Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010332.1 Kokia drynarioides strain JFW-HI SEQ_125197, 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: 55431
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Warning! 52 characters in sequence are not A, C, G, or T
Found at i:12999 original size:44 final size:44
Alignment explanation
Indices: 12932--13027 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
12922 TTTCCATTTT
* * *
12932 GGCTTGCACCCACTTGATCTTGCATTTAGA-CTGTCCGCCGCTTC
1 GGCTTGCACCCACTGGATCTTGCATTTAGATC-GTCCGCCACCTC
*
12976 GGCTTGCACCCACTCGGGT-TTGCATTTAGATCGTCCGCCACCTC
1 GGCTTGCACCCACT-GGATCTTGCATTTAGATCGTCCGCCACCTC
13020 GGCTTGCA
1 GGCTTGCA
13028 ATTCAACAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
44 43 0.93
45 3 0.07
ACGTcount: A:0.14, C:0.34, G:0.23, T:0.29
Consensus pattern (44 bp):
GGCTTGCACCCACTGGATCTTGCATTTAGATCGTCCGCCACCTC
Found at i:13105 original size:30 final size:30
Alignment explanation
Indices: 13044--13212 Score: 214
Period size: 30 Copynumber: 5.7 Consensus size: 30
13034 CAGGCTCACA
* * *
13044 CTTTGACAGACTCGCACTTT-GCTTGCTGT
1 CTTTAACAGGCTCGCACTTTGGCTTACTGT
* *
13073 CTTTAATAGGGTCGCACTTTGGCTTACTGT
1 CTTTAACAGGCTCGCACTTTGGCTTACTGT
*
13103 CTTTGACAGGCTCGCACTTTGGCTTACTGT
1 CTTTAACAGGCTCGCACTTTGGCTTACTGT
* *
13133 CTTTAACAAGCTCGCTCTTTGGCTTACTGT
1 CTTTAACAGGCTCGCACTTTGGCTTACTGT
* * *
13163 CTTTGACAGGCTTGCACTTTAGCTTACTGT
1 CTTTAACAGGCTCGCACTTTGGCTTACTGT
**
13193 CTTTAGTAGGCTCGCACTTT
1 CTTTAACAGGCTCGCACTTT
13213 TGATGGCTCG
Statistics
Matches: 119, Mismatches: 20, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
29 16 0.13
30 103 0.87
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.39
Consensus pattern (30 bp):
CTTTAACAGGCTCGCACTTTGGCTTACTGT
Found at i:15169 original size:15 final size:15
Alignment explanation
Indices: 15149--15231 Score: 53
Period size: 16 Copynumber: 5.3 Consensus size: 15
15139 GATCCTTTTA
15149 ATTTTATTTTTTAAT
1 ATTTTATTTTTTAAT
*
15164 ATTTTAAATTTTTTTAAA
1 ATTTT--A-TTTTTTAAT
*
15182 ATTATATATTTTTAAT
1 ATTTTAT-TTTTTAAT
* * *
15198 TTTTTAGTTTTTCAAG
1 ATTTTA-TTTTTTAAT
*
15214 A-TTTAGTTTTTAA-
1 ATTTTATTTTTTAAT
15227 ATTTT
1 ATTTT
15232 TCAATAATAT
Statistics
Matches: 52, Mismatches: 10, Indels: 13
0.69 0.13 0.17
Matches are distributed among these distances:
13 1 0.02
14 9 0.17
15 10 0.19
16 18 0.35
17 2 0.04
18 12 0.23
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (15 bp):
ATTTTATTTTTTAAT
Found at i:15178 original size:18 final size:18
Alignment explanation
Indices: 15155--15194 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
15145 TTTAATTTTA
* *
15155 TTTTTTAATATTTTAAAT
1 TTTTTTAAAATTATAAAT
*
15173 TTTTTTAAAATTATATAT
1 TTTTTTAAAATTATAAAT
15191 TTTT
1 TTTT
15195 AATTTTTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTTAAAATTATAAAT
Found at i:15218 original size:23 final size:23
Alignment explanation
Indices: 15192--15235 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
15182 ATTATATATT
* *
15192 TTTAATTTTTTAGTTTTTCAAGA
1 TTTAATTTTTAAATTTTTCAAGA
*
15215 TTTAGTTTTTAAATTTTTCAA
1 TTTAATTTTTAAATTTTTCAA
15236 TAATATATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (23 bp):
TTTAATTTTTAAATTTTTCAAGA
Found at i:16428 original size:29 final size:30
Alignment explanation
Indices: 16396--16454 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
16386 AGGCAAAACA
* *
16396 GTAA-TATTGGACACTCAGGGGCGAAAATG
1 GTAATTATTGAACACTCAGGGGCAAAAATG
* *
16425 GTAATTTTTGAACACTCGGGGGCAAAAATG
1 GTAATTATTGAACACTCAGGGGCAAAAATG
16455 TGACTTTTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.24
Consensus pattern (30 bp):
GTAATTATTGAACACTCAGGGGCAAAAATG
Found at i:16462 original size:29 final size:30
Alignment explanation
Indices: 16406--16463 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
16396 GTAATATTGG
* *
16406 ACACTCAGGGGCGAAAATGGTAATTTTTGA
1 ACACTCAGGGGCAAAAATGGTAACTTTTGA
* *
16436 ACACTCGGGGGCAAAAAT-GTGACTTTTG
1 ACACTCAGGGGCAAAAATGGTAACTTTTG
16464 GAAGTTTGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.26
Consensus pattern (30 bp):
ACACTCAGGGGCAAAAATGGTAACTTTTGA
Found at i:16494 original size:29 final size:29
Alignment explanation
Indices: 16459--16654 Score: 170
Period size: 29 Copynumber: 6.8 Consensus size: 29
16449 AAAATGTGAC
*
16459 TTTTGGAAGTTTGGGGGTAAAATGGTAAT
1 TTTTGGAAGTTTAGGGGTAAAATGGTAAT
* * * *
16488 TTATGGAAGTTT-GCGAGCAAAACGGTAA-
1 TTTTGGAAGTTTAG-GGGTAAAATGGTAAT
** * * *
16516 TTTTGGAAAATT-CGAGTAAAAAATGAT-AT
1 TTTTGGAAGTTTAGGGGT--AAAATGGTAAT
* *
16545 TTTTGGAAGTTCAGAGGTAAAATGGTAA-
1 TTTTGGAAGTTTAGGGGTAAAATGGTAAT
*
16573 TTTTGGAAGTTTAGGGGTAAAAAT-GTGAT
1 TTTTGGAAGTTTAGGGGT-AAAATGGTAAT
16602 TTTTGGAAAGTTTAGGGGTAAAATGGTAATT
1 TTTTGG-AAGTTTAGGGGTAAAATGGTAA-T
*
16633 TTTTGGAAATTTAGGGGTAAAA
1 TTTTGGAAGTTTAGGGGTAAAA
16655 ATGCAATTTT
Statistics
Matches: 133, Mismatches: 23, Indels: 21
0.75 0.13 0.12
Matches are distributed among these distances:
27 3 0.02
28 37 0.28
29 54 0.41
30 32 0.24
31 7 0.05
