Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold557
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: 108604
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.30
Warning! 11559 characters in sequence are not A, C, G, or T
Found at i:16564 original size:19 final size:19
Alignment explanation
Indices: 16540--16585 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
16530 TCTATTTTTT
* *
16540 TTTGCTGTCATTTGGTTTG
1 TTTGCTGTCATTCGGTTTC
*
16559 TTTGCTCTCATTCGGTTTC
1 TTTGCTGTCATTCGGTTTC
16578 TTTGCTGT
1 TTTGCTGT
16586 TTGTTGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.04, C:0.17, G:0.22, T:0.57
Consensus pattern (19 bp):
TTTGCTGTCATTCGGTTTC
Found at i:17364 original size:51 final size:51
Alignment explanation
Indices: 17254--17369 Score: 124
Period size: 51 Copynumber: 2.3 Consensus size: 51
17244 ATCCGCTCCA
* * * **
17254 CTTCAGCTTTAATTTATTCCACTGCAACGCCAAGGAAACAATATTTTCTAC
1 CTTCAGCTTTAATCTATTCCAATGCAACGCCAAGGAAACAAGATTCGCTAC
* * * * * * *
17305 CTTTAGCTTTAATCTATTCTAATGCAACGCTAAGGAGATAGGATTCGCTGC
1 CTTCAGCTTTAATCTATTCCAATGCAACGCCAAGGAAACAAGATTCGCTAC
17356 CTTCAGCTTTAATC
1 CTTCAGCTTTAATC
17370 CGCTCCACTT
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (51 bp):
CTTCAGCTTTAATCTATTCCAATGCAACGCCAAGGAAACAAGATTCGCTAC
Found at i:17434 original size:123 final size:123
Alignment explanation
Indices: 17215--17983 Score: 675
Period size: 123 Copynumber: 6.0 Consensus size: 123
17205 TTAACATCAG
*
17215 GGAGATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCCACTTCAGCTTTAATTTATTCCACTGCA
1 GGAGATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCA
* * ** * * *
17280 ACGCCAAGGAAACAATATTTTCTACCTTTAGCTTTAATCTATTCTAATGCAACGCTAA
66 ACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGCAACGCCAA
* * *
17338 GGAGATAGGATTCGCTGCCTTCAGCTTTAATCCGCTCCACTTCAGCTTTAATTTATTCCA-TAGA
1 GGAGATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTCCACT-GC
* * *
17402 AACGCCAGGGAAACAAGATTCGCTA-CTCTTAGCTTTAATCTGTTCTACTACCACACCAA
65 AACGCCAGGGAAACAAGATTCGCTACCT-TTAGCTTTAATCTGTTCTACTGCAACGCCAA
* * **
17461 GGAAATAAGATTCGCTGCCTTCAG-TCTTAATACCAGGGAGATAAGATTTGTTGCCTTCAGCTTT
1 GGAGATAAGATTCGCTGCCTTCAGCT-TTAAT-CC-----GCT-CCA--------CTTCAGCTTT
** * * *
17525 AATCTGCTCCACTGCAACGTCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTA
50 AATCTATTCCACTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTG
* **
17590 TAAATCCAA
115 CAACGCCAA
* * * * * * * *
17599 AGAGATAATATTCACTGCCTTTAGCTTTAATTCGCTCTACTTCAGCTTTAATCTATTCCATTGTA
1 GGAGATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCA
* ** *
17664 ATGCCAGGGAAACAAGATTCGCTAATTTTAGCTTTAATCTGTTCTACTGCAACGCCAG
66 ACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGCAACGCCAA
* * * ** * * * *
17722 GGAAATAAGATTCGCTGCGTTCAG-TCTTAACGTCACGGAGATAAGATTTGCTGCCTTTAGCTTT
1 GGAGATAAGATTCGCTGCCTTCAGCT-TTAA--TC-C---GCT-CCACTT-CAG-CTTTA-ATCT
** * *
17786 ATTTTGCTCCACTGCAACATCAGAGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTG
55 A---T--TCCACTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTG
**
17851 CAGGGCCAA
115 CAACGCCAA
* *
17860 AGAGATAAGATTCGCTGCCTTCAGCTTTAATCAGCTCCACTTCAGCTTTAATCTATTCCACTGCA
1 GGAGATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCA
* * *
17925 ACGCCAGGGAAACAAGATTCACTACCTTTAGCTTTAATCAGTTCCACTGCAACG-CAA
66 ACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGCAACGCCAA
17982 GG
1 GG
17984 GAAATAAGTT
Statistics
Matches: 513, Mismatches: 95, Indels: 77
0.75 0.14 0.11
Matches are distributed among these distances:
122 9 0.02
123 281 0.55
124 2 0.00
125 2 0.00
126 1 0.00
128 3 0.01
129 9 0.02
130 6 0.01
131 6 0.01
132 9 0.02
133 3 0.01
136 3 0.01
137 1 0.00
138 173 0.34
139 5 0.01
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (123 bp):
GGAGATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCA
ACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGCAACGCCAA
Found at i:17629 original size:138 final size:135
Alignment explanation
Indices: 17402--17972 Score: 476
Period size: 138 Copynumber: 4.4 Consensus size: 135
17392 ATTCCATAGA
* * *
17402 AACGCCAGGGAAACAAGATTCGCTA-CTCTTAGCTTTAATCTGTTCTACTACCACA-CCAAGGAA
1 AACGCCAGGGAAACAAGATTCGCTACCT-TTAGCTTTAATCTGTTCCACTA-CAAAGCCAAAGAA
*
17465 ATAAGATTCGCTGCCTTCAGTCTTAATACCAGGGAGATAAGATTTGTTGCCTTCAGCTTTAATCT
64 ATAAGATTCGCTGCCTTCAGTCTTAAT--CA-GGAGATAAGATTTGCTGCCTTCAGCTTTAATCT
17530 GCTCCACTGC
126 GCTCCACTGC
* * * *
17540 AACGTCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTATAAATCCAAAGAGAT
1 AACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTACAAAGCCAAAGAAAT
* * * ** * * **
17605 AATATTCACTGCCTTTAG-CTT--T----A-ATTCG--CT-CT-ACTTCAGCTTTAATCTATTCC
66 AAGATTCGCTGCCTTCAGTCTTAATCAGGAGATAAGATTTGCTGCCTTCAGCTTTAATCTGCTCC
* *
17658 ATTGT
131 ACTGC
* ** * * * **
17663 AATGCCAGGGAAACAAGATTCGCTAATTTTAGCTTTAATCTGTTCTACTGCAACGCCAGGGAAAT
1 AACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTACAAAGCCAAAGAAAT
* * * *
17728 AAGATTCGCTGCGTTCAGTCTTAACGTCACGGAGATAAGATTTGCTGCCTTTAGCTTTATTTTGC
66 AAGATTCGCTGCCTTCAGTCTTAA--TCA-GGAGATAAGATTTGCTGCCTTCAGCTTTAATCTGC
17793 TCCACTGC
128 TCCACTGC
** * * ** *
17801 AACATCAGAGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAGGGCCAAAGAGAT
1 AACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTACAAAGCCAAAGAAAT
* * **
17866 AAGATTCGCTGCCTTCAG-CTT--T----A-AT--CA---GCTCCACTTCAGCTTTAATCTATTC
66 AAGATTCGCTGCCTTCAGTCTTAATCAGGAGATAAGATTTGCTGC-CTTCAGCTTTAATCTGCTC
17918 CACTGC
130 CACTGC
* *
17924 AACGCCAGGGAAACAAGATTCACTACCTTTAGCTTTAATCAGTTCCACT
1 AACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACT
17973 GCAACGCAAG
Statistics
Matches: 345, Mismatches: 70, Indels: 51
0.74 0.15 0.11
Matches are distributed among these distances:
122 4 0.01
123 152 0.44
124 4 0.01
125 2 0.01
127 5 0.01
128 3 0.01
133 2 0.01
134 3 0.01
135 1 0.00
136 1 0.00
137 10 0.03
138 156 0.45
139 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (135 bp):
AACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTACAAAGCCAAAGAAAT
AAGATTCGCTGCCTTCAGTCTTAATCAGGAGATAAGATTTGCTGCCTTCAGCTTTAATCTGCTCC
ACTGC
Found at i:17728 original size:261 final size:261
Alignment explanation
Indices: 17254--17991 Score: 992
Period size: 261 Copynumber: 2.8 Consensus size: 261
17244 ATCCGCTCCA
** * * * **
17254 CTTCAGCTTTAATTTATTCCACTGCAACGCCAAGGAAACAATATTTTCTACCTTTAGCTTTAATC
1 CTTCAGCTTTAATTTGCTCCACTGCAACGTCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
* * * * * * * *
