCGCTTAATTGAGTTAATCCACTTCTCTGTATCTCATCAGGAAG
10538 GTGGATTTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (48 bp):
TCGCTTAATTGAGTTAATCCACTTCTCTGTATCTCATCAGGAAGATGA
Found at i:10602 original size:85 final size:85
Alignment explanation
Indices: 10459--10622 Score: 213
Period size: 85 Copynumber: 1.9 Consensus size: 85
10449 CTTCATTGAG
* * *
10459 TTGGTCTACTTTTCTGTATCTCATTAGGAAGATGATCGCTTAATTGATTTAATCCACTTCTCTGT
1 TTGGTCCACTTTTCTGTATCTCATTAGGAAGATGATCGCTTAATTGATTTAACCCACTTCTCTAT
10524 ATCTCATCAGGAAGGTGGAT
66 ATCTCATCAGGAAGGTGGAT
* * * ** * *
10544 TTGGTCCACTTCTT-TGTATCTCATTAGGAAGATGGTTGCTTTATTTCTTTGACCCACTTCTTTA
1 TTGGTCCACTT-TTCTGTATCTCATTAGGAAGATGATCGCTTAATTGATTTAACCCACTTCTCTA
*
10608 TATCTCATTAGGAAG
65 TATCTCATCAGGAAG
10623 ATGGGGTTTG
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
85 65 0.97
86 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (85 bp):
TTGGTCCACTTTTCTGTATCTCATTAGGAAGATGATCGCTTAATTGATTTAACCCACTTCTCTAT
ATCTCATCAGGAAGGTGGAT
Found at i:11355 original size:50 final size:49
Alignment explanation
Indices: 11232--11357 Score: 135
Period size: 50 Copynumber: 2.6 Consensus size: 49
11222 CGTCGTTACA
* ** *
11232 GCTTCAAGCTTTCCCTTCATGTCTTCATGGTACCGGGTTCGCCATCGCG
1 GCTTCAACCTTTCCCTTCAAATCTTCAAGGTACCGGGTTCGCCATCGCG
* * ** * * * *
11281 GCCTCAACCTTTCCCATCTCATCTTCTAAGGTACTGGGTTTGCCGTTGCG
1 GCTTCAACCTTTCCCTTCAAATCTTC-AAGGTACCGGGTTCGCCATCGCG
11331 GCTTCAACCTTTCCCTTCAAATCTTCA
1 GCTTCAACCTTTCCCTTCAAATCTTCA
11358 TGTTTCCTTG
Statistics
Matches: 61, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
49 21 0.34
50 40 0.66
ACGTcount: A:0.15, C:0.33, G:0.17, T:0.34
Consensus pattern (49 bp):
GCTTCAACCTTTCCCTTCAAATCTTCAAGGTACCGGGTTCGCCATCGCG
Found at i:12319 original size:13 final size:12
Alignment explanation
Indices: 12298--12331 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
12288 GACCTCTCCG
*
12298 TTTTGTTTTTTC
1 TTTTTTTTTTTC
12310 TTTTTTTTTTTC
1 TTTTTTTTTTTC
12322 TTTTTTTTTT
1 TTTTTTTTTT
12332 GGGTGAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:13198 original size:17 final size:17
Alignment explanation
Indices: 13176--13215 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
13166 TTTTTCGACC
*
13176 CTTTTTTCTTTTTTCTTT
1 CTTTTTT-TTTTTACTTT
*
13194 CTTTTTTTTTTTATTTT
1 CTTTTTTTTTTTACTTT
13211 CTTTT
1 CTTTT
13216 GATAACATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (17 bp):
CTTTTTTTTTTTACTTT
Found at i:17560 original size:30 final size:30
Alignment explanation
Indices: 17526--17761 Score: 221
Period size: 30 Copynumber: 7.9 Consensus size: 30
17516 ATTTATGGTG
17526 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
* ** *
17556 AAAATGTGATTTTCAAAAAGTTTGAGGTGTC
1 AAAATGTAATTTTGGAAAAGTTTAAGG-GTC
*
17587 AAAATGTGATTTTTGGAAAA-TTT-AGGTGTC
1 AAAATGT-AATTTTGGAAAAGTTTAAGG-GTC
* *
17617 AAAATGTAATTTTGGAAAAGTTT-GGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
* * *
17646 AAAATGCAATTTTGGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
* * *
17676 AAAATGTGATTTTGGAAAAATTT-AGAGGTT
1 AAAATGTAATTTTGGAAAAGTTTAAG-GGTC
* * * *
17706 AGAATATGATTTT-GAAAAATTTAAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
** *
17735 AAAATGTAATTTTTAAAAAGCTTAAGG
1 AAAATGTAATTTTGGAAAAGTTTAAGG
17762 ACCTCTTGGG
Statistics
Matches: 174, Mismatches: 25, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
29 58 0.33
30 95 0.55
31 13 0.07
32 8 0.05
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTAAGGGTC
Found at i:17680 original size:59 final size:58
Alignment explanation
Indices: 17526--17747 Score: 227
Period size: 59 Copynumber: 3.7 Consensus size: 58
17516 ATTTATGGTG
* ** *
17526 AAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAATGTGATTTTCAAAAAGTTTGAGGTGTC
1 AAAATG-AATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTG-GG-GTT
*
17587 AAAATGTGATTTTTGGAAAA-TTT-AGGTGTCAAAATGTAATTTTGGAAAAGTTTGGGGTT
1 AAAA--TGAATTTTGGAAAAGTTTAAGG-GTCAAAATGTAATTTTGGAAAAGTTTGGGGTT
* * * * *
17646 AAAATGCAATTTTGGAAAAGTTTAGGGGTTAAAATGTGATTTTGGAAAAATTTAGAGGTT
1 AAAATG-AATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTT-GGGGTT
*
17706 AGAATATG-ATTTT-GAAAAATTTAAGGGTCAAAATGTAATTTT
1 A-AA-ATGAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTT
17748 TAAAAAGCTT
Statistics
Matches: 137, Mismatches: 15, Indels: 20
0.80 0.09 0.12
Matches are distributed among these distances:
57 2 0.01
58 11 0.08
59 57 0.42
60 18 0.13
61 33 0.24
62 14 0.10
63 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (58 bp):
AAAATGAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTGGGGTT
Done.