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
TTTTGGAAGTTTAGGGGTAAAATGGTAAT
Found at i:16595 original size:57 final size:58
Alignment explanation
Indices: 16459--16666 Score: 187
Period size: 57 Copynumber: 3.6 Consensus size: 58
16449 AAAATGTGAC
* * * * * *
16459 TTTTGGAAGTTTGGGGGT-AAAATGGTAATTTATGGAAGTTTGC-GA-GCAAAACGGTAA
1 TTTTGGAAATTTAGGGGTAAAAATGATAATTTTTGGAAG-TT-CAGAGGTAAAATGGTAA
* * *
16516 TTTTGGAAAATT-CGAGTAAAAAATGAT-ATTTTTGGAAGTTCAGAGGTAAAATGGTAA
1 TTTTGGAAATTTAGGGGT-AAAAATGATAATTTTTGGAAGTTCAGAGGTAAAATGGTAA
* * * *
16573 TTTTGGAAGTTTAGGGGTAAAAATG-TGATTTTTGGAAAGTTTAGGGGTAAAATGGTAA
1 TTTTGGAAATTTAGGGGTAAAAATGATAATTTTTGG-AAGTTCAGAGGTAAAATGGTAA
*
16631 TTTTTTGGAAATTTAGGGGTAAAAATG-CAATTTTTG
1 --TTTTGGAAATTTAGGGGTAAAAATGATAATTTTTG
16667 TAAATTTGAG
Statistics
Matches: 125, Mismatches: 17, Indels: 15
0.80 0.11 0.10
Matches are distributed among these distances:
55 1 0.01
56 8 0.06
57 55 0.44
58 30 0.24
60 31 0.25
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (58 bp):
TTTTGGAAATTTAGGGGTAAAAATGATAATTTTTGGAAGTTCAGAGGTAAAATGGTAA
Found at i:16615 original size:30 final size:29
Alignment explanation
Indices: 16443--16666 Score: 158
Period size: 29 Copynumber: 7.7 Consensus size: 29
16433 TGAACACTCG
* * * *
16443 GGGGCAAAAATGTGACTTTTGGAAGTTTG
1 GGGGTAAAAATGTAATTTTTGGAAGTTTA
*
16472 GGGGT-AAAATGGTAATTTATGGAAGTTT-
1 GGGGTAAAAAT-GTAATTTTTGGAAGTTTA
* * ** **
16500 GCGAGCAAAACGGTAA-TTTTGGAAAATT-
1 G-GGGTAAAAATGTAATTTTTGGAAGTTTA
* * *
16528 CGAGTAAAAAATG-ATATTTTTGGAAGTTCA
1 GGGGT-AAAAATGTA-ATTTTTGGAAGTTTA
*
16558 GAGGT-AAAATGGTAA-TTTTGGAAGTTTA
1 GGGGTAAAAAT-GTAATTTTTGGAAGTTTA
*
16586 GGGGTAAAAATGTGATTTTTGGAAAGTTTA
1 GGGGTAAAAATGTAATTTTTGG-AAGTTTA
*
16616 GGGGT-AAAATGGTAATTTTTTGGAAATTTA
1 GGGGTAAAAAT-GTAA-TTTTTGGAAGTTTA
*
16646 GGGGTAAAAATGCAATTTTTG
1 GGGGTAAAAATGTAATTTTTG
16667 TAAATTTGAG
Statistics
Matches: 153, Mismatches: 27, Indels: 30
0.73 0.13 0.14
Matches are distributed among these distances:
27 4 0.03
28 45 0.29
29 57 0.37
30 35 0.23
31 12 0.08
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (29 bp):
GGGGTAAAAATGTAATTTTTGGAAGTTTA
Found at i:18556 original size:209 final size:209
Alignment explanation
Indices: 17980--19485 Score: 1764
Period size: 209 Copynumber: 7.2 Consensus size: 209
17970 ATTTGGTGTT
* * *
17980 ATTGATTTAGTCTACTTCTCAATATCTCATC-AGCAAGATGACTGCATCACTTGTTTTGATCCAC
1 ATTGATTTGGTCTACTTCTCAGTATCTCATCAAG-AAGATGACCGCATCACTTGTTTTGATCCAC
* * *
18044 TTCTCTGTGTCTCATCAGGAAGACGGATCTAGTTCACTTCTCTGTATCTCATCAGGAAGGTAACC
65 TTCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTATGTATCTCATCAGGAAGCTAA-C
* * * *
18109 GCTTTATTGGTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCAC
129 GATTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAC
18174 ATTGAGCTTTGGCTTC
194 ATTGAGCTTTGGCTTC
* * * *
18190 ATTGATTTGGTCTACTTCTCAGTATCTCATC-AGGA-ATAACTGCATC-TTTGTTTTGATCCACT
1 ATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACT
* * * * * *
18252 TCTCTGTATCTCATCAGGAAGACGGATCCGATTCACTTCTTTGTATCTAATCAGGAAGGTAACAG
66 TCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTATGTATCTCATCAGGAAGCTAAC-G
* * * * * * *
18317 TTTTATTGCTTCGACTTACATCTTAGTATCTCATCAGGAAGATGGGGTTCGAAGATTCGCTCACA
130 ATTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
*
18382 TCGAGCTTTGGCTTC
195 TTGAGCTTTGGCTTC
* *
18397 ATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATC-TTTATTTTGATCCACT
1 ATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACT
* * * * * *
18461 TCTTTGTATCTCATCAGGAAGATGGATCCGGTTCACTTCTATATATCTCATCAGGAAGGTAATCG
66 TCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTATGTATCTCATCAGGAAGCTAA-CG
*
18526 ATTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAG-TTTCGCTCAC
130 ATTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT-GCTCAC
* *
18590 ATCGAGCTTT-GTTTC
194 ATTGAGCTTTGGCTTC
* * * * * *
18605 ATTGAGTTGGTGTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTCTTTTGATCCACT
1 ATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACT
* * * * *
18670 TCTCTGAGTCTCATCAGGAAGACGAATCTGGTTCACTTCTTTGTATCTCATTAGGAAGCTATCTG
66 TCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTATGTATCTCATCAGGAAGCTAAC-G
* * * *
18735 CTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACT
130 ATTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
* **
18800 TTGAG-TCTGATTTC
195 TTGAGCTTTGGCTTC
* * * *
18814 ATTGATTTGGCCTTCTTCTTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACT
1 ATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACT
* * * * * *
18879 TCTCTATGTCTCATTAGGAAAACGGATTTGG-TCTACTACTCA-GTATCTCATCAGGAAGCTGAC
66 TCTCTGTGTCTCATCAGGAAGACGGATCTGGTTC-ACTTCT-ATGTATCTCATCAGGAAGCTAAC
* * * * *
18942 CATTTTATTGCTTCGTCCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCAAAGTTTTGCTCA
129 GA-TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* *
19007 CATTGAGCTTCGACTTC
193 CATTGAGCTTTGGCTTC
* * * **
19024 TTTGATTTGGTATACTTCTCAGTATCTCATCAAGAAGATGATCGTC-TTGCTTGTTTTGATCCAC
