Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 3 of 45
Found at i:455370 original size:18 final size:19
Alignment explanation
Indices: 455344--455384 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
455334 AATAAAATTT
*
455344 AATATAAATTATTAA-ATA
1 AATAAAAATTATTAATATA
*
455362 AATAAAAATTTTTAATATA
1 AATAAAAATTATTAATATA
455381 AATA
1 AATA
455385 TGATATTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAAAAATTATTAATATA
Found at i:456740 original size:12 final size:13
Alignment explanation
Indices: 456723--456755 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
456713 TAATAATTCC
456723 TCTTTCTTTCT-T
1 TCTTTCTTTCTCT
456735 TCTTTCTTTCTCT
1 TCTTTCTTTCTCT
456748 TCTCTTCT
1 TCT-TTCT
456756 CTTCCGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 4 0.21
14 4 0.21
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
TCTTTCTTTCTCT
Found at i:457041 original size:3 final size:3
Alignment explanation
Indices: 457035--457066 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
457025 TGCAATCTTC
457035 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
457067 TAAAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:457473 original size:15 final size:14
Alignment explanation
Indices: 457455--457491 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
457445 AAATAATTAG
457455 AAGAAAAAAAAAAGA
1 AAGAAAAAAAAAA-A
457470 AAGAAAGAAAAAAAA
1 AAGAAA-AAAAAAAA
457485 AAGAAAA
1 AAGAAAA
457492 GAGTTGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 13 0.62
16 7 0.33
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAAAAA
Found at i:458928 original size:21 final size:21
Alignment explanation
Indices: 458902--458948 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
458892 TAGATTGAGG
*
458902 GTGGTATTTTCACATGGGAAA
1 GTGGTATTTTCACATGAGAAA
*
458923 GTGGTATTTTGACATGAGAAA
1 GTGGTATTTTCACATGAGAAA
458944 GTGGT
1 GTGGT
458949 TTACAAACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.06, G:0.32, T:0.34
Consensus pattern (21 bp):
GTGGTATTTTCACATGAGAAA
Found at i:460913 original size:18 final size:18
Alignment explanation
Indices: 460875--460913 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
460865 AACTATAAAA
*
460875 TAAATTTTTATCAAATGT
1 TAAATTTTTATCAAATAT
* *
460893 TAAATTTTTATTAATTAT
1 TAAATTTTTATCAAATAT
460911 TAA
1 TAA
460914 TTATCATATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TAAATTTTTATCAAATAT
Found at i:461033 original size:21 final size:21
Alignment explanation
Indices: 460986--461040 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
460976 AATTTAAATG
* **
460986 CTAAAATAATAAAAATATTTAA
1 CTAAAA-AATAAAAAAATCAAA
*
461008 GTAAAAAATAAAAAAATCAAA
1 CTAAAAAATAAAAAAATCAAA
*
461029 CTAAAAACTAAA
1 CTAAAAAATAAA
461041 TTATAAAAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (21 bp):
CTAAAAAATAAAAAAATCAAA
Found at i:462415 original size:3 final size:3
Alignment explanation
Indices: 462407--462439 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
462397 TGTTGGAAAT
462407 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
462440 AATCATCAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:475992 original size:45 final size:45
Alignment explanation
Indices: 475925--476024 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 45
475915 AAGAGGAGTA
** * *
475925 AATGGTCCTGTACCAATGATGCCTAATCTCCCTTCACCACGAATG
1 AATGGTCCTGTACCAACAATGCCCAATCTCCCATCACCACGAATG
* * * * *
475970 AATGGTCCTGTTCCACCAATGCCCAATCTTCCATCTCCACGGATG
1 AATGGTCCTGTACCAACAATGCCCAATCTCCCATCACCACGAATG
*
476015 AATGGGCCTG
1 AATGGTCCTG
476025 CCCTGTTACC
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (45 bp):
AATGGTCCTGTACCAACAATGCCCAATCTCCCATCACCACGAATG
Found at i:478666 original size:18 final size:18
Alignment explanation
Indices: 478630--478663 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
478620 TATATTTTTA
478630 TATTTATTTTATATTAAT