17319 TATTCTAATGCAACGCTAAGGAGATAGGATTCGCTGCCTTCAGCTTTAATCCGCTCCACTTCAGC
66 TGTTCCACTGCAAAGCCAAAGAGATAAGATTCGCTGCCTTCAGCTTTAATTCGCTCCACTTCAGC
* * *
17384 TTTAATTTATTCCATAGAAACGCCAGGGAAACAAGATTCGCTACTCTTAGCTTTAATCTGTTCTA
131 TTTAATCTATTCCATTGAAACGCCAGGGAAACAAGATTCGCTACTTTTAGCTTTAATCTGTTCTA
* * * * * * *
17449 CTACCACACCAAGGAAATAAGATTCGCTGCCTTCAGTCTTAATACCAGGGAGATAAGATTTGTTG
196 CTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGTCTTAACACCACGGAGATAAGATTTGCTG
17514 C
261 C
*
17515 CTTCAGCTTTAATCTGCTCCACTGCAACGTCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
1 CTTCAGCTTTAATTTGCTCCACTGCAACGTCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
** * * * * *
17580 TGTTCCACTATAAATCCAAAGAGATAATATTCACTGCCTTTAGCTTTAATTCGCTCTACTTCAGC
66 TGTTCCACTGCAAAGCCAAAGAGATAAGATTCGCTGCCTTCAGCTTTAATTCGCTCCACTTCAGC
* * *
17645 TTTAATCTATTCCATTGTAATGCCAGGGAAACAAGATTCGCTAATTTTAGCTTTAATCTGTTCTA
131 TTTAATCTATTCCATTGAAACGCCAGGGAAACAAGATTCGCTACTTTTAGCTTTAATCTGTTCTA
* **
17710 CTGCAACGCCAGGGAAATAAGATTCGCTGCGTTCAGTCTTAACGTCACGGAGATAAGATTTGCTG
196 CTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGTCTTAACACCACGGAGATAAGATTTGCTG
17775 C
261 C
* * * *
17776 CTTTAGCTTTATTTTGCTCCACTGCAACATCAGAGAAACAAGATTCGCTACCTTTAGCTTTAATC
1 CTTCAGCTTTAATTTGCTCCACTGCAACGTCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
**
17841 TGTTCCACTGCAGGGCCAAAGAGATAAGATTCGCTGCCTTCAGCTTTAA-TCAGCTCCACTTCAG
66 TGTTCCACTGCAAAGCCAAAGAGATAAGATTCGCTGCCTTCAGCTTTAATTC-GCTCCACTTCAG
* * * * * *
17905 CTTTAATCTATTCCACTGCAACGCCAGGGAAACAAGATTCACTACCTTTAGCTTTAATCAGTTCC
130 CTTTAATCTATTCCATTGAAACGCCAGGGAAACAAGATTCGCTACTTTTAGCTTTAATCTGTTCT
*
17970 ACTGCAACGCAAGGGAAATAAG
195 ACTGCAACGCCAGGGAAATAAG
17992 TTTATTGGAT
Statistics
Matches: 414, Mismatches: 62, Indels: 2
0.87 0.13 0.00
Matches are distributed among these distances:
260 2 0.00
261 412 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (261 bp):
CTTCAGCTTTAATTTGCTCCACTGCAACGTCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
TGTTCCACTGCAAAGCCAAAGAGATAAGATTCGCTGCCTTCAGCTTTAATTCGCTCCACTTCAGC
TTTAATCTATTCCATTGAAACGCCAGGGAAACAAGATTCGCTACTTTTAGCTTTAATCTGTTCTA
CTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGTCTTAACACCACGGAGATAAGATTTGCTG
C
Found at i:17870 original size:51 final size:51
Alignment explanation
Indices: 17759--17900 Score: 158
Period size: 51 Copynumber: 2.8 Consensus size: 51
17749 TAACGTCACG
* * * * *
17759 GAGATAAGATTTGCTGCCTTTAGCTTTATTTTGCTCCACTGCAACATCAGA
1 GAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCACTGCAACACCAAA
* * * * ***
17810 GAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAGGGCCAAA
1 GAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCACTGCAACACCAAA
* *
17861 GAGATAAGATTCGCTGCCTTCAGCTTTAATCAGCTCCACT
1 GAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCACT
17901 TCAGCTTTAA
Statistics
Matches: 73, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 73 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.31
Consensus pattern (51 bp):
GAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCACTGCAACACCAAA
Found at i:17958 original size:72 final size:72
Alignment explanation
Indices: 17831--17972 Score: 185
Period size: 72 Copynumber: 2.0 Consensus size: 72
17821 CGCTACCTTT
* ** * * * *
17831 AGCTTTAATCTGTTCCACTGCAGGGCCAAAGAGATAAGATTCGCTGCCTTCAGCTTTAATCAGCT
1 AGCTTTAATCTATTCCACTGCAACGCCAAAGAAACAAGATTCACTACCTTCAGCTTTAATCAGCT
17896 CCACTTC
66 CCACTTC
** * *
17903 AGCTTTAATCTATTCCACTGCAACGCCAGGGAAACAAGATTCACTACCTTTAGCTTTAATCAGTT
1 AGCTTTAATCTATTCCACTGCAACGCCAAAGAAACAAGATTCACTACCTTCAGCTTTAATCAGCT
17968 CCACT
66 CCACT
17973 GCAACGCAAG
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30
Consensus pattern (72 bp):
AGCTTTAATCTATTCCACTGCAACGCCAAAGAAACAAGATTCACTACCTTCAGCTTTAATCAGCT
CCACTTC
Found at i:18386 original size:24 final size:24
Alignment explanation
Indices: 18354--18411 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
18344 CGGATTGCCC
*
18354 CCACTGTAATCTTCAAGGTTCAAT
1 CCACTGTAATCTTCAAAGTTCAAT
*
18378 CCACTGTAATCTTTAAAGTTCAAT
1 CCACTGTAATCTTCAAAGTTCAAT
*
18402 CCATTGTAAT
1 CCACTGTAAT
18412 TTCGGGACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.36
Consensus pattern (24 bp):
CCACTGTAATCTTCAAAGTTCAAT
Found at i:21989 original size:3 final size:3
Alignment explanation
Indices: 21983--22017 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
21973 CTAATAATAA
21983 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
22018 ATAATAAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:25596 original size:361 final size:361
Alignment explanation
Indices: 24922--25647 Score: 1384
Period size: 361 Copynumber: 2.0 Consensus size: 361
24912 TGGAATCTTA
* *
24922 TTTC-ATATTGTTAAGAACAAAACTTTATTAATTAATACATTCTAAATGTTATATTAAAATGGAT
1 TTTCTATATTATTAAGAACAAAACTTTATTAATTAATACATTCTAAATGTTACATTAAAATGGAT
24986 AAATTTCCTTTTTAATGGAAAATTCTATGGTAATTTAAATGAATTTTCTTTGTGAATGCCCTTTG
66 AAATTTCCTTTTTAATGGAAAATTCTATGGTAATTTAAATGAATTTTCTTTGTGAATGCCCTTTG
*
25051 AGATTTGTTAATTGTGTGCGTTTGATTTTGGCTTTTAGATTTGCTGTCACTATAGAGAGGTAAGT
131 AGATTTGTTAATTGTGTGCGTTTGATTTTGGCTTTTAGATTTGCTGTCACTATAGAGAGGTAAAT
25116 ATGTACTGACGAATAACTACTATTACTAAAAGATTATACAGAGATAAACCTATAGCGATGACTTC
196 ATGTACTGACGAATAACTACTATTACTAAAAGATTATACAGAGATAAACCTATAGCGATGACTTC
25181 ATTTGTGAGGGTATCCAATTTAATCGTTGGTATAGGTTTTTCTGGCCTATAGAGATTTTTTTATG
261 ATTTGTGAGGGTATCCAATTTAATCGTTGGTATAGGTTTTTCTGGCCTATAGAGATTTTTTTATG
25246 ATTTTAGTGACTATTTTGCATCCGTCAATATATGAT
326 ATTTTAGTGACTATTTTGCATCCGTCAATATATGAT
*
25282 TTTCTATATTATTAAGAACAAAACTTTATTAATTAATACATTCTAAATGTTGCATTAAAATGGAT
1 TTTCTATATTATTAAGAACAAAACTTTATTAATTAATACATTCTAAATGTTACATTAAAATGGAT
25347 AAATTTCCTTTTTAATGGAAAATTCTATGGTAATTTAAAATGAA-TTTCTTTGTGAATGCCCTTT
66 AAATTTCCTTTTTAATGGAAAATTCTATGGTAATTT-AAATGAATTTTCTTTGTGAATGCCCTTT
*
25411 GAGATTTGTTAATTGTGTGCGTTTGATTTTGGCTTTTGGATTTGCTGTCACTATAGAGAGGTAAA
130 GAGATTTGTTAATTGTGTGCGTTTGATTTTGGCTTTTAGATTTGCTGTCACTATAGAGAGGTAAA
25476 TATGTACTGACGAATAACTACTATTACTAAAAGATTATACAGAGATAAACCTATAGCGATGACTT
195 TATGTACTGACGAATAACTACTATTACTAAAAGATTATACAGAGATAAACCTATAGCGATGACTT
25541 CATTTGTGAGGGTATCCAATTTAATCGTTGGTATAGGTTTTTCTGGCCTATAGAGATTTTTTTAT
260 CATTTGTGAGGGTATCCAATTTAATCGTTGGTATAGGTTTTTCTGGCCTATAGAGATTTTTTTAT
25606 GATTTTAGTGACTATTTTGCATCCGTCAATATATGAT
325 GATTTTAGTGACTATTTTGCATCCGTCAATATATGAT
25643 TTTCT
1 TTTCT
25648 NNNNNNNNNN
Statistics
Matches: 359, Mismatches: 5, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
360 4 0.01
361 348 0.97
362 7 0.02
