Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold319
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: 745371
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.30
Warning! 60102 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:598570 original size:44 final size:45
Alignment explanation
Indices: 598521--598607 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 45
598511 TTATTTTGAA
*
598521 TATTTTGATATTATTTTATGTAA-AAGAATAGAAATTT-TTTGAGT
1 TATTTTGATATTATTTGATGTAATAA-AATAGAAATTTATTTGAGT
*
598565 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGA
598608 TGTAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
44 32 0.82
45 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
Found at i:598635 original size:30 final size:25
Alignment explanation
Indices: 598575--598642 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
598565 TATTTTGATA
598575 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
598600 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
* * *
598625 CTATTTTATTTAATAAAA
1 TTATTTGATGTAATAAAA
598643 ACCCTAACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.43
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:598690 original size:23 final size:23
Alignment explanation
Indices: 598632--598801 Score: 119
Period size: 23 Copynumber: 6.9 Consensus size: 23
598622 AGTCTATTTT
*
598632 ATTTAA-TAAAAACCCTAACTTA
1 ATTTAATTAAAAACCCTAACCTA
****
598654 ATTTAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
598677 ATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATT--AAA----AACCCTAACCTA
598706 ATTTAATTAAAAACCCTAACCTTA
1 ATTTAATTAAAAACCCTAACC-TA
**
598730 ACCTAATTTAATACAGAACCCTAACCTA
1 ATTTAA-TT-A-A-A-AACCCTAACCTA
*
598758 ATTTAA-TACAAAACCCTACCCTA
1 ATTTAATTA-AAAACCCTAACCTA
**
598781 ATTGGATTAAAAACCCTAACC
1 ATTTAATTAAAAACCCTAACC
598802 CTAACCTAAT
Statistics
Matches: 117, Mismatches: 17, Indels: 27
0.73 0.11 0.17
Matches are distributed among these distances:
22 6 0.05
23 54 0.46
24 9 0.08
25 5 0.04
26 2 0.02
27 4 0.03
28 7 0.06
29 30 0.26
ACGTcount: A:0.44, C:0.26, G:0.02, T:0.28
Consensus pattern (23 bp):
ATTTAATTAAAAACCCTAACCTA
Found at i:598720 original size:52 final size:52
Alignment explanation
Indices: 598664--598822 Score: 205
Period size: 52 Copynumber: 3.1 Consensus size: 52
598654 ATTTAACCCT
598664 AAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAA
1 AAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAA
** * * **
598716 AAACCCTAACCTTAACCTAATTTAATA-CAGAACCCTAACCTAATTTAA-TACA
1 AAACCCTAACC-TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTA-A
* **
598768 AAACCCTACCCTAATTGGATTAAAAACCCTAACCCTAACCTAATTTAATTAA
1 AAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAA
598820 AAA
1 AAA
598823 TCCNNNNNNN
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
51 11 0.12
52 64 0.73
53 13 0.15
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.27
Consensus pattern (52 bp):
AAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAA
Found at i:598818 original size:29 final size:29
Alignment explanation
Indices: 598658--598822 Score: 176
Period size: 29 Copynumber: 6.1 Consensus size: 29
598648 AACTTAATTT
598658 AACCCTAAACCCTAACCTAATTTAATTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
598688 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
598717 AACCCTAACCTTAACCTAATTTAA-T---
1 AACCCTAACCCTAACCTAATTTAATTAAA
**
598742 -A-CAGAACCCTAACCTAATTTAA-TACAA
1 AACCCTAACCCTAACCTAATTTAATTA-AA
**
598769 AACCCT-A--C---CCTAATTGGATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
598792 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
598821 AA
1 AA
598823 TCCNNNNNNN
Statistics
Matches: 112, Mismatches: 10, Indels: 27
0.75 0.07 0.18
Matches are distributed among these distances:
23 35 0.31
24 4 0.04
26 2 0.02
28 3 0.03
29 62 0.55
30 6 0.05
ACGTcount: A:0.45, C:0.27, G:0.02, T:0.27
Consensus pattern (29 bp):