1 TATTTATTTTATATTAAT
*
478648 TATTT-TTTTATGTTAA
1 TATTTATTTTATATTAA
478664 ATTTATAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTTATTTTATATTAAT
Found at i:478668 original size:28 final size:27
Alignment explanation
Indices: 478616--478670 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
478606 GTATATAAAT
*
478616 TTAATATATTTTTATATTTATTTTATA
1 TTAATATATTTTTATATTTAATTTATA
*
478643 TTAAT-TATTTTTTTATGTTAAATTTATA
1 TTAATATATTTTTATAT-TT-AATTTATA
478671 ATCGAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.42
27 7 0.29
28 7 0.29
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (27 bp):
TTAATATATTTTTATATTTAATTTATA
Found at i:479752 original size:13 final size:13
Alignment explanation
Indices: 479734--479771 Score: 53
Period size: 11 Copynumber: 3.1 Consensus size: 13
479724 TTATTTATCA
479734 ATTTAAAATATAT
1 ATTTAAAATATAT
479747 ATTT--AATATAT
1 ATTTAAAATATAT
*
479758 ATTTAAAATCTAT
1 ATTTAAAATATAT
479771 A
1 A
479772 CTCAATCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 11 0.50
13 11 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTAAAATATAT
Found at i:484322 original size:2 final size:2
Alignment explanation
Indices: 484315--484345 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
484305 TTTGTTTTGT
484315 TA 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 T
484346 TTATTAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:485549 original size:5 final size:5
Alignment explanation
Indices: 485534--485597 Score: 51
Period size: 5 Copynumber: 12.4 Consensus size: 5
485524 ATATGTTATG
* * *
485534 TAATA TAAATA TAATA TAAAA TAATA TAGTA TTAA-A -AAAA TAATA TAAATA
1 TAATA T-AATA TAATA TAATA TAATA TAATA -TAATA TAATA TAATA T-AATA
485585 TAATA TGAATA TA
1 TAATA T-AATA TA
485598 TAAATTTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 28 0.58
6 17 0.35
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (5 bp):
TAATA
Found at i:485550 original size:11 final size:11
Alignment explanation
Indices: 485534--485597 Score: 66
Period size: 11 Copynumber: 6.2 Consensus size: 11
485524 ATATGTTATG
485534 TAATATAAATA
1 TAATATAAATA
485545 TAATATAAA-A
1 TAATATAAATA
*
485555 TAATAT-AGTA
1 TAATATAAATA
485565 TTAA-A-AAA-A
1 -TAATATAAATA
485574 TAATATAAATA
1 TAATATAAATA
*
485585 TAATATGAATA
1 TAATATAAATA
485596 TA
1 TA
485598 TAAATTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
8 3 0.07
9 3 0.07
10 13 0.30
11 25 0.57
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (11 bp):
TAATATAAATA
Found at i:485653 original size:13 final size:14
Alignment explanation
Indices: 485617--485655 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
485607 AATGTATTAA
*
485617 AATTTATAAAATAT
1 AATTTTTAAAATAT
*
485631 AATATTTAAAATAT
1 AATTTTTAAAATAT
485645 -ATTTTTAAAAT
1 AATTTTTAAAAT
485656 TAAAAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AATTTTTAAAATAT
Found at i:486515 original size:2 final size:2
Alignment explanation
Indices: 486508--486533 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
486498 CCAAAAGTGG
486508 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
486534 CGTGATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:490202 original size:7 final size:7
Alignment explanation
Indices: 490186--490214 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
490176 TCGATTTGTT
490186 AAGA-CC
1 AAGATCC
490192 AAGATCC
1 AAGATCC
490199 AAGATCC
1 AAGATCC
490206 AAGATCC
1 AAGATCC
490213 AA
1 AA
490215 TTCCACACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.48, C:0.28, G:0.14, T:0.10
Consensus pattern (7 bp):
AAGATCC
Found at i:491485 original size:19 final size:21
Alignment explanation
Indices: 491448--491486 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
491438 ATTTTTTTCT
*
491448 TTTTGGGTTTTAATATTTCCA
1 TTTTGGGTTTAAATATTTCCA
491469 TTTTGGG-TTAAAT-TTTCC
1 TTTTGGGTTTAAATATTTCC