1 ATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCG-CATCACTTGTTTTGATCCAC
* * * * * * * *
19088 TTCTTTGTGTCTCATTAGGAAGGCGGATCTGGTTCACTTCTCTGTATCTCGTTAAGAAGCTAACC
65 TTCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTATGTATCTCATCAGGAAGCTAACG
* * * *
19153 ACTTTATTGCTTCGACTTGCTTCTCAATATCTCATCAGGAAGCTGGGGTTCGATGATTTGCTTAC
130 A-TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAC
* * *
19218 TTTGAGC-CTGG-TTAT
194 ATTGAGCTTTGGCTT-C
* * * * * *
19233 ATTGATTTGGTCTTCTTCTCAGTATTTCATCAGGAAGATGACCACATCACTTGTTTGGATTCACT
1 ATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACT
* * * * * *
19298 TCTTTGTGTCTCATCAGGAAGACGAATCTTGTCCACTTCTCA-GTATCTCATCAGGAAGCTGACC
66 TCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCT-ATGTATCTCATCAGGAAGCTAACG
* * * *
19362 ATTTTATTGCTTTGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCAAAGTTTTGCTCAC
130 A-TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAC
19427 ATT-ATGCTTTGGCTTC
194 ATTGA-GCTTTGGCTTC
* *
19443 TTTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACC
1 ATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACC
19486 ACTTTGTTGC
Statistics
Matches: 1112, Mismatches: 162, Indels: 44
0.84 0.12 0.03
Matches are distributed among these distances:
206 1 0.00
207 176 0.16
208 71 0.06
209 610 0.55
210 249 0.22
211 5 0.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (209 bp):
ATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACT
TCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTATGTATCTCATCAGGAAGCTAACGA
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
TGAGCTTTGGCTTC
Found at i:19186 original size:419 final size:418
Alignment explanation
Indices: 17980--19483 Score: 1898
Period size: 419 Copynumber: 3.6 Consensus size: 418
17970 ATTTGGTGTT
* * * * *
17980 ATTGATTTAGTCTACTTCTCAATATCTCATCAGCAAGATGACTGCATCACTTGTTTTGATCCACT
1 ATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACT
* * * *
18045 TCTCTGTGTCTCATCAGGAAGACGGATCTAGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCG
66 TCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * * * * *
18110 CTTTATTGGTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCACA
131 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCAAAGTTTCGCTCACA
* *
18175 TTGAGCTTTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATC-AGGA-AT-AAC-TGCATC
196 TTGAGCTTTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGAACGT-CTTC
* * * *
18236 TTTGTTTTGATCCACTTCTCTGTATCTCATCAGGAAGACGGATCCGATTCACTTCTTTGTATCTA
260 -TTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTTTGTATCTC
* * * * * *
18301 ATCAGGAAGGTAA-CAGTTTTATTGCTTCGACTTACATCTTAGTATCTCATCAGGAAGATGGGGT
324 ATTAGGAAGCTAACCA-CTTTATTGCTTCGACTTGCTTCTTAGTATCTCATCAGGAAGCTGGGGT
* * * * *
18365 TCGAAGATTCGCTCACATCGAGCTTTGGCTTC
388 TCGAAGATTTGCTCACTTTGAG-TCTGGTTTC
* * * *
18397 ATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATC-TTTATTTTGATCCACT
1 ATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACT
* * * * * *
18461 TCTTTGTATCTCATCAGGAAGATGGATCCGGTTCACTTCT-ATATATCTCATCAGGAAGGTAATC
66 TCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCA-GTATCTCATCAGGAAGCTAA-C
* *
18525 GA-TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGTTTCGCTCA
129 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCAAAGTTTCGCTCA
* * * * * * * *
18589 CATCGAGCTTT-GTTTCATTGAGTTGGTGTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTC
194 CATTGAGCTTTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGAACGTCT-
* * * *
18653 ACTTCTTTTGATCCACTTCTCTGAGTCTCATCAGGAAGACGAATCTGGTTCACTTCTTTGTATCT
258 TCTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTTTGTATCT
* ** * *
18718 CATTAGGAAGCTATCTGCTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTAGGGT
323 CATTAGGAAGCTAACCACTTTATTGCTTCGACTTGCTTCTTAGTATCTCATCAGGAAGCTGGGGT
*
18783 TCGAAGATTTGCTCACTTTGAGTCTGATTTC
388 TCGAAGATTTGCTCACTTTGAGTCTGGTTTC
* *
18814 ATTGATTTGGCCTTCTTCTTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACT
1 ATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACT
* * * * * *
18879 TCTCTATGTCTCATTAGGAAAACGGATTTGG-TCTACTACTCAGTATCTCATCAGGAAGCTGACC
66 TCTCTGTGTCTCATCAGGAAGACGGATCTGGTTC-ACTTCTCAGTATCTCATCAGGAAGCTAACC
* * * *
18943 ATTTTATTGCTTCGTCCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCAAAGTTTTGCTCAC
130 ATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCAAAGTTTCGCTCAC
* * * * *
19008 ATTGAGCTTCGACTTCTTTGATTTGGTATACTTCTCAGTATCTCATCAAGAAGATGATCGTCTTG
195 ATTGAGCTTTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGAACGTCTT-
* * * *
19073 CTTGTTTTGATCCACTTCTTTGTGTCTCATTAGGAAGGCGGATCTGGTTCACTTCTCTGTATCTC
259 CTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTTTGTATCTC
* * * *
19138 GTTAAGAAGCTAACCACTTTATTGCTTCGACTTGCTTCTCAATATCTCATCAGGAAGCTGGGGTT
324 ATTAGGAAGCTAACCACTTTATTGCTTCGACTTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTT
* * *
19203 CGATGATTTGCTTACTTTGAGCCTGGTTAT-
389 CGAAGATTTGCTCACTTTGAGTCTGGTT-TC
* * * *