AACCCTAACCCTAACCTAATTTAATTAAA
Found at i:602501 original size:126 final size:126
Alignment explanation
Indices: 602275--602628 Score: 591
Period size: 126 Copynumber: 2.8 Consensus size: 126
602265 ACCAAACATG
*
602275 CTACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
602340 TAGAAGTGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCTGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
* * * * *
602401 TTACTGTAGCAAAAGTGCGTCCTCGAGGGCGCGATTTCACAATTTCTTCTCACATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
602466 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
* * *
602527 CTACAGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAAAAATTCTTCCCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
602592 TAGAAGCGATTTTATACTATTTGATTAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
602629 CTCGAAATTA
Statistics
Matches: 210, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 210 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
Found at i:603669 original size:22 final size:21
Alignment explanation
Indices: 603631--603673 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
603621 TTTTATAAGA
*
603631 AATTTATCTTTTAAATAGAAAT
1 AATTTATCTATTAAATA-AAAT
603653 AATTTATACTATT-AATAAAAT
1 AATTTAT-CTATTAAATAAAAT
603674 CTCTAATCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (21 bp):
AATTTATCTATTAAATAAAAT
Found at i:604289 original size:18 final size:18
Alignment explanation
Indices: 604266--604301 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
604256 AGCAAAACTT
*
604266 TATTTTGATTTTCTTATG
1 TATTTTAATTTTCTTATG
*
604284 TATTTTAATTTTTTTATG
1 TATTTTAATTTTCTTATG
604302 CACACTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.08, T:0.69
Consensus pattern (18 bp):
TATTTTAATTTTCTTATG
Found at i:606777 original size:3 final size:3
Alignment explanation
Indices: 606769--606816 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
606759 AAAGAGTCTA
*
606769 ATT ATT ATT ATT ATT CTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
606817 TTGTAATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:628199 original size:29 final size:29
Alignment explanation
Indices: 628157--628483 Score: 352
Period size: 29 Copynumber: 11.2 Consensus size: 29
628147 GTGCTAAACA
* * *
628157 ATGGTCATAACCATCCCTTTTCATATTTG
1 ATGGTCGTCACCATCCCTTTTCATAGTTG
*
628186 ATGGTTGTCACCATCCCTTTTCATA-TTCG
1 ATGGTCGTCACCATCCCTTTTCATAGTT-G
* ** * *
628215 ATGGTTGGAACCATCCCTTTTCATTAATCG
1 ATGGTCGTCACCATCCCTTTTCA-TAGTTG
628245 ATGGTCGTCACCATCCCTTTTCATAGTTG
1 ATGGTCGTCACCATCCCTTTTCATAGTTG
* *
628274 ATGGTCATCACCATCCCTTTTCATAGTCG
1 ATGGTCGTCACCATCCCTTTTCATAGTTG
* *** * *
628303 ATAGTCAAAACTATCCCTTTTCATA-TTCA
1 ATGGTCGTCACCATCCCTTTTCATAGTT-G
* * *
628332 ATTGTCGTCACTATCCATTTTCATAGTTG
1 ATGGTCGTCACCATCCCTTTTCATAGTTG
*
628361 ATGGTTGTCACCATCCCTTTTCATAGTTG
1 ATGGTCGTCACCATCCCTTTTCATAGTTG
* ** * *
628390 ATAGTCGAAACTATCCCTTTTCATATTTG
1 ATGGTCGTCACCATCCCTTTTCATAGTTG
*
628419 ATGGTCGTCACCATTCCTTTTCATAGTTG
1 ATGGTCGTCACCATCCCTTTTCATAGTTG
*
628448 ATGGTCGTCCCCATCCCTTTTCATAGTTG
1 ATGGTCGTCACCATCCCTTTTCATAGTTG
*
628477 ATAGTCG
1 ATGGTCG
628484 AATTTATCCC
Statistics
Matches: 249, Mismatches: 44, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
28 3 0.01
29 220 0.88
30 25 0.10
31 1 0.00
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.39
Consensus pattern (29 bp):
ATGGTCGTCACCATCCCTTTTCATAGTTG
Found at i:628377 original size:87 final size:87
Alignment explanation
Indices: 628155--628508 Score: 474
Period size: 87 Copynumber: 4.1 Consensus size: 87
628145 GTGTGCTAAA
* * * * * *
628155 CAATGGTCATAACCATCCCTTTTCATATTTGATGGTTGTCACCATCCCTTTTCATATTCGATGGT
1 CAATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGT
* * * *
628220 TGGAACCATCCCTTTTCATTAAT
66 CGAAACTATCCCTTTTCA-TATT
* *
628243 CGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCATAGTCGATAGT
1 CAATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGT
*
628308 CAAAACTATCCCTTTTCATATT
66 CGAAACTATCCCTTTTCATATT
* * * * *
628330 CAATTGTCGTCACTATCCATTTTCATAGTTGATGGTTGTCACCATCCCTTTTCATAGTTGATAGT
1 CAATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGT
628395 CGAAACTATCCCTTTTCATATT
66 CGAAACTATCCCTTTTCATATT
** * * *
628417 TGATGGTCGTCACCATTCCTTTTCATAGTTGATGGTCGTCCCCATCCCTTTTCATAGTTGATAGT
1 CAATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGT
**
628482 CGAATTTATCCCTTTTCATATT
66 CGAAACTATCCCTTTTCATATT
628504 CAATG
1 CAATG
628509 CTCATCGATA
Statistics
Matches: 233, Mismatches: 33, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
87 162 0.70
88 71 0.30
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (87 bp):
CAATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGT
CGAAACTATCCCTTTTCATATT
Found at i:630308 original size:19 final size:19
Alignment explanation
Indices: 630257--630312 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
630247 AAAGTAAATT
630257 AAAAAAA-ATGAAA--AAA
1 AAAAAAACATGAAATGAAA
630273 AAAAGAAACAATGGAAATGAAA
1 AAAA-AAAC-AT-GAAATGAAA
630295 AAAAAAACATGAAATGAA
1 AAAAAAACATGAAATGAA
630313 TTTTAATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.12
17 3 0.09
19 10 0.29
20 6 0.18
21 4 0.12
22 7 0.21
ACGTcount: A:0.75, C:0.04, G:0.12, T:0.09
Consensus pattern (19 bp):
AAAAAAACATGAAATGAAA
Found at i:631978 original size:15 final size:17
Alignment explanation
Indices: 631958--631994 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
631948 ATTATTTTTG
631958 AATAAAT-AATCAG-TT
1 AATAAATAAATCAGTTT
631973 AATAAATAAATCAGTTT
1 AATAAATAAATCAGTTT
631990 AATAA
1 AATAA
631995 TCGAATCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.35
16 6 0.30
17 7 0.35
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (17 bp):
AATAAATAAATCAGTTT
Found at i:638411 original size:38 final size:39
Alignment explanation
Indices: 638369--638446 Score: 122
Period size: 38 Copynumber: 2.0 Consensus size: 39
638359 CTTATCACAT
*
638369 ATTAAAGATGTTCAAATTATGACATAGTTAAA-ACTCAA
1 ATTAAAGATGTTCAAATTATGACATAATTAAAGACTCAA
* *
638407 ATTAATGATGTTCAAATTATGGCATAATTAAAGACTCAA
1 ATTAAAGATGTTCAAATTATGACATAATTAAAGACTCAA
638446 A
1 A
638447 CTTTAATAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 29 0.81
39 7 0.19
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (39 bp):
ATTAAAGATGTTCAAATTATGACATAATTAAAGACTCAA
Found at i:642990 original size:19 final size:21
Alignment explanation
Indices: 642966--643010 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
642956 ATTTTAATAT
642966 TTTTTTGGATATAAA-AAAG-
1 TTTTTTGGATATAAATAAAGA
**
642985 TTTTTTTTATATAAATAAAGA
1 TTTTTTGGATATAAATAAAGA
643006 TTTTT
1 TTTTT
643011 CTATTCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.59
20 4 0.18
21 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (21 bp):
TTTTTTGGATATAAATAAAGA
Found at i:644422 original size:345 final size:347
Alignment explanation
Indices: 643778--644471 Score: 1374
Period size: 345 Copynumber: 2.0 Consensus size: 347
643768 TTTATAATAT
643778 AATATAATTTAATTTTAATTTTTTATTAAAAATGTAAATTATATTATTAATTGATTTTCTTAATT
1 AATATAATTTAATTTTAATTTTTTATTAAAAATGTAAATTATATTATTAATTGATTTTCTTAATT
643843 ATTAATTTCCCTAAACTATTATCAATTTTTTTCCTAAACCAGTCTTTCCTACTCACTGCAAACAA
66 ATTAATTTCCCTAAACTATTATCAATTTTTTTCCTAAACCAGTCTTTCCTACTCACTGCAAACAA
643908 CGAGCAAGGCAATTTGTTACGCTGTTACGGATGCATTTGTTGGACAAACCTATGAGGGTCGTTGG
131 CGAGCAAGGCAATTTGTTACGCTGTTACGGATGCATTTGTTGGACAAACCTATGAGGGTCGTTGG
643973 GTGCACGGAAGTTCATAGGGTGCACGGAAGTGGAACAGCAGAAGATGATGTTTAAGGGAATTATT
196 GTGCACGGAAGTTCATAGGGTGCACGGAAGTGGAACAGCAGAAGATGATGTTTAAGGGAATTATT
644038 ATTTTTATGCTATTAGGAATGTTTTTATTATTATTTTATTTAGAAAGTATTAAAGATTTTAATTA
261 ATTTTTATGCTATTAGGAATGTTTTTATTATTATTTTATTTAGAAAGTATTAAAGATTTTAATTA
644103 TGGATATTTCTTATTTTCTTAG
326 TGGATATTTCTTATTTTCTTAG
644125 AATATAATTT-A-TTTAATTTTTTATTAAAAATGTAAATTATATTATTAATTGATTTTCTTAATT