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.42
Consensus pattern (361 bp):
TTTCTATATTATTAAGAACAAAACTTTATTAATTAATACATTCTAAATGTTACATTAAAATGGAT
AAATTTCCTTTTTAATGGAAAATTCTATGGTAATTTAAATGAATTTTCTTTGTGAATGCCCTTTG
AGATTTGTTAATTGTGTGCGTTTGATTTTGGCTTTTAGATTTGCTGTCACTATAGAGAGGTAAAT
ATGTACTGACGAATAACTACTATTACTAAAAGATTATACAGAGATAAACCTATAGCGATGACTTC
ATTTGTGAGGGTATCCAATTTAATCGTTGGTATAGGTTTTTCTGGCCTATAGAGATTTTTTTATG
ATTTTAGTGACTATTTTGCATCCGTCAATATATGAT
Found at i:28663 original size:3 final size:3
Alignment explanation
Indices: 28651--28874 Score: 439
Period size: 3 Copynumber: 74.7 Consensus size: 3
28641 CAACTAATAA
*
28651 TAC TAA TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
28699 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
28747 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
28795 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
28843 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
28875 ATAATAATAA
Statistics
Matches: 219, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
3 219 1.00
ACGTcount: A:0.34, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TAC
Found at i:28879 original size:3 final size:3
Alignment explanation
Indices: 28873--28916 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
28863 CTACTACTAC
28873 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
28917 GTAACAGTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:29773 original size:19 final size:19
Alignment explanation
Indices: 29749--29792 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
29739 TGTTATTTTT
**
29749 TTTGCTATCATTTGGTTTC
1 TTTGCTATCATTCAGTTTC
*
29768 TTTGCTCTCATTCAGTTTC
1 TTTGCTATCATTCAGTTTC
29787 TTTGCT
1 TTTGCT
29793 GTTTGTTGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.09, C:0.20, G:0.14, T:0.57
Consensus pattern (19 bp):
TTTGCTATCATTCAGTTTC
Found at i:30519 original size:51 final size:51
Alignment explanation
Indices: 30420--30557 Score: 168
Period size: 51 Copynumber: 2.7 Consensus size: 51
30410 AGTCTTCACG
**
30420 TCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTACTCCGCTGCAACA
1 TCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTACTCCAATGCAACA
* * * * * **
30471 TCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCTAATGCAATG
1 TCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTACTCCAATGCAACA
* * *
30522 CCAAGGAGATAGGATTCGCTGCCTTTAGCTTTAATC
1 TCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATC
30558 CGCTCCACTT
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 72 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (51 bp):
TCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTACTCCAATGCAACA
Found at i:30665 original size:123 final size:123
Alignment explanation
Indices: 30472--30950 Score: 489
Period size: 123 Copynumber: 3.8 Consensus size: 123
30462 GCTGCAACAT
* * * * * **
30472 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCTAATGCA-ATGCCAAGGAGATAGGA
1 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAGCT-CCAAAGAGATAACA
* *
30536 TTCGCTGCCTTTAGCTTTAATCCGCTCCACTTCAGCTTTAATTTATTCCATTGAAATGC
65 TTCGCTGCCTTTAGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTCCATTGCAATGC
* * * * *
30595 CAGGGAAACAAGATGCGCTA-CTCTTAGCTTTAATCTGTTCTACTGCCA-CTCCAAGGAAATAAG
1 CAGGGAAACAAGATTCGCTACCT-TTAGCTTTAATCTGTTCCACTG-CAGCTCCAAAGAGATAAC
* * ** **
30658 ATTCGCTGCCTTCAG-TCTTAATACCAGGGAGATAAGATTTGTTGCCTTCAGCTTTAATCTGCTC
64 ATTCGCTGCCTTTAGCT-TTAAT-CC-----GCT-CCA--------CTTCAGCTTTAATCTATTC
* * *
30722 CACTGCAACGT
113 CATTGCAATGC
*
30733 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGTAGCTCCAAAGAGATAACAT
1 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAGCTCCAAAGAGATAACAT
* * *
30798 TCGCTGCCTTTAGCTTTAATTCGCTCTACTTCATCTTTAATCTATTCCATTGCAATGC
66 TCGCTGCCTTTAGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTCCATTGCAATGC
* *
30856 CAGGGAAACAAGATTCGCTACCTTTAGCGTTAATCTGTTCCACTGTAGCTCCAAAGAGATAACAT
1 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAGCTCCAAAGAGATAACAT
*
30921 TCGCTGCCTTTAGCTTTAATCTGCTCCACT
66 TCGCTGCCTTTAGCTTTAATCCGCTCCACT
30951 GCAACATCAG
Statistics
Matches: 297, Mismatches: 38, Indels: 42
0.79 0.10 0.11
Matches are distributed among these distances:
122 3 0.01
123 184 0.62
124 5 0.02
129 2 0.01
130 1 0.00
131 1 0.00
132 2 0.01
137 2 0.01
138 94 0.32
139 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (123 bp):
CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAGCTCCAAAGAGATAACAT
TCGCTGCCTTTAGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTCCATTGCAATGC
Found at i:30763 original size:261 final size:261
Alignment explanation
Indices: 30293--30930 Score: 850
Period size: 261 Copynumber: 2.4 Consensus size: 261
30283 TTGGTGTTTC
* * * * **
30293 AATCCACTCCACTTCAGCTTTAATCTATTCCACTGCAATGCCAAGGAAACAATATTTACTACAT-
1 AATCCGCTCCACTTCAGCTTTAATCTATTCCATTGCAATGCCAGGGAAACAAGATTCGCTAC-TC
* * * * * **
30357 TTAGCTTTAATTTGTTCCACTGCAACGCCAGGGAAATAAGATTTGCTGCCTTCAGTCTTCACGTC
65 TTAGCTTTAATCTGTTCCACTGCAACTCCAAGGAAATAAGATTCGCTGCCTTCAGTCTTAACACC
* *
30422 AGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTACTCCGCTGCAACATCAGGGAAACAAGATT
130 AGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTACTCCACTGCAACATCAGGGAAACAAGATT
* * **
30487 CGCTACCTTTAGCTTTAATCTATTCTAATGCA-ATGCCAAGGAGATAGGATTCGCTGCCTTTAGC
195 CGCTACCTTTAGCTTTAATCTATTCCAATGCAGAT-CCAAAGAGATAACATTCGCTGCCTTTAGC
30551 TTT
259 TTT
* * *
30554 AATCCGCTCCACTTCAGCTTTAATTTATTCCATTGAAATGCCAGGGAAACAAGATGCGCTACTCT
1 AATCCGCTCCACTTCAGCTTTAATCTATTCCATTGCAATGCCAGGGAAACAAGATTCGCTACTCT
* * *
30619 TAGCTTTAATCTGTTCTACTGCCACTCCAAGGAAATAAGATTCGCTGCCTTCAGTCTTAATACCA
66 TAGCTTTAATCTGTTCCACTGCAACTCCAAGGAAATAAGATTCGCTGCCTTCAGTCTTAACACCA
* * * *
30684 GGGAGATAAGATTTGTTGCCTTCAGCTTTAATCTGCTCCACTGCAACGTCAGGGAAACAAGATTC
131 GGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTACTCCACTGCAACATCAGGGAAACAAGATTC
* * * *
30749 GCTACCTTTAGCTTTAATCTGTTCCACTGTAGCTCCAAAGAGATAACATTCGCTGCCTTTAGCTT
196 GCTACCTTTAGCTTTAATCTATTCCAATGCAGATCCAAAGAGATAACATTCGCTGCCTTTAGCTT
30814 T
261 T
* * *
30815 AATTCGCTCTACTTCATCTTTAATCTATTCCATTGCAATGCCAGGGAAACAAGATTCGCTAC-CT
1 AATCCGCTCCACTTCAGCTTTAATCTATTCCATTGCAATGCCAGGGAAACAAGATTCGCTACTC-
* * * * * *
30879 TTAGCGTTAATCTGTTCCACTGTAGCTCCAAAGAGATAACATTCGCTGCCTT
65 TTAGCTTTAATCTGTTCCACTGCAACTCCAAGGAAATAAGATTCGCTGCCTT
30931 TAGCTTTAAT
Statistics
Matches: 327, Mismatches: 47, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
260 2 0.01
261 324 0.99