19233 ATTGATTTGGTCTTCTTCTCAGTATTTCATCAGGAAGATGACCACATCACTTGTTTGGATTCACT
1 ATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACT
* * * * *
19298 TCTTTGTGTCTCATCAGGAAGACGAATCTTGTCCACTTCTCAGTATCTCATCAGGAAGCTGACCA
66 TCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* *
19363 TTTTATTGCTTTGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCAAAGTTTTGCTCACA
131 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCAAAGTTTCGCTCACA
* *
19428 TT-ATGCTTTGGCTTCTTTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGA
196 TTGA-GCTTTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGA
19484 CCACTTTGTT
Statistics
Matches: 936, Mismatches: 134, Indels: 32
0.85 0.12 0.03
Matches are distributed among these distances:
415 32 0.03
416 138 0.15
417 100 0.11
418 257 0.27
419 407 0.43
420 2 0.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (418 bp):
ATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACT
TCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCA
TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCAAAGTTTCGCTCACA
TTGAGCTTTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGAACGTCTTCT
TGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTTTGTATCTCAT
TAGGAAGCTAACCACTTTATTGCTTCGACTTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCG
AAGATTTGCTCACTTTGAGTCTGGTTTC
Found at i:19312 original size:628 final size:625
Alignment explanation
Indices: 17973--19485 Score: 1944
Period size: 628 Copynumber: 2.4 Consensus size: 625
17963 TTCAGTGATT
* * * *
17973 TGGTGTTATTGATTTAGTCTACTTCTCAATATCTCATCAGCAAGATGACTGCATCACTTGTTTTG
1 TGGT-TTATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
*
18038 ATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTAGTTCACTTCTCTGTATCTCATCAGGAAG
65 ATCCACTTCTCTGTGTCTCATCAGGAAGACGAATCTAGTTCACTTCTCTGTATCTCATCAGGAAG
* * * * *
18103 GTAACCGCTTTATTGGTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTC
130 CTAACTGCTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTT
* * *
18168 GCTCACATTGAGCTTTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGG-A-ATAACT
195 GCTCACTTTGAG-TTTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACC
* * * * **
18231 GCATCTTTGTTTTGATCCACTTCTCTGTATCTCATCAGGAAGACGGATCCGATTCACTTCTTTGT
259 GCATCCTTGTTTTGATCCACTTCTCTATATCTCATCAGGAAAACGGATCCGATTCACTACTCAGT
* * * *
18296 ATCTAATCAGGAAGGTAACAGTTTTATTGCTTCGACTTACATCTTAGTATCTCATCAGGAAGATG
324 ATCTAATCAGGAAGCTAACAGTTTTATTGCTTCGACCTACATCTCAGTATCTCATCAGAAAGATG
* * * *
18361 GGGTTCGAAGATTCGCTCACATCGAGCTTTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCA
389 GGGTTCAAAGATTCGCTCACATCGAGCTTCGACTTCATTGATTTGGTATACTTCTCAGTATCTCA
*
18426 TCAAGAAGATGACCGCATCTTTATTTTGATCCACTTCTTTGTATCTCATCAGGAAGATGGATCCG
454 TCAAGAAGATGACCGCATCTTTATTTTGATCCACTTCTTTGTATCTCATCAGGAAGACGGATCCG
* * * *
18491 GTTCACTTCTATATATCTCATCAGGAAGGTAATCGATTTATTGCTTCGACCTGCTTCTCAGTATC
519 GTTCACTTCTATATATCTCATCAAGAAGCTAATCCATTTATTGCTTCGACCTGCTTCTCAATATC
*
18556 TCATCAGGAAGCTAGGGTTCGAAGTTTCGCTCACATCGAGCT
584 TCATCAGGAAGCTAGGGTTCGAAGTTTCGCTCACATCGAGCC
* * * * * *
18598 TTGTTTCATTGAGTTGGTGTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTCTTTTG
1 TGGTTT-ATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
* * * *
18663 ATCCACTTCTCTGAGTCTCATCAGGAAGACGAATCTGGTTCACTTCTTTGTATCTCATTAGGAAG
65 ATCCACTTCTCTGTGTCTCATCAGGAAGACGAATCTAGTTCACTTCTCTGTATCTCATCAGGAAG
*
18728 CTATCTGCTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTT
130 CTAACTGCTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTT
* ** * * *
18793 GCTCACTTTGAGTCTGATTTCATTGATTTGGCCTTCTTCTTAGTATCTCATCAGGAAGATGACCG
195 GCTCACTTTGAGTTTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCG
* * ** *
18858 CATCACTTGTTTTGATCCACTTCTCTATGTCTCATTAGGAAAACGGATTTG-GTCTACTACTCAG
260 CATC-CTTGTTTTGATCCACTTCTCTATATCTCATCAGGAAAACGGATCCGATTC-ACTACTCAG
* * * * * *
18922 TATCTCATCAGGAAGCTGACCA-TTTTATTGCTTCGTCCTGCTTCTCAGTATCTCATCAGAAAGC
323 TATCTAATCAGGAAGCT-AACAGTTTTATTGCTTCGACCTACATCTCAGTATCTCATCAGAAAGA
* * * *
18986 TGGGGTTCAAAGTTTTGCTCACATTGAGCTTCGACTTCTTTGATTTGGTATACTTCTCAGTATCT
387 TGGGGTTCAAAGATTCGCTCACATCGAGCTTCGACTTCATTGATTTGGTATACTTCTCAGTATCT
* * * * * *
19051 CATCAAGAAGATGATCGTCTTGC-TTGTTTTGATCCACTTCTTTGTGTCTCATTAGGAAGGCGGA
452 CATCAAGAAGATGACCG-CAT-CTTTATTTTGATCCACTTCTTTGTATCTCATCAGGAAGACGGA
* * * * * *
19115 TCTGGTTCACTTCTCTGTATCTCGTTAAGAAGCTAA-CCACTTTATTGCTTCGACTTGCTTCTCA
515 TCCGGTTCACTTCTATATATCTCATCAAGAAGCTAATCCA-TTTATTGCTTCGACCTGCTTCTCA
* * * * *
19179 ATATCTCATCAGGAAGCTGGGGTTCGATGATTT-GCTTACTTTGAGCC
579 ATATCTCATCAGGAAGCTAGGGTTCGAAG-TTTCGCTCACATCGAGCC
* * * *
19226 TGGTTATATTGATTTGGTCTTCTTCTCAGTATTTCATCAGGAAGATGACCACATCACTTGTTTGG
1 TGGTT-TATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
* * * * *
19291 ATTCACTTCTTTGTGTCTCATCAGGAAGACGAATCTTGTCCACTTCTCAGTATCTCATCAGGAAG
65 ATCCACTTCTCTGTGTCTCATCAGGAAGACGAATCTAGTTCACTTCTCTGTATCTCATCAGGAAG
* *** * * * *
19356 CTGACCATTTTATTGCTTTGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCAAAGTTTT
130 CTAACTGCTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTT
* *
19421 GCTCACATTATG-CTTTGGCTTCTTTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGAC
195 GCTCAC-TT-TGAGTTTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGAC
19485 C
258 C
19486 ACTTTGTTGC
Statistics
Matches: 758, Mismatches: 117, Indels: 22
0.85 0.13 0.02
Matches are distributed among these distances:
624 39 0.05
625 183 0.24
626 11 0.01
627 170 0.22
628 301 0.40
629 52 0.07
630 2 0.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (625 bp):
TGGTTTATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGA
TCCACTTCTCTGTGTCTCATCAGGAAGACGAATCTAGTTCACTTCTCTGTATCTCATCAGGAAGC
TAACTGCTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTG
CTCACTTTGAGTTTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGC
ATCCTTGTTTTGATCCACTTCTCTATATCTCATCAGGAAAACGGATCCGATTCACTACTCAGTAT
CTAATCAGGAAGCTAACAGTTTTATTGCTTCGACCTACATCTCAGTATCTCATCAGAAAGATGGG
GTTCAAAGATTCGCTCACATCGAGCTTCGACTTCATTGATTTGGTATACTTCTCAGTATCTCATC
AAGAAGATGACCGCATCTTTATTTTGATCCACTTCTTTGTATCTCATCAGGAAGACGGATCCGGT
TCACTTCTATATATCTCATCAAGAAGCTAATCCATTTATTGCTTCGACCTGCTTCTCAATATCTC
ATCAGGAAGCTAGGGTTCGAAGTTTCGCTCACATCGAGCC
Found at i:28105 original size:2 final size:2
Alignment explanation
Indices: 28093--28127 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
28083 AAATTATTTG
*
28093 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28128 CTATTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:28898 original size:30 final size:29
Alignment explanation
Indices: 28743--29055 Score: 170
Period size: 29 Copynumber: 10.7 Consensus size: 29
28733 GAACACTCGG
* * * *
28743 GGGTAAAAAAGTGACTTTTGGAAGTTTGA
1 GGGTAAAAATGTAATTTTTGGAAGTTTAA
* *
28772 CGGT-AAAATGGTAATTTTTGGAAATTT-A
1 GGGTAAAAAT-GTAATTTTTGGAAGTTTAA
* * *** * *
28800 GGAGCAAAAAAGTAATTTTCAAAAAATTT-G
1 GG-GTAAAAATGTAATTTT-TGGAAGTTTAA
*
28830 GGGTCAAAAATG-ATATTTTTGGAAGTTCAA
1 GGGT-AAAAATGTA-ATTTTTGGAAGTTTAA
*
28860 GGGT-AAAATGGTAATTTTTTGAAGTTTAA
1 GGGTAAAAAT-GTAATTTTTGGAAGTTTAA
* * * **
28889 GCGTAAAAATATGATTTTTGGAAAGTTCGA
1 GGGTAAAAATGTAATTTTTGG-AAGTTTAA
* * * * *
28919 TGG-CAAAATGGCAATTTTTGGAAATTTAG
1 GGGTAAAAAT-GTAATTTTTGGAAGTTTAA
* *
28948 GGGTAAAAAAGTAATTTTTGGAAATTTAA
1 GGGTAAAAATGTAATTTTTGGAAGTTTAA
* *
28977 GGGTAAAAATGTAATTTTTATGAAGTTTAG
1 GGGTAAAAATGTAATTTTT-GGAAGTTTAA
* * **
29007 GGGTCAAAATATAATTTTTTAAAAGTTTAA
1 GGGTAAAAATGTAA-TTTTTGGAAGTTTAA
* * *
29037 GGATCAAAATGTGATTTTT
1 GGGTAAAAATGTAATTTTT
29056 AAACAGTTCA
Statistics
Matches: 214, Mismatches: 55, Indels: 30
0.72 0.18 0.10
Matches are distributed among these distances:
28 11 0.05
29 109 0.51
30 89 0.42
31 5 0.02
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTAA
Found at i:28927 original size:59 final size:59
Alignment explanation
Indices: 28829--29025 Score: 206
Period size: 59 Copynumber: 3.3 Consensus size: 59
28819 CAAAAAATTT
*
28829 GGGGTCAAAAATGAT-ATTTTTGG-AAGTTCAAGGGTAAAATGGTAATTTTTTGAAGTTTA
1 GGGGT-AAAAAT-ATAATTTTTGGAAAGTTCAAGGGAAAAATGGTAATTTTTTGAAGTTTA
* * * * * * * * *
28888 AGCGTAAAAATATGATTTTTGGAAAGTTCGATGGCAAAATGGCAATTTTTGGAAATTTA
1 GGGGTAAAAATATAATTTTTGGAAAGTTCAAGGGAAAAATGGTAATTTTTTGAAGTTTA
*
28947 GGGGTAAAAA-AGTAATTTTTGGAAA-TTTAAGGGTAAAAAT-GTAATTTTTATGAAGTTTA
1 GGGGTAAAAATA-TAATTTTTGGAAAGTTCAAGGG-AAAAATGGTAATTTTT-TGAAGTTTA
*
29006 GGGGTCAAAATATAATTTTT
1 GGGGTAAAAATATAATTTTT
29026 TAAAAGTTTA
Statistics
Matches: 113, Mismatches: 19, Indels: 12
0.78 0.13 0.08
Matches are distributed among these distances:
57 2 0.02
58 28 0.25
59 82 0.73
60 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.37
Consensus pattern (59 bp):
GGGGTAAAAATATAATTTTTGGAAAGTTCAAGGGAAAAATGGTAATTTTTTGAAGTTTA
Found at i:29023 original size:88 final size:87
Alignment explanation
Indices: 28773--29025 Score: 226
Period size: 88 Copynumber: 2.9 Consensus size: 87
28763 GAAGTTTGAC
* * * * *
28773 GGTAAAATGGTAATTTTTGGAAATTT-AGGAGCAAAAAAGTAATTTTCAAAAAATTTGGGGTCAA
1 GGTAAAATGGTAATTTTTGGAAATTTAAGG-GTAAAAATGTAATTTTTAAGAAGTTTGGGGTCAA
*
28837 AA-ATGATATTTTTGGAAGTTCAAG
65 AATAT-A-ATTTTTGGAAATTCAAG
* * * * * * * *
28861 GGTAAAATGGTAATTTTTTGAAGTTTAAGCGTAAAAATATGATTTTT-GGAAAGTTCGATGG-CA
1 GGTAAAATGGTAATTTTTGGAAATTTAAGGGTAAAAATGTAATTTTTAAG-AAGTTTG-GGGTCA
** * *
28924 AAATGGCAATTTTTGGAAATTTAGG
64 AAAT-ATAATTTTTGGAAATTCAAG
** *
28949 GGTAAAAAAGTAATTTTTGGAAATTTAAGGGTAAAAATGTAATTTTTATGAAGTTTAGGGGTCAA
1 GGTAAAATGGTAATTTTTGGAAATTTAAGGGTAAAAATGTAATTTTTAAGAAGTTT-GGGGTCAA
29014 AATATAATTTTT
65 AATATAATTTTT
29026 TAAAAGTTTA
Statistics
Matches: 127, Mismatches: 30, Indels: 16
0.73 0.17 0.09
Matches are distributed among these distances:
88 114 0.90
89 13 0.10
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.36
Consensus pattern (87 bp):
GGTAAAATGGTAATTTTTGGAAATTTAAGGGTAAAAATGTAATTTTTAAGAAGTTTGGGGTCAAA
ATATAATTTTTGGAAATTCAAG
Found at i:30192 original size:3 final size:3
Alignment explanation
Indices: 30124--30173 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