1 AATATAATTTAATTTTAATTTTTTATTAAAAATGTAAATTATATTATTAATTGATTTTCTTAATT
644188 ATTAATTTCCCTAAACTATTATCAATTTTTTTCCTAAACCAGTCTTTCCTACTCACTGCAAACAA
66 ATTAATTTCCCTAAACTATTATCAATTTTTTTCCTAAACCAGTCTTTCCTACTCACTGCAAACAA
644253 CGAGCAAGGCAATTTGTTACGCTGTTACGGATGCATTTGTTGGACAAACCTATGAGGGTCGTTGG
131 CGAGCAAGGCAATTTGTTACGCTGTTACGGATGCATTTGTTGGACAAACCTATGAGGGTCGTTGG
644318 GTGCACGGAAGTTCATAGGGTGCACGGAAGTGGAACAGCAGAAGATGATGTTTAAGGGAATTATT
196 GTGCACGGAAGTTCATAGGGTGCACGGAAGTGGAACAGCAGAAGATGATGTTTAAGGGAATTATT
644383 ATTTTTATGCTATTAGGAATGTTTTTATTATTATTTTATTTAGAAAGTATTAAAGATTTTAATTA
261 ATTTTTATGCTATTAGGAATGTTTTTATTATTATTTTATTTAGAAAGTATTAAAGATTTTAATTA
644448 TGGATATTTCTTATTTTCTTAG
326 TGGATATTTCTTATTTTCTTAG
644470 AA
1 AA
644472 GTCTTTCCTT
Statistics
Matches: 347, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
345 336 0.97
346 1 0.00
347 10 0.03
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (347 bp):
AATATAATTTAATTTTAATTTTTTATTAAAAATGTAAATTATATTATTAATTGATTTTCTTAATT
ATTAATTTCCCTAAACTATTATCAATTTTTTTCCTAAACCAGTCTTTCCTACTCACTGCAAACAA
CGAGCAAGGCAATTTGTTACGCTGTTACGGATGCATTTGTTGGACAAACCTATGAGGGTCGTTGG
GTGCACGGAAGTTCATAGGGTGCACGGAAGTGGAACAGCAGAAGATGATGTTTAAGGGAATTATT
ATTTTTATGCTATTAGGAATGTTTTTATTATTATTTTATTTAGAAAGTATTAAAGATTTTAATTA
TGGATATTTCTTATTTTCTTAG
Found at i:651656 original size:18 final size:18
Alignment explanation
Indices: 651635--651674 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
651625 ATATTTAATT
651635 TTTTAATAATTTTTTAGA
1 TTTTAATAATTTTTTAGA
* *
651653 TTTTCATGATTTTTTAGA
1 TTTTAATAATTTTTTAGA
651671 TTTT
1 TTTT
651675 TAGGGCACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (18 bp):
TTTTAATAATTTTTTAGA
Found at i:651718 original size:16 final size:16
Alignment explanation
Indices: 651694--651731 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
651684 TTTGGTTCGC
* *
651694 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
651710 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
651726 TGTAAT
1 TGTAAT
651732 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:651982 original size:16 final size:16
Alignment explanation
Indices: 651945--651986 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
651935 TTAATCATAT
*
651945 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
651961 TT-AAATATATTATAA
1 TTAAAATATATTATAA
651976 TTAAAATATAT
1 TTAAAATATAT
651987 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:651993 original size:14 final size:15
Alignment explanation
Indices: 651954--651995 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
651944 TTTAAACATA
*
651954 ATTATTATTAAATAT
1 ATTATAATTAAATAT
651969 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
651983 A-TATAATTTAATA
1 ATTATAATTAAATA
651996 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:652207 original size:24 final size:25
Alignment explanation
Indices: 652161--652208 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
652151 TATGAATTTG
652161 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
652187 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
652209 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:652212 original size:92 final size:92
Alignment explanation
Indices: 652116--652344 Score: 236
Period size: 92 Copynumber: 2.5 Consensus size: 92
652106 TGATTTAATA
* * *
652116 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
652178 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
652208 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
652273 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* * *
652298 ATAATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 A-AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
652345 CTAAAATCAA
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
90 2 0.02
91 27 0.23
92 81 0.68
93 9 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:656555 original size:20 final size:22
Alignment explanation