491487 TTATATTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.18, C:0.10, G:0.15, T:0.56
Consensus pattern (21 bp):
TTTTGGGTTTAAATATTTCCA
Found at i:495627 original size:2 final size:2
Alignment explanation
Indices: 495620--495660 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
495610 CTTCAAGGCA
495620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
495661 ATTCACCAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:496204 original size:12 final size:12
Alignment explanation
Indices: 496187--496225 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
496177 TATCTGATTA
496187 TAATTATATTTG
1 TAATTATATTTG
* *
496199 TAATTATAATTA
1 TAATTATATTTG
496211 TAATTATATTTG
1 TAATTATATTTG
496223 TAA
1 TAA
496226 CATTTATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (12 bp):
TAATTATATTTG
Found at i:496238 original size:6 final size:6
Alignment explanation
Indices: 496183--496218 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
496173 ATTTTATCTG
* *
496183 ATTATA ATTATA TTTGTA ATTATA ATTATA ATTATA
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA
496219 TTTGTAACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
ATTATA
Found at i:499916 original size:24 final size:24
Alignment explanation
Indices: 499884--499937 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
499874 TGATCATGGA
*
499884 TTAACTGTCTTTTAAACTCAAATG
1 TTAAATGTCTTTTAAACTCAAATG
499908 TTAAATGTCTTTTAAACTCAAATG
1 TTAAATGTCTTTTAAACTCAAATG
*
499932 CTAAAT
1 TTAAAT
499938 TCAATGGGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (24 bp):
TTAAATGTCTTTTAAACTCAAATG
Found at i:505673 original size:23 final size:23
Alignment explanation
Indices: 505647--505693 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
505637 CTATTCGAGG
505647 TATTAATTTGTTACCACTACTTT
1 TATTAATTTGTTACCACTACTTT
505670 TATTAATTTGTTACCACTACTTT
1 TATTAATTTGTTACCACTACTTT
505693 T
1 T
505694 GTTACTACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.04, T:0.53
Consensus pattern (23 bp):
TATTAATTTGTTACCACTACTTT
Found at i:505754 original size:2 final size:2
Alignment explanation
Indices: 505742--505772 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
505732 ATTCTAAGGA
*
505742 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
505773 AGTAGAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:507238 original size:5 final size:5
Alignment explanation
Indices: 507225--507255 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
507215 TTACTTCAGG
*
507225 AAAGC AAAGA AAAGA AAAGA AAAGA AAAGA A
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA A
507256 GAAAACAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:508145 original size:47 final size:47
Alignment explanation
Indices: 508092--508188 Score: 176
Period size: 47 Copynumber: 2.1 Consensus size: 47
508082 TGAACTTATC
*
508092 AGTTCAAAGGCACTAAATAAAAGGAAAAGACAAATAGATAAAAGTGG
1 AGTTCAAAGGCACTAAAGAAAAGGAAAAGACAAATAGATAAAAGTGG
*
508139 AGTTCAAAGGCACTAAAGAAAAGGAAAAGATAAATAGATAAAAGTGG
1 AGTTCAAAGGCACTAAAGAAAAGGAAAAGACAAATAGATAAAAGTGG
508186 AGT
1 AGT
508189 GGTGATTACA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.55, C:0.07, G:0.23, T:0.15
Consensus pattern (47 bp):
AGTTCAAAGGCACTAAAGAAAAGGAAAAGACAAATAGATAAAAGTGG
Found at i:510024 original size:17 final size:17
Alignment explanation
Indices: 510008--510048 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
509998 TTTTTATTAT
510008 TAAAATAA-TAATTTTA
1 TAAAATAATTAATTTTA
510024 TAAAATTAATTTAATTTTA
1 TAAAA-TAA-TTAATTTTA
510043 TAAAAT
1 TAAAAT
510049 TTTTATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.23
17 3 0.14
18 1 0.05
19 13 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAATAATTAATTTTA
Found at i:510361 original size:5 final size:5
Alignment explanation
Indices: 510351--510376 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
510341 AATGTACCTC
510351 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