30114 TTTATTTCAT
30124 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30172 TT
1 TT
30174 TAATGCTATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:30835 original size:6 final size:6
Alignment explanation
Indices: 30824--30886 Score: 67
Period size: 6 Copynumber: 10.8 Consensus size: 6
30814 TTTAATGAAT
** **
30824 TTTAAA TTTAAA AGTAAA TTTAAA TTTAAA -GCAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
30871 TTTAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAA
30887 TCTTAAGATA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
5 7 0.16
6 38 0.84
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:30881 original size:11 final size:11
Alignment explanation
Indices: 30844--30886 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
30834 AAAGTAAATT
*
30844 TAAATTTAAAG
1 TAAATTTAAAA
* *
30855 CAAATTTAAATT
1 TAAATTTAAA-A
30867 TAAATTTAAAA
1 TAAATTTAAAA
30878 TAAATTTAA
1 TAAATTTAA
30887 TCTTAAGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:30886 original size:17 final size:18
Alignment explanation
Indices: 30824--30870 Score: 78
Period size: 17 Copynumber: 2.7 Consensus size: 18
30814 TTTAATGAAT
*
30824 TTTAAATTTAAAAGTAAA
1 TTTAAATTTAAAAGCAAA
30842 TTTAAATTT-AAAGCAAA
1 TTTAAATTTAAAAGCAAA
30859 TTTAAATTTAAA
1 TTTAAATTTAAA
30871 TTTAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (18 bp):
TTTAAATTTAAAAGCAAA
Found at i:30892 original size:17 final size:16
Alignment explanation
Indices: 30861--30903 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
30851 AAAGCAAATT
30861 TAAATTTAAATTTAAAA
1 TAAATTT-AATTTAAAA
*
30878 TAAATTTAATCTTAAGA
1 TAAATTTAAT-TTAAAA
*
30895 TAATTTTAA
1 TAAATTTAA
30904 AAAGAGGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
TAAATTTAATTTAAAA
Found at i:30892 original size:23 final size:23
Alignment explanation
Indices: 30838--30886 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
30828 AATTTAAAAG
*
30838 TAAATTTAAATTTAAAGCAAATT
1 TAAATTTAAATTTAAAACAAATT
*
30861 TAAATTTAAATTTAAAATAAATT
1 TAAATTTAAATTTAAAACAAATT
30884 TAA
1 TAA
30887 TCTTAAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TAAATTTAAATTTAAAACAAATT
Found at i:31208 original size:22 final size:21
Alignment explanation
Indices: 31183--31239 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
31173 GGGTCAAAAT
* *
31183 TAAATTATAATTTTTATAATAG
1 TAAATTATAATTTTTA-AAGAA
* *
31205 TAAAATGTAATTTTTAAAGAA
1 TAAATTATAATTTTTAAAGAA
*
31226 TAAATCATAATTTT
1 TAAATTATAATTTT
31240 ATCATTTTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (21 bp):
TAAATTATAATTTTTAAAGAA
Found at i:31445 original size:25 final size:27
Alignment explanation
Indices: 31401--31451 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
31391 AACATCAATT
31401 TTTTTAAAAAAAATAGAATTT-ATTTA
1 TTTTTAAAAAAAATAGAATTTCATTTA
*
31427 TTTTTAAAAAAAAT-TAATTTCATTT
1 TTTTTAAAAAAAATAGAATTTCATTT
31452 TTAGTACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTTTAAAAAAAATAGAATTTCATTTA
Found at i:31576 original size:18 final size:16
Alignment explanation
Indices: 31555--31596 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
31545 TTTTTTTCAA
31555 TTTTATAATTTTTTGAGC
1 TTTTATAATTTTTT-A-C
*
31573 TTTTAT-ACTTTTTAC
1 TTTTATAATTTTTTAC
31588 TTTTATAAT
1 TTTTATAAT
31597 ATATATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 7 0.33
16 2 0.10
17 6 0.29
18 6 0.29
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTTATAATTTTTTAC
Found at i:33598 original size:29 final size:29
Alignment explanation
Indices: 33566--33644 Score: 68
Period size: 31 Copynumber: 2.6 Consensus size: 29
33556 GTTCAATTGA
*
33566 ATACATGAACTTTAATTTGGTGCAATTAT
1 ATACATGAACTTTAATTTGGTGCAAATAT
* * * *
33595 ATACGTGAAACTCTAATTATGGTTCAAATGT
1 ATACATG-AACTTTAATT-TGGTGCAAATAT
* *
33626 ATACTTTAAACTTTAATTT
1 ATAC-ATGAACTTTAATTT
33645 TGATTTAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
29 6 0.15
30 10 0.26
31 22 0.56
32 1 0.03
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.42
Consensus pattern (29 bp):
ATACATGAACTTTAATTTGGTGCAAATAT
Found at i:39395 original size:22 final size:21
Alignment explanation
Indices: 39352--39395 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
39342 TTATTAAAAA
*
39352 TAATTTATTCAACTAATTTTT
1 TAATTTATTCAACTAATATTT
* *
39373 TAATTTAATTCAATTTATATTT
1 TAATTT-ATTCAACTAATATTT
39395 T
1 T
39396 TCACAAATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATTTATTCAACTAATATTT
Found at i:39522 original size:42 final size:42
Alignment explanation
Indices: 39463--39548 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
39453 CTAACCGGCC
39463 AACCGATCCGATTTAGTTTCTAGGCAGCCAAACCTGAATAAA
1 AACCGATCCGATTTAGTTTCTAGGCAGCCAAACCTGAATAAA
39505 AACCGATCCGATTTAGTTTCTAGGCAGCCAAACCTGAATAAA
1 AACCGATCCGATTTAGTTTCTAGGCAGCCAAACCTGAATAAA
39547 AA
1 AA
39549 GATAGCATCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.23
Consensus pattern (42 bp):
AACCGATCCGATTTAGTTTCTAGGCAGCCAAACCTGAATAAA
Found at i:42071 original size:13 final size:14