Indices: 656500--656554 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
656490 AACATGATGT
*
656500 TATATTT--TAAAAATTTTATA
1 TATATTTAATAAAAATTATATA
656520 TATATTTAATAAAAATTATATA
1 TATATTTAATAAAAATTATATA
*
656542 T-TTTTTAATAAAA
1 TATATTTAATAAAA
656555 TAAAGACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 7 0.23
21 11 0.35
22 13 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATTTAATAAAAATTATATA
Found at i:668159 original size:17 final size:17
Alignment explanation
Indices: 668108--668152 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
668098 GCAATAATTG
668108 ACGTTTTGAAAATGAATA
1 ACGTTTTGAAAA-GAATA
*
668126 ACGTTTTGCAAGAGAATA
1 ACGTTTTG-AAAAGAATA
668144 AC-TTTTGAA
1 ACGTTTTGAA
668153 TACGAATCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 2 0.08
17 5 0.20
18 15 0.60
19 3 0.12
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (17 bp):
ACGTTTTGAAAAGAATA
Found at i:676900 original size:25 final size:25
Alignment explanation
Indices: 676840--676900 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
676830 CTCCTAAATT
*
676840 TTAATTTAATTATCTAATTTTTCAA
1 TTAATTAAATTATCTAATTTTTCAA
* *
676865 TTTATTGAATTAT-TAATATTTT-ATA
1 TTAATTAAATTATCTAAT-TTTTCA-A
676890 TTAATTAAATT
1 TTAATTAAATT
676901 TTTGAGAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 5 0.17
25 25 0.83
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTATCTAATTTTTCAA
Found at i:689489 original size:2 final size:2
Alignment explanation
Indices: 689482--689509 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
689472 TGACGTGTAA
689482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
689510 GTTGATTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:698245 original size:8 final size:8
Alignment explanation
Indices: 698232--698283 Score: 52
Period size: 8 Copynumber: 6.1 Consensus size: 8
698222 TTTAAGATTT
698232 ATTATAAA
1 ATTATAAA
698240 ATTATAAA
1 ATTATAAA
698248 ATTATTAAAA
1 ATTA-T-AAA
*
698258 ATTTATCAA
1 A-TTATAAA
698267 ATTAT-AA
1 ATTATAAA
698274 ATCTATAAA
1 AT-TATAAA
698283 A
1 A
698284 AGTATTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
7 4 0.11
8 19 0.50
9 7 0.18
10 5 0.13
11 3 0.08
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (8 bp):
ATTATAAA
Found at i:698254 original size:19 final size:19
Alignment explanation
Indices: 698230--698271 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
698220 TTTTTAAGAT
698230 TTATTATAAAA-TTATAAAA
1 TTATTA-AAAATTTATAAAA
*
698249 TTATTAAAAATTTATCAAA
1 TTATTAAAAATTTATAAAA
698268 TTAT
1 TTAT
698272 AAATCTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
TTATTAAAAATTTATAAAA
Found at i:698284 original size:27 final size:27
Alignment explanation
Indices: 698233--698302 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
698223 TTAAGATTTA
*
698233 TTATAAAATTATAAAATTATTAAAAAT
1 TTATAAAATTATAAAATTATAAAAAAT
* *
698260 TTATCAAATTAT-AAATCTATAAAAAGT
1 TTATAAAATTATAAAAT-TATAAAAAAT
*
698287 ATTA-AAAACTATAAAA
1 -TTATAAAATTATAAAA
698303 AAAAAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
26 4 0.11
27 25 0.71
28 6 0.17
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (27 bp):
TTATAAAATTATAAAATTATAAAAAAT
Found at i:698411 original size:6 final size:6
Alignment explanation
Indices: 698400--698428 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
698390 AAACCATAAA
698400 AATTTG AATTTG AATTTG AATTTG AATTT
1 AATTTG AATTTG AATTTG AATTTG AATTT
698429 AAAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (6 bp):
AATTTG
Found at i:698592 original size:20 final size:20
Alignment explanation
Indices: 698542--698598 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
698532 AAAATTATGA
* *
698542 TTTATTTTTATAATTTGT-G
1 TTTATTTTTATAATTTTTAC
698561 TTT-TTTTTATAATTTTTAC
1 TTTATTTTTATAATTTTTAC
*
698580 TTTATTTTGATAATTTTTA
1 TTTATTTTTATAATTTTTA
698599 TAAAATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 13 0.39
19 6 0.18
20 14 0.42