262 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (261 bp):
AATCCGCTCCACTTCAGCTTTAATCTATTCCATTGCAATGCCAGGGAAACAAGATTCGCTACTCT
TAGCTTTAATCTGTTCCACTGCAACTCCAAGGAAATAAGATTCGCTGCCTTCAGTCTTAACACCA
GGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTACTCCACTGCAACATCAGGGAAACAAGATTC
GCTACCTTTAGCTTTAATCTATTCCAATGCAGATCCAAAGAGATAACATTCGCTGCCTTTAGCTT
T
Found at i:30897 original size:51 final size:50
Alignment explanation
Indices: 30832--31004 Score: 186
Period size: 51 Copynumber: 3.4 Consensus size: 50
30822 TCTACTTCAT
* *
30832 CTTTAATCTATTCCATTGCAATGCCAGGGAAACAAGATTCGCTACCTTTAG
1 CTTTAATCTGTTCCACTGCAAT-CCAGGGAAACAAGATTCGCTACCTTTAG
* * * ** * * * *
30883 CGTTAATCTGTTCCACTGTAGCTCCAAAGAGATAACATTCGCTGCCTTTAG
1 CTTTAATCTGTTCCACTGCA-ATCCAGGGAAACAAGATTCGCTACCTTTAG
*
30934 CTTTAATCTGCTCCACTGCAA-CATCAGGGAAACAAGATTCGCTACCTTTAG
1 CTTTAATCTGTTCCACTGCAATC--CAGGGAAACAAGATTCGCTACCTTTAG
*
30985 CTTTAATCAGTTCCACTGCA
1 CTTTAATCTGTTCCACTGCA
31005 GGGCCAAAGA
Statistics
Matches: 96, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
49 1 0.01
51 94 0.98
52 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (50 bp):
CTTTAATCTGTTCCACTGCAATCCAGGGAAACAAGATTCGCTACCTTTAG
Found at i:31012 original size:102 final size:102
Alignment explanation
Indices: 30856--31052 Score: 313
Period size: 102 Copynumber: 1.9 Consensus size: 102
30846 ATTGCAATGC
* * *
30856 CAGGGAAACAAGATTCGCTACCTTTAGCGTTAATCTGTTCCACTGTAGCTCCAAAGAGATAACAT
1 CAGGGAAACAAGATTCGCTACCTTTAGCGTTAATCAGTTCCACTGCAGCGCCAAAGAGATAACAT
* *
30921 TCGCTGCCTTTAGCTTTAATCTGCTCCACTGCAACAT
66 TCGCTGCCTTCACCTTTAATCTGCTCCACTGCAACAT
* * *
30958 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCAGTTCCACTGCAGGGCCAAAGAGATAAGAT
1 CAGGGAAACAAGATTCGCTACCTTTAGCGTTAATCAGTTCCACTGCAGCGCCAAAGAGATAACAT
*
31023 TCGTTGCCTTCACCTTTAATCTGCTCCACT
66 TCGCTGCCTTCACCTTTAATCTGCTCCACT
31053 TCAGCTTTAA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 86 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (102 bp):
CAGGGAAACAAGATTCGCTACCTTTAGCGTTAATCAGTTCCACTGCAGCGCCAAAGAGATAACAT
TCGCTGCCTTCACCTTTAATCTGCTCCACTGCAACAT
Found at i:31022 original size:51 final size:51
Alignment explanation
Indices: 30865--31057 Score: 197
Period size: 51 Copynumber: 3.8 Consensus size: 51
30855 CCAGGGAAAC
* * * *
30865 AAGATTCGCTACCTTTAGCGTTAATCTGTTCCACTGTAGCTCCAAAGAGAT
1 AAGATTCGCTACCTTTAGCTTTAATCTGCTCCACTGCAGCACCAAAGAGAT
* * * * ** * *
30916 AACATTCGCTGCCTTTAGCTTTAATCTGCTCCACTGCAACATCAGGGAAAC
1 AAGATTCGCTACCTTTAGCTTTAATCTGCTCCACTGCAGCACCAAAGAGAT
* * **
30967 AAGATTCGCTACCTTTAGCTTTAATCAGTTCCACTGCAGGGCCAAAGAGAT
1 AAGATTCGCTACCTTTAGCTTTAATCTGCTCCACTGCAGCACCAAAGAGAT
* * * * *
31018 AAGATTCGTTGCCTTCACCTTTAATCTGCTCCACTTCAGC
1 AAGATTCGCTACCTTTAGCTTTAATCTGCTCCACTGCAGC
31058 TTTAATCTAT
Statistics
Matches: 110, Mismatches: 32, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
51 110 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (51 bp):
AAGATTCGCTACCTTTAGCTTTAATCTGCTCCACTGCAGCACCAAAGAGAT
Found at i:31071 original size:21 final size:21
Alignment explanation
Indices: 31030--31073 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
31020 GATTCGTTGC
*
31030 CTTCACCTTTAATCTGCTCCA
1 CTTCACCTTTAATCTACTCCA
* *
31051 CTTCAGCTTTAATCTATTCCA
1 CTTCACCTTTAATCTACTCCA
31072 CT
1 CT
31074 GCAACGCCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.34, G:0.05, T:0.41
Consensus pattern (21 bp):
CTTCACCTTTAATCTACTCCA
Found at i:31090 original size:225 final size:225
Alignment explanation
Indices: 30686--31125 Score: 666
Period size: 225 Copynumber: 2.0 Consensus size: 225
30676 TAATACCAGG
* * * *
30686 GAGATAAGATTTGTTGCCTTCAGCTTTAATCTGCTCCACTGCAACGTCAGGGAAACAAGATTCGC
1 GAGATAACATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACATCAGGGAAACAAGATTCGC
* * * * *
30751 TACCTTTAGCTTTAATCTGTTCCACTGTAGCTCCAAAGAGATAACATTCGCTGCCTTTAGCTTTA
66 TACCTTTAGCTTTAATCAGTTCCACTGCAGCGCCAAAGAGATAACATTCGCTGCCTTCACCTTTA
* * * * * *
30816 ATTCGCTCTACTTCATCTTTAATCTATTCCATTGCAATGCCAGGGAAACAAGATTCGCTACCTTT
131 ATTCGCTCCACTTCAGCTTTAATCTATTCCACTGCAACGCCACGGAAACAAGATTCACTACCTTT
* *
30881 AGCGTTAATCTGTTCCACTGTAGCTCCAAA
196 AGAGTTAATCAGTTCCACTGTAGCTCCAAA
*
30911 GAGATAACATTCGCTGCCTTTAGCTTTAATCTGCTCCACTGCAACATCAGGGAAACAAGATTCGC
1 GAGATAACATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACATCAGGGAAACAAGATTCGC
* * *
30976 TACCTTTAGCTTTAATCAGTTCCACTGCAGGGCCAAAGAGATAAGATTCGTTGCCTTCACCTTTA
66 TACCTTTAGCTTTAATCAGTTCCACTGCAGCGCCAAAGAGATAACATTCGCTGCCTTCACCTTTA
31041 A-TCTGCTCCACTTCAGCTTTAATCTATTCCACTGCAACGCCACGGAAACAAGATTCACTACCTT
131 ATTC-GCTCCACTTCAGCTTTAATCTATTCCACTGCAACGCCACGGAAACAAGATTCACTACCTT
*
31105 TAGATTTAATCAGTTCCACTG
195 TAGAGTTAATCAGTTCCACTG
31126 CAACGTAAGG
Statistics
Matches: 192, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
224 2 0.01
225 190 0.99
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (225 bp):
GAGATAACATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACATCAGGGAAACAAGATTCGC
TACCTTTAGCTTTAATCAGTTCCACTGCAGCGCCAAAGAGATAACATTCGCTGCCTTCACCTTTA
ATTCGCTCCACTTCAGCTTTAATCTATTCCACTGCAACGCCACGGAAACAAGATTCACTACCTTT
AGAGTTAATCAGTTCCACTGTAGCTCCAAA
Found at i:39552 original size:18 final size:18
Alignment explanation
Indices: 39529--39570 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
39519 GATCTGATTC
39529 TAACTCATAATTCACGCT
1 TAACTCATAATTCACGCT
39547 TAACTCATAATTCACGCT
1 TAACTCATAATTCACGCT
39565 TAACTC
1 TAACTC
39571 TTGCCCTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (18 bp):
TAACTCATAATTCACGCT
Found at i:45128 original size:17 final size:17
Alignment explanation
Indices: 45106--45158 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
45096 TATTCTATTA
45106 ATTTATTAAGATTTAAT
1 ATTTATTAAGATTTAAT
*
45123 ATTTATTAAGA-TAAAT
1 ATTTATTAAGATTTAAT
*
45139 ATTAGATTAA-ATTTAAT
1 ATT-TATTAAGATTTAAT
45156 ATT
1 ATT
45159 AAGGTGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 8 0.26
17 23 0.74
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (17 bp):
ATTTATTAAGATTTAAT
Found at i:60468 original size:40 final size:40
Alignment explanation
Indices: 60406--60498 Score: 141
Period size: 40 Copynumber: 2.3 Consensus size: 40
60396 AGGTTCTGTT
***
60406 TCTAGCAGGCTTATTTTTAGTGAAATTTTCAGACTTAATG
1 TCTAGCAGGCTTATTGCCAGTGAAATTTTCAGACTTAATG
*
60446 TCTTGCAGGCTTATTGCCAGTGAAATTTTCAGACTTAATG
1 TCTAGCAGGCTTATTGCCAGTGAAATTTTCAGACTTAATG
*
60486 TGTAGCAGGCTTA
1 TCTAGCAGGCTTA
60499 ATGTCGGTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (40 bp):