Alignment explanation
Indices: 42053--42089 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
42043 TTTTTATTGC
42053 TAATATTATAT-AA
1 TAATATTATATAAA
42066 TAATATTAT-TAAA
1 TAATATTATATAAA
42079 TATATATTATA
1 TA-ATATTATA
42090 CTTTGACCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 1 0.05
13 13 0.62
14 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TAATATTATATAAA
Found at i:42554 original size:2 final size:2
Alignment explanation
Indices: 42547--42573 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42537 TGCATGCATG
42547 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
42574 GATGTATGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42963 original size:31 final size:32
Alignment explanation
Indices: 42928--43009 Score: 85
Period size: 33 Copynumber: 2.6 Consensus size: 32
42918 TTTTTGGTTC
*
42928 AATTTGGTACTTAAATTTGACA-CTTTTTCCT
1 AATTTGGTACTTAAATTTGACATCTTTTTACT
* * * * *
42959 AATTTGATATTTAAACTTGACATTTTTTTTATT
1 AATTTGGTACTTAAATTTGACA-TCTTTTTACT
*
42992 AAGTTGGTACTTAAATTT
1 AATTTGGTACTTAAATTT
43010 TTTGGGGTTC
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
31 19 0.49
33 20 0.51
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (32 bp):
AATTTGGTACTTAAATTTGACATCTTTTTACT
Found at i:44074 original size:29 final size:29
Alignment explanation
Indices: 44033--44351 Score: 220
Period size: 29 Copynumber: 10.9 Consensus size: 29
44023 ATTTTGGGGT
* *
44033 TAAAAATGAAATTTTTAGAAGTTTAAGGG
1 TAAAAATGGAATTTTTGGAAGTTTAAGGG
* **
44062 TAAAAGTGGAATTTTTGGAAGTTTCGGGG
1 TAAAAATGGAATTTTTGGAAGTTTAAGGG
*
44091 TCAAAAAT-GAGATTTTTGGAAGTTTTA-GG
1 T-AAAAATGGA-ATTTTTGGAAGTTTAAGGG
* * * * * *
44120 TTAAAATGGGATTTTTTGAAATTTGAGGC
1 TAAAAATGGAATTTTTGGAAGTTTAAGGG
* *
44149 TAAAAATGGAATTTTTGGAGGTTT-CGAGG
1 TAAAAATGGAATTTTTGGAAGTTTAAG-GG
* **
44178 TCAAAAATGGGATTTTTGGATA-TTTTGGGG
1 T-AAAAATGGAATTTTTGGA-AGTTTAAGGG
* * *
44208 TTAAAAATGGGATTTTTGGAAATTTTAGGG
1 -TAAAAATGGAATTTTTGGAAGTTTAAGGG
* * *
44238 TTAAAAATGGGATTTTTGAAAGTTCT-GGGG
1 -TAAAAATGGAATTTTTGGAAGTT-TAAGGG
* * *
44268 TGAAAATGGAATTTTTGGAAGTTT-CGAG
1 TAAAAATGGAATTTTTGGAAGTTTAAGGG
* * **
44296 TCAAAAATGGGATTTTTGGAA-ATTCGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTAAGGG
44325 CTAAAAATGGAATTTTTGGATAGTTTA
1 -TAAAAATGGAATTTTTGGA-AGTTTA
44352 GGGACCTCCA
Statistics
Matches: 233, Mismatches: 41, Indels: 30
0.77 0.13 0.10
Matches are distributed among these distances:
28 25 0.11
29 110 0.47
30 93 0.40
31 5 0.02
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTAAGGG
Found at i:44091 original size:59 final size:57
Alignment explanation
Indices: 44022--44354 Score: 323
Period size: 58 Copynumber: 5.7 Consensus size: 57
44012 AATTTTGGTA
* * * * *
44022 AATTTTGGGGTTAAAAATGAAATTTTTAGAAGTTTAAGGGTAAAAGTGGAATTTTTGG
1 AATTTCGGGGTTAAAAATGGAATTTTTGGAAGTTT-AGGGTAAAAATGGGATTTTTGG
* * *
44080 AAGTTTCGGGGTCAAAAAT-GAGATTTTTGGAAGTTTTA-GGTTAAAATGGGATTTTTTGA
1 AA-TTTCGGGGTTAAAAATGGA-ATTTTTGGAAG-TTTAGGGTAAAAATGGGA-TTTTTGG
* * * *
44139 AATTT-GAGGCTAAAAATGGAATTTTTGGAGGTTTCGAGGTCAAAAATGGGATTTTTGG
1 AATTTCGGGGTTAAAAATGGAATTTTTGGAAGTTTAG-GGT-AAAAATGGGATTTTTGG
* * * *
44197 ATATTTTGGGGTTAAAAATGGGATTTTTGGAAATTTTAGGGTTAAAAATGGGATTTTTGA
1 A-ATTTCGGGGTTAAAAATGGAATTTTTGG-AAGTTTAGGG-TAAAAATGGGATTTTTGG
* * * *
44257 AAGTTCTGGGG-TGAAAATGGAATTTTTGGAAGTTTCGAGTCAAAAATGGGATTTTTGG
1 AATTTC-GGGGTTAAAAATGGAATTTTTGGAAGTTTAGGGT-AAAAATGGGATTTTTGG
* *
44315 AAATTCGGGGCTAAAAATGGAATTTTTGGATAGTTTAGGG
1 AATTTCGGGGTTAAAAATGGAATTTTTGGA-AGTTTAGGG
44355 ACCTCCAAGG
Statistics
Matches: 225, Mismatches: 34, Indels: 31
0.78 0.12 0.11
Matches are distributed among these distances:
56 3 0.01
57 24 0.11
58 74 0.33
59 72 0.32
60 46 0.20
61 6 0.03
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (57 bp):
AATTTCGGGGTTAAAAATGGAATTTTTGGAAGTTTAGGGTAAAAATGGGATTTTTGG
Found at i:44108 original size:30 final size:30
Alignment explanation
Indices: 44014--44350 Score: 255
Period size: 30 Copynumber: 11.4 Consensus size: 30
44004 TAATTGGTAA
* * * **
44014 TTTTGGTAAATTTTGGGGTTAAAAATGAAAT
1 TTTTGG-AAGTTTCGGGGTCAAAAATGGGAT
* ** * *
44045 TTTTAGAAGTTTAAGGGT-AAAAGTGGAAT
1 TTTTGGAAGTTTCGGGGTCAAAAATGGGAT
*
44074 TTTTGGAAGTTTCGGGGTCAAAAATGAGAT
1 TTTTGGAAGTTTCGGGGTCAAAAATGGGAT
** *
44104 TTTTGGAAGTTT-TAGGT-TAAAATGGGAT
1 TTTTGGAAGTTTCGGGGTCAAAAATGGGAT
* * * *
44132 TTTTTGAAATTT-GAGG-CTAAAAATGGAAT
1 TTTTGGAAGTTTCGGGGTC-AAAAATGGGAT
* *
44161 TTTTGGAGGTTTCGAGGTCAAAAATGGGAT
1 TTTTGGAAGTTTCGGGGTCAAAAATGGGAT
* *
44191 TTTTGGATA-TTTTGGGGTTAAAAATGGGAT
1 TTTTGGA-AGTTTCGGGGTCAAAAATGGGAT
* ** *
44221 TTTTGGAAATTTTAGGGTTAAAAATGGGAT
1 TTTTGGAAGTTTCGGGGTCAAAAATGGGAT
* * *
44251 TTTTGAAAG-TTCTGGGGT-GAAAATGGAAT
1 TTTTGGAAGTTTC-GGGGTCAAAAATGGGAT
*
44280 TTTTGGAAGTTTC-GAGTCAAAAATGGGAT
1 TTTTGGAAGTTTCGGGGTCAAAAATGGGAT
* *
44309 TTTTGGAA-ATTCGGGG-CTAAAAATGGAAT
1 TTTTGGAAGTTTCGGGGTC-AAAAATGGGAT
44338 TTTTGGATAGTTT
1 TTTTGGA-AGTTT
44351 AGGGACCTCC
Statistics
Matches: 248, Mismatches: 44, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