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTATTTTTATAATTTTTAC
Found at i:701224 original size:25 final size:24
Alignment explanation
Indices: 701187--701234 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
701177 GTCATTGATA
*
701187 ATTTATATTGTGTTATTAT-TATGC
1 ATTTATAATGTGTT-TTATGTATGC
701211 ATTTAATAATGTGTTTTATGTATG
1 ATTT-ATAATGTGTTTTATGTATG
701235 GTAAAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.56
Consensus pattern (24 bp):
ATTTATAATGTGTTTTATGTATGC
Found at i:702318 original size:24 final size:24
Alignment explanation
Indices: 702303--702354 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
702293 AATCAAAGTC
702303 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
702327 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
702351 AAAT
1 AAAT
702355 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:706761 original size:24 final size:24
Alignment explanation
Indices: 706746--706797 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
706736 AATCAAAGTC
706746 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
706770 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
706794 AAAT
1 AAAT
706798 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:710276 original size:41 final size:41
Alignment explanation
Indices: 710161--710255 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
710151 NNNNNNNNNN
*
710161 GTGATCTGAATCAGGTTATAAACCTAGCAGGCTACGTGCCG
1 GTGATCTGAATCAGGTTATAAACCTAGCAGGCTACGTGCCA
*
710202 GTGATTTGAATCAGGTTATAAACCTAGCAGGCTACGTGCCA
1 GTGATCTGAATCAGGTTATAAACCTAGCAGGCTACGTGCCA
*
710243 GTGATCTAAATCA
1 GTGATCTGAATCA
710256 AGCTATAAGT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Consensus pattern (41 bp):
GTGATCTGAATCAGGTTATAAACCTAGCAGGCTACGTGCCA
Found at i:715532 original size:43 final size:43
Alignment explanation
Indices: 715470--715605 Score: 159
Period size: 43 Copynumber: 3.2 Consensus size: 43
715460 TTTTAAAAAT
* *
715470 AAACGCCGCTAAA-AGTCATGATCTTTAACGGCGCTT-TTCTCAC
1 AAACGCCGCTAAAGA-TCATGAACTTTAACGGCGCTTCTAC-CAC
*
715513 AAACGCCGCTAAAGATCATGAACTTTAGCGGCGCTTCTACCAC
1 AAACGCCGCTAAAGATCATGAACTTTAACGGCGCTTCTACCAC
* * * * * *
715556 AAACGCCGCTAAAGAACATGACCTTTAGCGACACTTATACCAC
1 AAACGCCGCTAAAGATCATGAACTTTAACGGCGCTTCTACCAC
715599 AAACGCC
1 AAACGCC
715606 ACTGTAAATA
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
43 80 0.96
44 3 0.04
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGAACTTTAACGGCGCTTCTACCAC
Found at i:715664 original size:41 final size:41
Alignment explanation
Indices: 715470--715664 Score: 153
Period size: 43 Copynumber: 4.6 Consensus size: 41
715460 TTTTAAAAAT
* * *
715470 AAACGCCGCTAAAAGTCATGA-TCTTTAACGGCGCTTTTCTCAC
1 AAACGCCGCTAAAA-ACATGACT-TTTAGCGGCGCTTTT-ACAC
* *
715513 AAACGCCGCTAAAGATCATGAAC-TTTAGCGGCGCTTCTACCAC
1 AAACGCCGCTAAA-AACATG-ACTTTTAGCGGCGCTTTTA-CAC
* * * *
715556 AAACGCCGCTAAAGAACATGACCTTTAGCGACACTTATACCAC
1 AAACGCCGCTAAA-AACATGACTTTTAGCGGCGCTTTTA-CAC
* ** * * *
715599 AAACGCCACTGTAAATATGGCTTTTAGCAGCGCTTTTTA-AC
1 AAACGCCGCTAAAAACATGACTTTTAGCGGCGC-TTTTACAC
715640 AAACGCCGCTAAAAACATGACTTTT
1 AAACGCCGCTAAAAACATGACTTTT
715665 TAAAAAATAT
Statistics
Matches: 124, Mismatches: 22, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
41 22 0.18
42 16 0.13
43 84 0.68
44 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (41 bp):
AAACGCCGCTAAAAACATGACTTTTAGCGGCGCTTTTACAC
Found at i:718711 original size:107 final size:108
Alignment explanation
Indices: 718589--718869 Score: 296
Period size: 123 Copynumber: 2.5 Consensus size: 108
718579 TGGCCTATTT
* *
718589 GCTATTTTTTAAAAGTAAAATTATTTTTTGCGGCGTTTTTCATAAAAACGCGGC-AAAAAATTAT
1 GCTATTTTTTAAAAGTAAAATTATTTTTTGTGGCGTTTTTCATAAAAACGCGCCAAAAAAATTAT
718653 TTCATTTGGAATAAAACGACACTGTTTTGCTATATAAAATGGC
66 TTCATTTGGAATAAAACGACACTGTTTTGCTATATAAAATGGC
* * * * **
718696 GCTATTTTTTAAAAGTAAAATTATTTTTTGTATTGCTTACCTTTTGCGGCGTTTTCCATAAAAAC