510377 AACATGTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:511181 original size:21 final size:23
Alignment explanation
Indices: 511155--511197 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
511145 AATAAAAATA
511155 TAATAAA-A-AATATGATATATT
1 TAATAAACATAATATGATATATT
*
511176 TAATAAACATAATATTATATAT
1 TAATAAACATAATATGATATAT
511198 AAATATGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 1 0.05
23 11 0.58
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TAATAAACATAATATGATATATT
Found at i:511939 original size:2 final size:2
Alignment explanation
Indices: 511932--511962 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
511922 TTCAATTATT
511932 TA 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 T
511963 TAAAAAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:512620 original size:20 final size:20
Alignment explanation
Indices: 512597--512648 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
512587 TTATATTTAA
512597 TATTTATTTAAAATTAAAAT
1 TATTTATTTAAAATTAAAAT
* *
512617 TATTTATTCAATATTTAAAAT
1 TATTTATTTAA-AATTAAAAT
*
512638 T-TTTAATTAAA
1 TATTTATTTAAA
512649 TAATTCAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 17 0.63
21 9 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTTATTTAAAATTAAAAT
Found at i:512650 original size:21 final size:21
Alignment explanation
Indices: 512597--512650 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
512587 TTATATTTAA
512597 TATTTATTTAAA-A-TTAAAAT
1 TATTTA-TTAAATATTTAAAAT
*
512617 TATTTATTCAATATTTAAAAT
1 TATTTATTAAATATTTAAAAT
512638 T-TTTAATTAAATA
1 TATTT-ATTAAATA
512651 ATTCAATCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 4 0.14
20 10 0.34
21 15 0.52
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTATTAAATATTTAAAAT
Found at i:512898 original size:12 final size:11
Alignment explanation
Indices: 512877--512923 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
512867 TAGGTATAGA
512877 TTAAAATTATT
1 TTAAAATTATT
512888 TTAATAATTATT
1 TTAA-AATTATT
*
512900 TT-ACATTATT
1 TTAAAATTATT
* *
512910 TTACATTTATT
1 TTAAAATTATT
512921 TTA
1 TTA
512924 TTTTTATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
10 8 0.27
11 13 0.43
12 9 0.30
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (11 bp):
TTAAAATTATT
Found at i:512931 original size:11 final size:11
Alignment explanation
Indices: 512895--512923 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
512885 ATTTTAATAA
512895 TTATTTTACA-
1 TTATTTTACAT
512905 TTATTTTACAT
1 TTATTTTACAT
512916 TTATTTTA
1 TTATTTTA
512924 TTTTTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATTTTACAT
Found at i:513351 original size:2 final size:2
Alignment explanation
Indices: 513344--513372 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
513334 ATCAGGACAG
513344 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 T
513373 TAGCTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:519252 original size:33 final size:35
Alignment explanation
Indices: 519174--519253 Score: 83
Period size: 33 Copynumber: 2.3 Consensus size: 35
519164 ATTTGAAGAT
* *
519174 AAAAATAATAAATACTAATAATTGTATATTATATAA
1 AAAAATAA-AAATACAAAAAATTGTATATTATATAA
** * *
519210 CTAATTAAAAATA-AAAAAATT-TATATTATTTAA
1 AAAAATAAAAATACAAAAAATTGTATATTATATAA
519243 AAAAATAAAAA
1 AAAAATAAAAA
519254 ATATATGTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
33 19 0.54
34 6 0.17
35 5 0.14
36 5 0.14
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (35 bp):
AAAAATAAAAATACAAAAAATTGTATATTATATAA
Found at i:519289 original size:18 final size:17
Alignment explanation
Indices: 519268--519315 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
519258 ATGTTAATAT
*
519268 ATAAATTTATTCATGCAC
1 ATAAATTTATT-ATGAAC
* *
519286 ATAAGATATAATATGAAC
1 ATAA-ATTTATTATGAAC
519304 ATAAATTTATTA
1 ATAAATTTATTA
519316 AAATTAAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 6 0.25