28 29 0.12
29 101 0.41
30 110 0.44
31 8 0.03
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (30 bp):
TTTTGGAAGTTTCGGGGTCAAAAATGGGAT
Found at i:45119 original size:26 final size:25
Alignment explanation
Indices: 45084--45156 Score: 103
Period size: 25 Copynumber: 2.9 Consensus size: 25
45074 TAAAAAAAAC
*
45084 ACTTCCCTTTTCCCCTTTTTTTTTAA
1 ACTTCTCTTTT-CCCTTTTTTTTTAA
*
45110 ACTTCTCTTTT-CCTTTTTCGTTTAA
1 ACTTCTCTTTTCCCTTTTT-TTTTAA
45135 ACTTCTCTTTTCCCTTTTTTTT
1 ACTTCTCTTTTCCCTTTTTTTT
45157 AAAAAACTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
24 7 0.17
25 18 0.43
26 17 0.40
ACGTcount: A:0.10, C:0.27, G:0.01, T:0.62
Consensus pattern (25 bp):
ACTTCTCTTTTCCCTTTTTTTTTAA
Found at i:45133 original size:25 final size:25
Alignment explanation
Indices: 45084--45159 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 25
45074 TAAAAAAAAC
* *
45084 ACTTCCCTTTTCCCCTTTTTTTTTAA
1 ACTTCTCTTTT-CCCTTTTTGTTTAA
45110 ACTTCTCTTTT-CCTTTTTCGTTTAA
1 ACTTCTCTTTTCCCTTTTT-GTTTAA
45135 ACTTCTCTTTTCCCTTTTT-TTTAA
1 ACTTCTCTTTTCCCTTTTTGTTTAA
45159 A
1 A
45160 AAACTTATCA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
24 13 0.28
25 16 0.35
26 17 0.37
ACGTcount: A:0.13, C:0.26, G:0.01, T:0.59
Consensus pattern (25 bp):
ACTTCTCTTTTCCCTTTTTGTTTAA
Found at i:46166 original size:17 final size:17
Alignment explanation
Indices: 46126--46183 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
46116 GGACATTCAA
46126 AATAAATTTTAAATTTCAG
1 AATAAA-TTTAAATTT-AG
*
46145 -CTAAATTTAAATTTAG
1 AATAAATTTAAATTTAG
* * *
46161 AATAAACTTAATTTTAA
1 AATAAATTTAAATTTAG
46178 AATAAA
1 AATAAA
46184 CAGCTACCCC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 2 0.06
17 27 0.82
18 4 0.12
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (17 bp):
AATAAATTTAAATTTAG
Found at i:47327 original size:203 final size:205
Alignment explanation
Indices: 46798--47555 Score: 1223
Period size: 205 Copynumber: 3.7 Consensus size: 205
46788 AGAAAGATGG
* * * * * *
46798 TCAGGAAGCTAACTGTTTTATTACTTCGACTTGCTTCTCAGTATCTCATCAGGAAGCTATGGTTC
1 TCAGGAAGTTAAC-CTTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGTGGTTC
* *
46863 GAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAATGTTTAATCAGGAAGAT
65 GAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAATATTTCATCAGGAAGAT
* * *
46928 TACTGCATCATTTGTTTCAATCCGCTACTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTC
130 GACTGCGTCATTTGTTTCAATCCGCTACTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTC
*
46993 TCAATATCTCA
195 TCAGTATCTCA
47004 TCAGGAAGTTAACCTTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGTGGTTCG
1 TCAGGAAGTTAACCTTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGTGGTTCG
*
47069 AAGATTTGCTCACATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAATATTTCATCAGGAAGATG
66 AAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAATATTTCATCAGGAAGATG
47134 ACTGCGTCATTTGTTTCAATCCGCTACTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCT
131 ACTGCGTCATTTGTTTCAATCCGCTACTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCT
47199 CAGTATCTCA
196 CAGTATCTCA
*
47209 TCAGGAA-TTAACCTTTTATTGCTTCGA-CTACTTCTCAGTATCTAATCAGGAAGCTGTGGTTCG
1 TCAGGAAGTTAACCTTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGTGGTTCG
* *
47272 AAGATTTTCTCACATCGAGCGTGGTTTTGATTTGGTCTTCTTCTCAATATTTCATCAGGAAGATG
66 AAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAATATTTCATCAGGAAGATG
*
47337 ACTGCGTCGTTTGTTTCAATCCGCTACTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCT
131 ACTGCGTCATTTGTTTCAATCCGCTACTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCT
47402 CAGTATCTCA
196 CAGTATCTCA
* * *
47412 TCAAGAAGTTAACCTTTTATTGCTTCGACCTACTTCTCAGTATCTTATCAGGAAGCTGGGGTTCG
1 TCAGGAAGTTAACCTTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGTGGTTCG
** * * * * * * *
47477 TGGATTTGTTCACATCAAGCGTAGGTTTGACTTGGTCTTCTTCTCAGTATCTCATCAGGTAGATG
66 AAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAATATTTCATCAGGAAGATG
*
47542 ACTGCGTCGTTTGT
131 ACTGCGTCATTTGT
47556 GGATAATCGC
Statistics
Matches: 518, Mismatches: 32, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
203 177 0.34
204 40 0.08
205 289 0.56
206 12 0.02
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (205 bp):
TCAGGAAGTTAACCTTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGTGGTTCG
AAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAATATTTCATCAGGAAGATG
ACTGCGTCATTTGTTTCAATCCGCTACTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCT
CAGTATCTCA
Found at i:48085 original size:27 final size:26
Alignment explanation
Indices: 48048--48099 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
48038 AAAATTCTAT
*
48048 TAAAAAGAGGATCAAAGGAAACAATA
1 TAAAAAGAGGATCAAAGAAAACAATA
48074 TAAACAAGAGGATCAAAGAAAACAAT
1 TAAA-AAGAGGATCAAAGAAAACAAT
48100 CATTAATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.62, C:0.10, G:0.17, T:0.12
Consensus pattern (26 bp):
TAAAAAGAGGATCAAAGAAAACAATA
Done.