1 GCTATTTTTTAAAAGTAAAATTATTTTTTG--TGGCGT---TTTT----C---AT--AAAAACGC
*
718761 GCCACAAAAAATTATTTCATTTGGAATAAAATGACACTGTTTTGCTATATAAAATGGC
52 GCCA-AAAAAATTATTTCATTTGGAATAAAACGACACTGTTTTGCTATATAAAATGGC
* * *
718819 ACTATTTTTTTTAAAGTAAAATTA-TTTTTGTGGCGTTTTTTATAAAAACGC
1 GCTA-TTTTTTAAAAGTAAAATTATTTTTTGTGGCGTTTTTCATAAAAACGC
718870 CGCTATTGCT
Statistics
Matches: 139, Mismatches: 18, Indels: 32
0.74 0.10 0.17
Matches are distributed among these distances:
107 30 0.22
109 8 0.06
111 1 0.01
112 4 0.03
116 1 0.01
118 4 0.03
119 1 0.01
121 11 0.08
123 61 0.44
124 18 0.13
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (108 bp):
GCTATTTTTTAAAAGTAAAATTATTTTTTGTGGCGTTTTTCATAAAAACGCGCCAAAAAAATTAT
TTCATTTGGAATAAAACGACACTGTTTTGCTATATAAAATGGC
Found at i:718747 original size:123 final size:124
Alignment explanation
Indices: 718614--718847 Score: 407
Period size: 123 Copynumber: 1.9 Consensus size: 124
718604 TAAAATTATT
* **
718614 TTTTGCGGCGTTTTTCATAAAAACGCGGCAAAAAATTATTTCATTTGGAATAAAACGACACTGTT
1 TTTTGCGGCGTTTTCCATAAAAACGCCACAAAAAATTATTTCATTTGGAATAAAACGACACTGTT
*
718679 TTGCTATATAAAATGGCGCTA-TTTTTTAAAAGTAAAATTATTTTTTGTATTGCTTACC
66 TTGCTATATAAAATGGCACTATTTTTTTAAAAGTAAAATTATTTTTTGTATTGCTTACC
*
718737 TTTTGCGGCGTTTTCCATAAAAACGCCACAAAAAATTATTTCATTTGGAATAAAATGACACTGTT
1 TTTTGCGGCGTTTTCCATAAAAACGCCACAAAAAATTATTTCATTTGGAATAAAACGACACTGTT
*
718802 TTGCTATATAAAATGGCACTATTTTTTTTAAAGTAAAATTATTTTT
66 TTGCTATATAAAATGGCACTATTTTTTTAAAAGTAAAATTATTTTT
718848 GTGGCGTTTT
Statistics
Matches: 104, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
123 81 0.78
124 23 0.22
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (124 bp):
TTTTGCGGCGTTTTCCATAAAAACGCCACAAAAAATTATTTCATTTGGAATAAAACGACACTGTT
TTGCTATATAAAATGGCACTATTTTTTTAAAAGTAAAATTATTTTTTGTATTGCTTACC
Found at i:719827 original size:14 final size:14
Alignment explanation
Indices: 719808--719850 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
719798 ATTACTAACT
719808 CTTAACCCCAAACC
1 CTTAACCCCAAACC
**
719822 CTTAACCCTTAACC
1 CTTAACCCCAAACC
*
719836 CCTAACCCCTAAACC
1 CTTAACCCC-AAACC
719851 TTATTTAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.33, C:0.49, G:0.00, T:0.19
Consensus pattern (14 bp):
CTTAACCCCAAACC
Found at i:719827 original size:21 final size:21
Alignment explanation
Indices: 719803--719853 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
719793 CCAAGATTAC
*
719803 TAACTCTTAACCCCAAACCCT
1 TAACCCTTAACCCCAAACCCT
* *
719824 TAACCCTTAACCCCTAACCCC
1 TAACCCTTAACCCCAAACCCT
*
719845 TAAACCTTA
1 TAACCCTTA
719854 TTTAATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.43, G:0.00, T:0.24
Consensus pattern (21 bp):
TAACCCTTAACCCCAAACCCT
Found at i:719937 original size:96 final size:96
Alignment explanation
Indices: 719824--720005 Score: 292
Period size: 96 Copynumber: 1.9 Consensus size: 96
719814 CCCAAACCCT
* * * *
719824 TAACCCTTAACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAATACTAATTAATCTA
1 TAACCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAACTAATCTA
*
719889 AACCCTAAACCCTAACCTGACCTCGAATCCC
66 AACCATAAACCCTAACCTGACCTCGAATCCC
* *
719920 TAACCCCTAACCTCTAACCCCTAAACATTATTTAATATATAAATTAAAATACACTAACTAATCTA
1 TAACCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAACTAATCTA
*
719985 AACCATAAACCCTAACTTGAC
66 AACCATAAACCCTAACCTGAC
720006 ACCAAATCCA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 78 1.00
ACGTcount: A:0.42, C:0.29, G:0.02, T:0.27
Consensus pattern (96 bp):
TAACCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAACTAATCTA
AACCATAAACCCTAACCTGACCTCGAATCCC
Found at i:720014 original size:96 final size:95
Alignment explanation
Indices: 719814--720025 Score: 291
Period size: 96 Copynumber: 2.2 Consensus size: 95
719804 AACTCTTAAC
* * *
719814 CCCAAA-CCCTTAACCCTTAACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAATAC
1 CCCAAATCCC-TAACCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACAC
* *
719878 TAATTAATCTAAACCCTAAACCCTAACCTGA