TCTAGCAGGCTTATTGCCAGTGAAATTTTCAGACTTAATG
Found at i:71260 original size:266 final size:266
Alignment explanation
Indices: 70786--71317 Score: 881
Period size: 266 Copynumber: 2.0 Consensus size: 266
70776 TTTTAGAAAT
**
70786 CCTTAACTCAAGATAACAAAATATCATATCTGGTGAGTTAGGACACAACATTTTGAAATCCTGAG
1 CCTTAACTCAAGATAACAAAATATCATATCAAGTGAGTTAGGACACAACATTTTGAAATCCTGAG
70851 AATAAACTTTTATTTAAAATCTATACGATTTTATTGAAAAAGGGTACTCGATTATCTAAATTTAA
66 AATAAACTTTTATTTAAAATCTATACGATTTTATTGAAAAAGGGTACTCGATTATCTAAATTTAA
* *
70916 CGAGAAAAATTGAAGCCCAGTAAGTTAGGGCAAAATCTTCTCGAGAATCTTTGGATACCAAGTGT
131 CGAGAAAAAATGAAGCACAGTAAGTTAGGGCAAAATCTTCTCGAGAATCTTTGGATACCAAGTGT
* *
70981 TTTGAAAACTTATGGATAAAATGATTTTAGTGTTTTAATCAAATGCGATCTTTTAAACAAACGTA
196 TTTGAAAACTTATGGATAAAATGAATTTAGTGTTTTAATCAAATGCAATCTTTTAAACAAACGTA
71046 GTGCAA
261 GTGCAA
* * *
71052 CCTTAACTCAAGGTAACAAAATGTCATATCAAGTGATTTA-GATCACAACATTTTGAAAT-CTCG
1 CCTTAACTCAAGATAACAAAATATCATATCAAGTGAGTTAGGA-CACAACATTTTGAAATCCT-G
* * * *
71115 AGAGTAAATTTTTATTTAAAATCTGTATGATTTTATTGAAAAAGGGTACTC-AGTTATCTAAATT
64 AGAATAAACTTTTATTTAAAATCTATACGATTTTATTGAAAAAGGGTACTCGA-TTATCTAAATT
**
71179 TAACGAGAAAAAATGAAGCACAGTAAGTTAGGGCACTATCTTCTCGAGAATCTTTGGATACCAAG
128 TAACGAGAAAAAATGAAGCACAGTAAGTTAGGGCAAAATCTTCTCGAGAATCTTTGGATACCAAG
71244 TGTTTTGAAAACTTATGGATAAAATGAATTTAGTGTTTTAATCAAATGCAATCTTTTAAACAAAC
193 TGTTTTGAAAACTTATGGATAAAATGAATTTAGTGTTTTAATCAAATGCAATCTTTTAAACAAAC
71309 GTAGTGCAA
258 GTAGTGCAA
71318 TTGAATGATG
Statistics
Matches: 248, Mismatches: 15, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
265 5 0.02
266 243 0.98
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (266 bp):
CCTTAACTCAAGATAACAAAATATCATATCAAGTGAGTTAGGACACAACATTTTGAAATCCTGAG
AATAAACTTTTATTTAAAATCTATACGATTTTATTGAAAAAGGGTACTCGATTATCTAAATTTAA
CGAGAAAAAATGAAGCACAGTAAGTTAGGGCAAAATCTTCTCGAGAATCTTTGGATACCAAGTGT
TTTGAAAACTTATGGATAAAATGAATTTAGTGTTTTAATCAAATGCAATCTTTTAAACAAACGTA
GTGCAA
Found at i:73787 original size:51 final size:51
Alignment explanation
Indices: 73691--73790 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 51
73681 GACAACATTC
* *
73691 GCTTTAATCTATTCCACTGCAACGCCAGAGAAACAATATTCGCTACCTTTA
1 GCTTTAATCTATTCCACTGCAACACCAGAGAAACAAGATTCGCTACCTTTA
* * *
73742 GCTTTAATCTATTCCACTGCAACACCAGGGAAATAAGATTTGCTACCTT
1 GCTTTAATCTATTCCACTGCAACACCAGAGAAACAAGATTCGCTACCTT
73791 CAGTCTTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (51 bp):
GCTTTAATCTATTCCACTGCAACACCAGAGAAACAAGATTCGCTACCTTTA
Found at i:74043 original size:123 final size:123
Alignment explanation
Indices: 73824--74564 Score: 587
Period size: 123 Copynumber: 5.8 Consensus size: 123
73814 GATTCGTTGC
* * *
73824 CTTCAGCTTTAATCTACTCCGCTGCAACATTAGGGAAACAAGATTTGCTACCTTTAGCTTTAATC
1 CTTCAGCTTTAATCTATTCCACTGCAACACTAGGGAAACAAGATTTGCTACCTTTAGCTTTAATC
* * ** * *
73889 TATTCTAATATAACGCCAAGGAGATAGGATTCGCTGCCTTCAGCTTTAATCCACTCCA
66 TATTCCACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCCACTCCA
* * *
73947 CTTCAGCTTTACTCTATTCCACTGCAACACTAGAGAAACAAGATTCGCTA-CTCTTAGCTTTAAT
1 CTTCAGCTTTAATCTATTCCACTGCAACACTAGGGAAACAAGATTTGCTACCT-TTAGCTTTAAT
* * ** *
74011 CTGTTCTACTGCAACGCCAAGGAAATAAGATTCATTGCCTTCAG-TCTTAACGCCAGGGAGATAA
65 CTATTCCACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCT-TTAA-TCC----------
*
74075 GATTTGCTGCA
118 -A----CTCCA
* **
74086 -TTCCGCTTTAATCTGCTCCACTGCAACA-TCAGGGAAACAAGATTTGCTACCTTTAGCTTTAAT
1 CTTCAGCTTTAATCTATTCCACTGCAACACT-AGGGAAACAAGATTTGCTACCTTTAGCTTTAAT
* * * ***
74149 CTATTCCACTGCAACGCCAAAGAGATAAGATTCGCTGCCTTCAGTTTTAATTTGCTCCA
65 CTATTCCACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCCACTCCA
* * * * * *
74208 CTTCAGCTTTAATCTATTCCACTACAACGCCAGGGAAACAAGATTCGGTA-ATCTTAGCTTTAAT
1 CTTCAGCTTTAATCTATTCCACTGCAACACTAGGGAAACAAGATTTGCTACCT-TTAGCTTTAAT
* * * * * **
74272 CTGTTCTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCCTTAATGCCAAGGAGATAAG
65 CTATTCCACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAAT-CC----A-CT-CC
74337 A
123 A
* * ** * * * *
74338 TTTGTTGCCTTTAGCTTGAATCTGCTCCACTACAAC-GTCAGGGAAATAAGATTTGCTACATTTA
1 --------CTTCAGCTTTAATCTATTCCACTGCAACACT-AGGGAAACAAGATTTGCTACCTTTA
* * * * *
74402 TCTTTAATCTGTTCCACTGCAACACCAAAGAAATAAGATTCGCTGCCTTCAGCTTTAATCCGCTC
57 GCTTTAATCTATTCCACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCCACTC
74467 CA
122 CA
* * *
74469 CTTCAGCTCTGATCTATTCCACTGCAACGCTAGGGAAACAAGATTTGCTACCTTTAGCTTTAATC
1 CTTCAGCTTTAATCTATTCCACTGCAACACTAGGGAAACAAGATTTGCTACCTTTAGCTTTAATC
*
74534 AATTCCACTGCAACG-CAAGGGAAATAAGATT
66 TATTCCACTGCAACGCCAA-GGAAATAAGATT
74565 ATTAGCTTTA
Statistics
Matches: 486, Mismatches: 89, Indels: 86
0.74 0.13 0.13
Matches are distributed among these distances:
122 11 0.02
123 265 0.55
124 3 0.01
129 1 0.00
130 1 0.00
131 1 0.00
132 1 0.00
135 1 0.00
137 3 0.01
138 190 0.39
139 9 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (123 bp):
CTTCAGCTTTAATCTATTCCACTGCAACACTAGGGAAACAAGATTTGCTACCTTTAGCTTTAATC
TATTCCACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCCACTCCA
Found at i:74167 original size:261 final size:261
Alignment explanation
Indices: 73691--74564 Score: 1178
Period size: 261 Copynumber: 3.3 Consensus size: 261
73681 GACAACATTC
*
73691 GCTTTAATCTATTCCACTGCAACGCCAGAGAAACAATATTCGCTACCTTTAGCTTTAATCTATTC
1 GCTTTAATCTATTCCACTGCAACGCCAGAGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTC
* * * * * * * *
73756 CACTGCAACACCAGGGAAATAAGATTTGCTACCTTCAGTCTTAATGTCAGGGAAACAAGATTCGT
66 CACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGTCTTAATGCCAGGGAGATAAGATTTGT
* * *
73821 TGCCTTCAGCTTTAATCTACTCCGCTGCAACATTAGGGAAACAAGATTTGCTACCTTTAGCTTTA
131 TGCCTTCAGCTTTAATCTGCTCCACTGCAACATCAGGGAAACAAGATTTGCTACCTTTAGCTTTA
* * ** * * *
73886 ATCTATTCTAATATAACGCCAAGGAGATAGGATTCGCTGCCTTCAGCTTTAATCCACTCCACTTC
196 ATCTATTCCACTGCAACGCCAAAGAGATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCCACTTC
73951 A
261 A
* * * *
73952 GCTTTACTCTATTCCACTGCAACACTAGAGAAACAAGATTCGCTA-CTCTTAGCTTTAATCTGTT
1 GCTTTAATCTATTCCACTGCAACGCCAGAGAAACAAGATTCGCTACCT-TTAGCTTTAATCTATT
* ** *
74016 CTACTGCAACGCCAAGGAAATAAGATTCATTGCCTTCAGTCTTAACGCCAGGGAGATAAGATTTG
65 CCACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGTCTTAATGCCAGGGAGATAAGATTTG
* * *
74081 CTGCATTCCGCTTTAATCTGCTCCACTGCAACATCAGGGAAACAAGATTTGCTACCTTTAGCTTT
130 TTGCCTTCAGCTTTAATCTGCTCCACTGCAACATCAGGGAAACAAGATTTGCTACCTTTAGCTTT
* **
74146 AATCTATTCCACTGCAACGCCAAAGAGATAAGATTCGCTGCCTTCAGTTTTAATTTGCTCCACTT
195 AATCTATTCCACTGCAACGCCAAAGAGATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCCACTT
74211 CA
260 CA
* * * * *
74213 GCTTTAATCTATTCCACTACAACGCCAGGGAAACAAGATTCGGTA-ATCTTAGCTTTAATCTGTT
1 GCTTTAATCTATTCCACTGCAACGCCAGAGAAACAAGATTCGCTACCT-TTAGCTTTAATCTATT
* * * *
74277 CTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCCTTAATGCCAAGGAGATAAGATTTG
65 CCACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGTCTTAATGCCAGGGAGATAAGATTTG
* * * * * * *
74342 TTGCCTTTAGCTTGAATCTGCTCCACTACAACGTCAGGGAAATAAGATTTGCTACATTTATCTTT
130 TTGCCTTCAGCTTTAATCTGCTCCACTGCAACATCAGGGAAACAAGATTTGCTACCTTTAGCTTT
* * *
74407 AATCTGTTCCACTGCAACACCAAAGAAATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCCACTT
195 AATCTATTCCACTGCAACGCCAAAGAGATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCCACTT
74472 CA
260 CA
* * * * * *
74474 GCTCTGATCTATTCCACTGCAACGCTAGGGAAACAAGATTTGCTACCTTTAGCTTTAATCAATTC
1 GCTTTAATCTATTCCACTGCAACGCCAGAGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTC
74539 CACTGCAACG-CAAGGGAAATAAGATT
66 CACTGCAACGCCAA-GGAAATAAGATT
74565 ATTAGCTTTA
Statistics
Matches: 537, Mismatches: 73, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
260 4 0.01
261 532 0.99
262 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (261 bp):
GCTTTAATCTATTCCACTGCAACGCCAGAGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTC
CACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGTCTTAATGCCAGGGAGATAAGATTTGT
TGCCTTCAGCTTTAATCTGCTCCACTGCAACATCAGGGAAACAAGATTTGCTACCTTTAGCTTTA
ATCTATTCCACTGCAACGCCAAAGAGATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCCACTTC
A
Found at i:74179 original size:51 final size:51
Alignment explanation
Indices: 74059--74209 Score: 158
Period size: 51 Copynumber: 3.0 Consensus size: 51
74049 CTTCAGTCTT
* * *
74059 AACGCCAGGGAGATAAGATTTGCTGCATTCCGCTTTAATCTGCTCCACTGC
1 AACGCCAGGGAGATAAGATTTGCTGCCTTCAGCTTTAATCTACTCCACTGC
** * * * * *
74110 AACATCAGGGAAACAAGATTTGCTACCTTTAGCTTTAATCTATTCCACTGC
1 AACGCCAGGGAGATAAGATTTGCTGCCTTCAGCTTTAATCTACTCCACTGC
** * * * *
74161 AACGCCAAAGAGATAAGATTCGCTGCCTTCAGTTTTAATTTGCTCCACT
1 AACGCCAGGGAGATAAGATTTGCTGCCTTCAGCTTTAATCTACTCCACT
74210 TCAGCTTTAA
Statistics
Matches: 77, Mismatches: 23, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
51 77 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (51 bp):
AACGCCAGGGAGATAAGATTTGCTGCCTTCAGCTTTAATCTACTCCACTGC
Found at i:74270 original size:72 final size:71
Alignment explanation
Indices: 74127--74271 Score: 166
Period size: 72 Copynumber: 2.0 Consensus size: 71
74117 GGGAAACAAG
* * * * *
74127 ATTTGCTACCTTTAGCTTTAATCTATTCCACTGCAACGCCAAAGAGATAAGATTCGCTGCCTTCA
1 ATTTGCTACCTTCAGCTTTAATCTATTCCACTACAACGCCAAAGAAACAAGATTCGCTACCTTCA
*
74192 GTTTTA
66 GCTTTA
* ** * *
74198 ATTTGCTCCACTTCAGCTTTAATCTATTCCACTACAACGCCAGGGAAACAAGATTCGGTAATCTT
1 ATTTGCTAC-CTTCAGCTTTAATCTATTCCACTACAACGCCAAAGAAACAAGATTCGCT-ACCTT
74263 -AGCTTTA
64 CAGCTTTA
74270 AT
1 AT
74272 CTGTTCTACT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
71 8 0.13
72 50 0.82
73 3 0.05
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (71 bp):
ATTTGCTACCTTCAGCTTTAATCTATTCCACTACAACGCCAAAGAAACAAGATTCGCTACCTTCA
GCTTTA
Found at i:74322 original size:51 final size:52
Alignment explanation
Indices: 74208--74322 Score: 144
Period size: 51 Copynumber: 2.2 Consensus size: 52
74198 ATTTGCTCCA
* *
74208 CTTCAGCTTTAATCTATTCCACTACAACGCCAGGGAAACAAGATTCGGTAAT
1 CTTCAGCTTTAATCTATTCCACTACAACGCCAGGGAAACAAGATTCGCTAAC
* * * * *
74260 CTT-AGCTTTAATCTGTTCTACTGCAACGCCAGGGAAATAAGATTCGCT-GC
1 CTTCAGCTTTAATCTATTCCACTACAACGCCAGGGAAACAAGATTCGCTAAC
*
74310 CTTCAGCCTTAAT
1 CTTCAGCTTTAAT
74323 GCCAAGGAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
50 3 0.06
51 48 0.89
52 3 0.06
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (52 bp):
CTTCAGCTTTAATCTATTCCACTACAACGCCAGGGAAACAAGATTCGCTAAC
Found at i:74411 original size:51 final size:51
Alignment explanation
Indices: 74332--74470 Score: 152
Period size: 51 Copynumber: 2.7 Consensus size: 51
74322 TGCCAAGGAG
* * ** **
74332 ATAAGATTTGTTGCCTTTAGCTTGAATCTGCTCCACTACAACGTCAGGGAA
1 ATAAGATTTGCTGCCTTTAGCTTTAATCTGCTCCACTACAACACCAAAGAA
* * * * *
74383 ATAAGATTTGCTACATTTATCTTTAATCTGTTCCACTGCAACACCAAAGAA
1 ATAAGATTTGCTGCCTTTAGCTTTAATCTGCTCCACTACAACACCAAAGAA
* * *
74434 ATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCCACT
1 ATAAGATTTGCTGCCTTTAGCTTTAATCTGCTCCACT
74471 TCAGCTCTGA
Statistics
Matches: 70, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 70 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.32
Consensus pattern (51 bp):
ATAAGATTTGCTGCCTTTAGCTTTAATCTGCTCCACTACAACACCAAAGAA
Found at i:74541 original size:72 final size:72
Alignment explanation
Indices: 74408--74542 Score: 162
Period size: 72 Copynumber: 1.9 Consensus size: 72
74398 TTTATCTTTA
* * * **
74408 ATCTGTTCCACTGCAACACCAAAGAAATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCCACTTC
1 ATCTATTCCACTGCAACACCAAAGAAACAAGATTCGCTACCTTCAGCTTTAATCAACTCCACTTC
74473 AGCTCTG
66 AGCTCTG
* * ** * * *
74480 ATCTATTCCACTGCAACGCTAGGGAAACAAGATTTGCTACCTTTAGCTTTAATCAATTCCACT
1 ATCTATTCCACTGCAACACCAAAGAAACAAGATTCGCTACCTTCAGCTTTAATCAACTCCACT
74543 GCAACGCAAG
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
72 51 1.00
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (72 bp):
ATCTATTCCACTGCAACACCAAAGAAACAAGATTCGCTACCTTCAGCTTTAATCAACTCCACTTC
AGCTCTG
Found at i:74771 original size:24 final size:24
Alignment explanation
Indices: 74739--74787 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
74729 GATTGCCCTT
*
74739 ACTGTAATCTTCAAGGTTCAATCC
1 ACTGTAATCTTCAAAGTTCAATCC
74763 ACTGTAATCTTCAAAGTTCAATCC
1 ACTGTAATCTTCAAAGTTCAATCC
74787 A
1 A
74788 TTGTCATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (24 bp):
ACTGTAATCTTCAAAGTTCAATCC
Found at i:75818 original size:48 final size:48
Alignment explanation
Indices: 75765--75856 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
75755 CATTTTTATA
* *
75765 TTTTTTATT-ACTCAAAG-AGCCCTTTGTGGGTTTTCACCTTGGTCTGG
1 TTTTTTTTTAACT-AAAGCAGCCCTTTGTGGGTTTTAACCTTGGTCTGG
* *
75812 TTTTTTTTTAACTTAAGCAGCCCTTTGTGGGTTTTAACTTTGGTC
1 TTTTTTTTTAACTAAAGCAGCCCTTTGTGGGTTTTAACCTTGGTC
75857 CCTCTCTCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
47 11 0.28
48 28 0.72
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.48
Consensus pattern (48 bp):
TTTTTTTTTAACTAAAGCAGCCCTTTGTGGGTTTTAACCTTGGTCTGG
Found at i:84536 original size:17 final size:18
Alignment explanation
Indices: 84509--84544 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