18 13 0.54
19 5 0.21
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (17 bp):
ATAAATTTATTATGAAC
Found at i:519467 original size:3 final size:3
Alignment explanation
Indices: 519459--519493 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
519449 TGAATCTCGT
519459 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
519494 GTAATATTAT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:519544 original size:16 final size:17
Alignment explanation
Indices: 519525--519559 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
519515 AATAATTTTA
*
519525 ATTTTTTATAA-TAAAT
1 ATTTATTATAATTAAAT
519541 ATTTATTATAATTAAAT
1 ATTTATTATAATTAAAT
519558 AT
1 AT
519560 AATAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTATTATAATTAAAT
Found at i:524124 original size:29 final size:28
Alignment explanation
Indices: 524092--524179 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 28
524082 ATAGAACGAG
*
524092 AAAAATAATTAAAATATTATATGATATAA
1 AAAAATAATTAAAATATTATAT-AAATAA
*
524121 AAAAATAA-TATAAATATTATATAAATAT
1 AAAAATAATTA-AAATATTATATAAATAA
* * *
524149 ATAAATAAATTAAAATTTTTTAT-AATAA
1 AAAAAT-AATTAAAATATTATATAAATAA
524177 AAA
1 AAA
524180 TTATTAATGT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
28 17 0.35
29 30 0.61
30 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (28 bp):
AAAAATAATTAAAATATTATATAAATAA
Found at i:524142 original size:24 final size:23
Alignment explanation
Indices: 524110--524158 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
524100 TTAAAATATT
524110 ATATGATATAAAAAAATAATATAA
1 ATATGATATAAAAAAATAA-ATAA
* * *
524134 ATATTATATAAATATATAAATAA
1 ATATGATATAAAAAAATAAATAA
524157 AT
1 AT
524159 TAAAATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
ATATGATATAAAAAAATAAATAA
Found at i:524669 original size:2 final size:2
Alignment explanation
Indices: 524655--524691 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
524645 ACAATATTCG
*
524655 TC TC TC -C TA TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
524692 ATTAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:528524 original size:2 final size:2
Alignment explanation
Indices: 528517--528546 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
528507 GAAATTTAAA
*
528517 AT AT AT AT GT 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 AT
528547 CCGATTAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:529090 original size:17 final size:17
Alignment explanation
Indices: 529051--529084 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
529041 AACGTGATTC
*
529051 AATATAAATTATTATTT
1 AATAAAAATTATTATTT
529068 AATAAAAATTATT-TTT
1 AATAAAAATTATTATTT
529084 A
1 A
529085 TTTAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATAAAAATTATTATTT
Found at i:529838 original size:2 final size:2
Alignment explanation
Indices: 529831--529855 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
529821 TTAAACTACC
529831 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
529856 GTAATTATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:530801 original size:31 final size:30
Alignment explanation
Indices: 530753--530826 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
530743 TGGTTTAAAT
*
530753 AAATT-TTATTATAATTTAAATTA-AATTAAGA
1 AAATTATT-TTATAATTTAAAATATAATT-A-A
* *
530784 AAATTATTTTATTATTTAAAATATTATTAA
1 AAATTATTTTATAATTTAAAATATAATTAA
530814 AAATTATTTTATA
1 AAATTATTTTATA
530827 TTAATATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 13 0.35
31 19 0.51
32 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (30 bp):
AAATTATTTTATAATTTAAAATATAATTAA
Found at i:530849 original size:22 final size:20
Alignment explanation
Indices: 530818--530857 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
530808 TATTAAAAAT
530818 TATTTTATATTAATATTTATA
1 TATTTTATATTAA-ATTTATA
530839 TATTATTATATTAAATTTA
1 TATT-TTATATTAAATTTA