65 TAACTAATCTAAACCATAAACCCTAACCTGA
* * *
719909 CCTCGAATCCCTAACCCCTAACCTCTAACCCCTAAACATTATTTAATATATAAATTAAAATACAC
1 CC-CAAATCCCTAACCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACAC
*
719974 TAACTAATCTAAACCATAAACCCTAACTTGA
65 TAACTAATCTAAACCATAAACCCTAACCTGA
* *
720005 CACCAAATCCATAAACCCTAA
1 C-CCAAATCCCTAACCCCTAA
720026 ATTCCTAACT
Statistics
Matches: 102, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
95 2 0.02
96 96 0.94
97 4 0.04
ACGTcount: A:0.42, C:0.31, G:0.01, T:0.25
Consensus pattern (95 bp):
CCCAAATCCCTAACCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACT
AACTAATCTAAACCATAAACCCTAACCTGA
Found at i:720119 original size:14 final size:15
Alignment explanation
Indices: 720102--720135 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
720092 CTTAAATCAG
720102 AATCTCTAA-TCCAT
1 AATCTCTAATTCCAT
*
720116 AATCCCTAATTCCAT
1 AATCTCTAATTCCAT
720131 AATCT
1 AATCT
720136 ATAAACCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (15 bp):
AATCTCTAATTCCAT
Found at i:720647 original size:41 final size:42
Alignment explanation
Indices: 720555--720697 Score: 141
Period size: 41 Copynumber: 3.5 Consensus size: 42
720545 ACGCTTCTTG
** * *
720555 AAAAACGTTGCTAAAGCCTC-GAGCATTAGCGGCGC-TTATTG
1 AAAAACGCCGCTAAAGCCCCTGAGCATTAGCGGCGCTTTA-TC
* * *
720596 ATAAATGCCGCTATAGCCCCT-AGCATTAGCGGCGCTTTATC
1 AAAAACGCCGCTAAAGCCCCTGAGCATTAGCGGCGCTTTATC
** * * *
720637 AAAAACGCCGCTAAAG-ATCTGAGCACTAGCGGCGCTTTTTT
1 AAAAACGCCGCTAAAGCCCCTGAGCATTAGCGGCGCTTTATC
720678 AAAAACGCCGCTAAAGCCCC
1 AAAAACGCCGCTAAAGCCCC
720698 GAAAGGTAGC
Statistics
Matches: 81, Mismatches: 17, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
40 2 0.02
41 75 0.93
42 4 0.05
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGCCCCTGAGCATTAGCGGCGCTTTATC
Found at i:739889 original size:40 final size:40
Alignment explanation
Indices: 739858--739935 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 40
739848 GATTTGTGTC
* *
739858 CACGTAAGC-AAATCGCGCTGACGTGGACGCGATGTTCTGA
1 CACGTAACCGAAATCGCCCTGACGTGGACGCGAT-TTCTGA
* *
739898 CACGTACCCTGACATCGCCCTGACGTGGACGCGATTTC
1 CACGTAACC-GAAATCGCCCTGACGTGGACGCGATTTC
739936 GCGGAAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 7 0.22
41 3 0.09
42 22 0.69
ACGTcount: A:0.22, C:0.31, G:0.27, T:0.21
Consensus pattern (40 bp):
CACGTAACCGAAATCGCCCTGACGTGGACGCGATTTCTGA
Found at i:741644 original size:24 final size:25
Alignment explanation
Indices: 741591--741641 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
741581 ATTGTAAATC
*
741591 AATAAATATATGTACAAAAATTTAA
1 AATAAATATATATACAAAAATTTAA
741616 AATAAATA-ATATACAAGAAATTTAA
1 AATAAATATATATACAA-AAATTTAA
741641 A
1 A
741642 TAAGCAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (25 bp):
AATAAATATATATACAAAAATTTAA
Found at i:745290 original size:20 final size:19
Alignment explanation
Indices: 745267--745328 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
745257 TTTCTAGAAG
745267 TTTTAACTATTTTTTTATAA
1 TTTTAACTA-TTTTTTATAA
*
745287 TTTTAA--ATTTTTTAGAA
1 TTTTAACTATTTTTTATAA
* *
745304 -TTTAACTAATCTTTTATAT
1 TTTTAACT-ATTTTTTATAA
745323 TTTTAA
1 TTTTAA
745329 TTTTTCTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 5 0.15
17 9 0.26
18 1 0.03
19 8 0.24
20 11 0.32
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTAACTATTTTTTATAA
Found at i:745299 original size:17 final size:17
Alignment explanation
Indices: 745277--745343 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
745267 TTTTAACTAT
745277 TTTTTTATAATTTTAAA
1 TTTTTTATAATTTTAAA
* *
745294 TTTTTTAGAATTTAACTAA
1 TTTTTTATAATTTTA--AA
* *
745313 TCTTTTAT-ATTTTTAA
1 TTTTTTATAATTTTAAA
*
745329 TTTTTCTATACTTTT
1 TTTTT-TATAATTTT
745344 TTGGATATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
16 6 0.16
17 16 0.42
18 8 0.21
19 8 0.21
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.64
Consensus pattern (17 bp):
TTTTTTATAATTTTAAA
Done.