84499 ATACTCTAAC
*
84509 AAATGACAAATAATCAAT
1 AAATGACAAATAAACAAT
84527 AAAT-ACAAATAAACAAT
1 AAATGACAAATAAACAAT
84544 A
1 A
84545 CCATACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.67, C:0.11, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATGACAAATAAACAAT
Found at i:85213 original size:3 final size:3
Alignment explanation
Indices: 85207--85268 Score: 61
Period size: 3 Copynumber: 20.7 Consensus size: 3
85197 TGATAAAAAA
* * * * * * *
85207 AAT AAT ACT ACT ACT AAT AAT AAT AGT AGT AGT AGT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
85255 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
85269 CAGTATTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:89906 original size:17 final size:17
Alignment explanation
Indices: 89884--89936 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
89874 TATTCTATTA
89884 ATTTATTAAGATTTAAT
1 ATTTATTAAGATTTAAT
* *
89901 ATTTATCAAGA-TAAAT
1 ATTTATTAAGATTTAAT
*
89917 ATTAGATTAA-ATTTAAT
1 ATT-TATTAAGATTTAAT
89934 ATT
1 ATT
89937 AGAGTGATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (17 bp):
ATTTATTAAGATTTAAT
Found at i:93113 original size:51 final size:51
Alignment explanation
Indices: 93029--93129 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
93019 ACTCCACTTC
* * *
93029 AGCTTTAATCTATTCCACTGCAATGCCAAGGAAACAATATTTGCTACCTTT
1 AGCTTTAATCCATTCCACTGCAACGCCAAGGAAACAAGATTTGCTACCTTT
* * * *
93080 AGCTTTAATCCGTTCCACTGCAACGCCAGGGAAATAAGATTTGCTGCCTT
1 AGCTTTAATCCATTCCACTGCAACGCCAAGGAAACAAGATTTGCTACCTT
93130 CAGTCTTAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (51 bp):
AGCTTTAATCCATTCCACTGCAACGCCAAGGAAACAAGATTTGCTACCTTT
Found at i:93240 original size:51 final size:51
Alignment explanation
Indices: 93141--93278 Score: 168
Period size: 51 Copynumber: 2.7 Consensus size: 51
93131 AGTCTTAACG
* **
93141 TCAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTACTATGCTGCAACA
1 TCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTACTATAATGCAACA
* * * * * *
93192 TCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCTAATGCAACG
1 TCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTACTATAATGCAACA
* * *
93243 CCAAGGAGATAGGATTCGCTGCCTTTAGCTTTAATC
1 TCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATC
93279 CGCTCCACTT
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 72 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (51 bp):
TCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTACTATAATGCAACA
Found at i:93382 original size:123 final size:123
Alignment explanation
Indices: 93193--93900 Score: 618
Period size: 123 Copynumber: 5.5 Consensus size: 123
93183 GCTGCAACAT
* * * *
93193 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCTAATGCAACGCCAAGGAGATAGGAT
1 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGCAACGCCAAGGAAATAAGAT
* *
93258 TCGCTGCCTTTAGCTTTAATCCGCTCCACTTCAGCTTTAATTTATTCCATTGAAATGC
66 TCGCTGCCTTTAGCTTTAATCCGCTCCACTTCAGCTTTAATTTATTCCACTGCAATGC
*
93316 CAGGGAAACAAGATTCGCTA-CTCTTAGCTTTAATCTGTTCTACTGCCACGCCAAGGAAATAAGA
1 CAGGGAAACAAGATTCGCTACCT-TTAGCTTTAATCTGTTCTACTGCAACGCCAAGGAAATAAGA
* * ** * *
93380 TTCGCTGCCTTCAG-TCTTAATACCAGAGAGATAAGATTTGTTGCCTTCAGCTTTAA-TCAGCTC
65 TTCGCTGCCTTTAGCT-TTAAT-CC-----GCT-CCA--------CTTCAGCTTTAATTTA-TTC
* *
93443 CACTGCAACGT
113 CACTGCAATGC
* * ** * * *
93454 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGTAAATCCAAAGAGATAATAT
1 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGCAACGCCAAGGAAATAAGAT
* * *
93519 TCGCTGCCTTTAGCTTTAATCCGCTCTACTTCAGCTTTAATCTATTCCATTGCAATGC
66 TCGCTGCCTTTAGCTTTAATCCGCTCCACTTCAGCTTTAATTTATTCCACTGCAATGC
* * * *
93577 CAGGGAAACAAGATTCGCTACTTTTAGCTTTCATCTGTTCTACTGCAACGCCAGGGAATTAAGAT
1 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGCAACGCCAAGGAAATAAGAT
** * * **
93642 TCGCTG-CTTTCAGTCTTAACGCCAGGGAGATAAGATTTGCTGC-CTTTAGCTTTAATTTGCTCC
66 TCGCTGCCTTT-AG-CTT-------------T-A-ATCCGCTCCACTTCAGCTTTAATTTATTCC
***
93705 ACTGCAACAT
114 ACTGCAATGC
* * * *
93715 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAGGCCAAAGAGATAAGAT
1 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGCAACGCCAAGGAAATAAGAT
* * *
93780 TCGCTGCCTTCAGCTTTAATCTGCTCCACTTCAGCTTTAATCTATTCCACTGCAATGC
66 TCGCTGCCTTTAGCTTTAATCCGCTCCACTTCAGCTTTAATTTATTCCACTGCAATGC
* * *
93838 TAGGGAAACAAGATTCACTACCTTTAGCTTTAATCAGTTCTACTGCAACG-CAAGGGAAATAAG
1 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGCAACGCCAA-GGAAATAAG
93901 TTTATTGGAT
Statistics
Matches: 463, Mismatches: 81, Indels: 82
0.74 0.13 0.13
Matches are distributed among these distances:
122 17 0.04
123 234 0.51
124 7 0.02
129 2 0.00
130 1 0.00
131 1 0.00
132 2 0.00
137 8 0.02
138 180 0.39
139 11 0.02
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (123 bp):
CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGCAACGCCAAGGAAATAAGAT
TCGCTGCCTTTAGCTTTAATCCGCTCCACTTCAGCTTTAATTTATTCCACTGCAATGC
Found at i:93484 original size:261 final size:261
Alignment explanation
Indices: 93014--93900 Score: 1303
Period size: 261 Copynumber: 3.4 Consensus size: 261
93004 TTGGTGTTTC
* * * *
93014 AATCCACTCCACTTCAGCTTTAATCTATTCCACTGCAATGCCAAGGAAACAATATTTGCTACCTT
1 AATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCAATGCCAGGGAAACAAGATTCGCTACCTT
* * * * *
93079 TAGCTTTAATCCGTTCCACTGCAACGCCAGGGAAATAAGATTTGCTGCCTTCAGTCTTAACGTCA
66 TAGCTTTAATCTGTTCTACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGTCTTAACGCCA
* ***
93144 GGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTA-CTATGCTGCAACATCAGGGAAACAAGATT
131 GGGAGATAAGATTTGCTGCCTTCAGCTTTAATC-AGCTCCACTGCAACATCAGGGAAACAAGATT
* * * * * *
93208 CGCTACCTTTAGCTTTAATCTATTCTAATGCAACGCCAAGGAGATAGGATTCGCTGCCTTTAGCT
195 CGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAAAGAGATAAGATTCGCTGCCTTTAGCT
93273 TT
260 TT
* * *
93275 AATCCGCTCCACTTCAGCTTTAATTTATTCCATTGAAATGCCAGGGAAACAAGATTCGCTA-CTC
1 AATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCAATGCCAGGGAAACAAGATTCGCTACCT-
* **
93339 TTAGCTTTAATCTGTTCTACTGCCACGCCAAGGAAATAAGATTCGCTGCCTTCAGTCTTAATACC
65 TTAGCTTTAATCTGTTCTACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGTCTTAACGCC
* * *
93404 AGAGAGATAAGATTTGTTGCCTTCAGCTTTAATCAGCTCCACTGCAACGTCAGGGAAACAAGATT
130 AGGGAGATAAGATTTGCTGCCTTCAGCTTTAATCAGCTCCACTGCAACATCAGGGAAACAAGATT
* * *
93469 CGCTACCTTTAGCTTTAATCTGTTCCACTGTAAATCCAAAGAGATAATATTCGCTGCCTTTAGCT
195 CGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAAAGAGATAAGATTCGCTGCCTTTAGCT
93534 TT
260 TT
* * *
93536 AATCCGCTCTACTTCAGCTTTAATCTATTCCATTGCAATGCCAGGGAAACAAGATTCGCTACTTT
1 AATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCAATGCCAGGGAAACAAGATTCGCTACCTT
* * * *
93601 TAGCTTTCATCTGTTCTACTGCAACGCCAGGGAATTAAGATTCGCTGCTTTCAGTCTTAACGCCA
66 TAGCTTTAATCTGTTCTACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGTCTTAACGCCA
* **
93666 GGGAGATAAGATTTGCTGCCTTTAGCTTTAATTTGCTCCACTGCAACATCAGGGAAACAAGATTC
131 GGGAGATAAGATTTGCTGCCTTCAGCTTTAATCAGCTCCACTGCAACATCAGGGAAACAAGATTC
* *
93731 GCTACCTTTAGCTTTAATCTGTTCCACTGCAAGGCCAAAGAGATAAGATTCGCTGCCTTCAGCTT
196 GCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAAAGAGATAAGATTCGCTGCCTTTAGCTT
93796 T
261 T
* * *
93797 AATCTGCTCCACTTCAGCTTTAATCTATTCCACTGCAATGCTAGGGAAACAAGATTCACTACCTT
1 AATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCAATGCCAGGGAAACAAGATTCGCTACCTT
*
93862 TAGCTTTAATCAGTTCTACTGCAACG-CAAGGGAAATAAG
66 TAGCTTTAATCTGTTCTACTGCAACGCCAA-GGAAATAAG
93901 TTTATTGGAT
Statistics
Matches: 559, Mismatches: 63, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
260 5 0.01
261 553 0.99
262 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (261 bp):
AATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCAATGCCAGGGAAACAAGATTCGCTACCTT
TAGCTTTAATCTGTTCTACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGTCTTAACGCCA
GGGAGATAAGATTTGCTGCCTTCAGCTTTAATCAGCTCCACTGCAACATCAGGGAAACAAGATTC
GCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAAAGAGATAAGATTCGCTGCCTTTAGCTT
T
Found at i:93538 original size:138 final size:136
Alignment explanation
Indices: 93316--93800 Score: 511
Period size: 138 Copynumber: 3.6 Consensus size: 136
93306 ATTGAAATGC
* * * *
93316 CAGGGAAACAAGATTCGCTA-CTCTTAGCTTTAATCTGTTCTACTGCCACGCCAAGGAAATAAGA
1 CAGGGAAACAAGATTCGCTACCT-TTAGCTTTAATCTGTTCCACTGCAACGCCAAAGAGATAAGA
*
93380 TTCGCTGCCTTCAGTCTTAATACCAGAGAGATAAGATTTGTTGCCTTCAGCTTTAATCAGCTCCA
65 TTCGCTGCCTTCAGTCTTAAT-CCAG-GAGATAAGATTTGCTGCCTTCAGCTTTAATCAGCTCCA
93445 CTGCAACGT
128 CTGCAACGT
* ** *
93454 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGTAAATCCAAAGAGATAATAT
1 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAAAGAGATAAGAT
* * * * *
93519 TCGCTGCCTTTAG-CTTTAATCC---------G--CT-CT-ACTTCAGCTTTAATCTA-TTCCAT
66 TCGCTGCCTTCAGTC-TTAATCCAGGAGATAAGATTTGCTGCCTTCAGCTTTAATC-AGCTCCAC
* *
93569 TGCAATGC
129 TGCAACGT
* * * **
93577 CAGGGAAACAAGATTCGCTACTTTTAGCTTTCATCTGTTCTACTGCAACGCCAGGGA-ATTAAGA
1 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAAAGAGA-TAAGA
* * * **
93641 TTCGCTGCTTTCAGTCTTAACGCCAGGGAGATAAGATTTGCTGCCTTTAGCTTTAATTTGCTCCA
65 TTCGCTGCCTTCAGTCTTAA-TCCA-GGAGATAAGATTTGCTGCCTTCAGCTTTAATCAGCTCCA
*
93706 CTGCAACAT
128 CTGCAACGT
*
93715 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAGGCCAAAGAGATAAGAT
1 CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAAAGAGATAAGAT
93780 TCGCTGCCTTCAG-CTTTAATC
66 TCGCTGCCTTCAGTC-TTAATC
93801 TGCTCCACTT
Statistics
Matches: 278, Mismatches: 46, Indels: 47
0.75 0.12 0.13
Matches are distributed among these distances:
122 1 0.00
123 93 0.33
124 5 0.02
125 1 0.00
127 1 0.00
134 1 0.00
136 1 0.00
137 7 0.03
138 165 0.59
139 3 0.01
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (136 bp):
CAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAAAGAGATAAGAT
TCGCTGCCTTCAGTCTTAATCCAGGAGATAAGATTTGCTGCCTTCAGCTTTAATCAGCTCCACTG
CAACGT
Found at i:93624 original size:51 final size:51
Alignment explanation
Indices: 93551--93651 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
93541 GCTCTACTTC
* *
93551 AGCTTTAATCTATTCCATTGCAATGCCAGGGAAACAAGATTCGCTACTTTT
1 AGCTTTAATCTATTCCACTGCAACGCCAGGGAAACAAGATTCGCTACTTTT
* * * ** *
93602 AGCTTTCATCTGTTCTACTGCAACGCCAGGGAATTAAGATTCGCTGCTTT
1 AGCTTTAATCTATTCCACTGCAACGCCAGGGAAACAAGATTCGCTACTTT
93652 CAGTCTTAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (51 bp):
AGCTTTAATCTATTCCACTGCAACGCCAGGGAAACAAGATTCGCTACTTTT
Found at i:93721 original size:87 final size:87
Alignment explanation
Indices: 93575--93733 Score: 201
Period size: 87 Copynumber: 1.8 Consensus size: 87
93565 CCATTGCAAT
* * * * * **
93575 GCCAGGGAAACAAGATTCGCTACTTTTAGCTTTCATCTGTTCTACTGCAACGCCAGGGAATTAAG
1 GCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGCTCCACTGCAACACCAGGGAAACAAG
93640 ATTCGCTGCTTTCAGTCTTAAC
66 ATTCGCTGCTTTCAGTCTTAAC
* * * * * *
93662 GCCAGGGAGATAAGATTTGCTGCCTTTAGCTTTAATTTGCTCCACTGCAACATCAGGGAAACAAG
1 GCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGCTCCACTGCAACACCAGGGAAACAAG
93727 ATTCGCT
66 ATTCGCT
93734 ACCTTTAGCT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
87 59 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (87 bp):
GCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGCTCCACTGCAACACCAGGGAAACAAG
ATTCGCTGCTTTCAGTCTTAAC
Found at i:93740 original size:51 final size:51
Alignment explanation
Indices: 93663--93809 Score: 186
Period size: 51 Copynumber: 2.9 Consensus size: 51
93653 AGTCTTAACG
* *
93663 CCAGGGAGATAAGATTTGCTGCCTTTAGCTTTAATTTGCTCCACTGCAACA
1 CCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCACTGCAACA
* * * * * **
93714 TCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAGG
1 CCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCACTGCAACA
** *
93765 CCAAAGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACT
1 CCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCACT
93810 TCAGCTTTAA
Statistics
Matches: 79, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 79 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (51 bp):
CCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCACTGCAACA
Found at i:93828 original size:21 final size:21
Alignment explanation
Indices: 93787--93830 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
93777 GATTCGCTGC
*
93787 CTTCAGCTTTAATCTGCTCCA
1 CTTCAGCTTTAATCTACTCCA
*
93808 CTTCAGCTTTAATCTATTCCA
1 CTTCAGCTTTAATCTACTCCA
93829 CT
1 CT
93831 GCAATGCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.32, G:0.07, T:0.41
Consensus pattern (21 bp):
CTTCAGCTTTAATCTACTCCA
Found at i:108233 original size:17 final size:17
Alignment explanation
Indices: 108211--108263 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
108201 TATTCTATTA
108211 ATTTATTAAGATTTAAT
1 ATTTATTAAGATTTAAT
*
108228 ATTTATTAAGA-TAAAT
1 ATTTATTAAGATTTAAT
*
108244 ATTAGATTAA-ATTTAAT
1 ATT-TATTAAGATTTAAT
108261 ATT
1 ATT
108264 AAAGTGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 8 0.26
17 23 0.74
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (17 bp):
ATTTATTAAGATTTAAT
Done.