530858 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTTATATTAAATTTATA
Found at i:533628 original size:5 final size:5
Alignment explanation
Indices: 533616--533659 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
533606 ACAAATTATA
* * * *
533616 TGCCC TTCCC TTCCC TGCCC TGCCC TGCCC TGCAC TGCAC TGCC
1 TGCCC TGCCC TGCCC TGCCC TGCCC TGCCC TGCCC TGCCC TGCC
533660 GTGAATTGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.05, C:0.55, G:0.16, T:0.25
Consensus pattern (5 bp):
TGCCC
Found at i:536316 original size:6 final size:6
Alignment explanation
Indices: 536305--536345 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
536295 CGTACGGCTA
* *
536305 TATATG TATATG TATATG TATATG TATATA TATATA TATAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TATAT
536346 ATAAACACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:536336 original size:2 final size:2
Alignment explanation
Indices: 536303--536348 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
536293 AACGTACGGC
* * * *
536303 TA TA TA TG TA TA TG TA TA TG TA TA TG TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
536345 TA TA
1 TA TA
536349 AACACACCCC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (2 bp):
TA
Found at i:542341 original size:2 final size:2
Alignment explanation
Indices: 542334--542366 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
542324 TGACCCAATT
*
542334 TA TA TA TA CA 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 T
542367 TTGTATAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:543684 original size:2 final size:2
Alignment explanation
Indices: 543679--543720 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
543669 ATATATATAG
*
543679 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AT AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
543721 TTACTTCTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:544392 original size:12 final size:13
Alignment explanation
Indices: 544372--544434 Score: 57
Period size: 12 Copynumber: 5.3 Consensus size: 13
544362 AATTTGTTAT
544372 AAATATTATGATA
1 AAATATTATGATA
544385 AAAT-TTATG--A
1 AAATATTATGATA
*
544395 AAAT-TTATTAT-
1 AAATATTATGATA
544406 AAATATTATGAT-
1 AAATATTATGATA
* *
544418 AAATACTACGATA
1 AAATATTATGATA
544431 AAAT
1 AAAT
544435 CTATGGTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
10 9 0.21
11 4 0.10
12 21 0.50
13 8 0.19
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.38
Consensus pattern (13 bp):
AAATATTATGATA
Found at i:544399 original size:10 final size:11
Alignment explanation
Indices: 544360--544421 Score: 63
Period size: 12 Copynumber: 5.5 Consensus size: 11
544350 ATTTAAATTT
* *
544360 TAAATTTGTTA
1 TAAATTTATGA
544371 TAAATATTATGA
1 TAAAT-TTATGA
544383 TAAAATTTATGA
1 T-AAATTTATGA
*
544395 -AAATTTATTA
1 TAAATTTATGA
544405 TAAATATTATGA
1 TAAAT-TTATGA
544417 TAAAT
1 TAAAT
544422 ACTACGATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
10 9 0.21
11 9 0.21
12 21 0.49
13 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (11 bp):
TAAATTTATGA
Found at i:544407 original size:22 final size:24
Alignment explanation
Indices: 544370--544432 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 24
544360 TAAATTTGTT
544370 ATAAATATTATGATAAA-ATTTATG
1 ATAAATATTATGATAAATA-TTATG
*
544394 A-AAAT-TTATTATAAATATTATG
1 ATAAATATTATGATAAATATTATG
* *
544416 ATAAATACTACGATAAA
1 ATAAATATTATGATAAA
544433 ATCTATGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
22 15 0.47
23 9 0.28
24 8 0.25
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.38
Consensus pattern (24 bp):
ATAAATATTATGATAAATATTATG
Found at i:545263 original size:23 final size:23
Alignment explanation
Indices: 545211--545265 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
545201 TGAAATATAA
* **
545211 ATATTTT-TAAATTTTTTAAATT
1 ATATTTTATATATTTTAAAAATT
545233 -TATTTTATATATTTTAAAAATT
1 ATATTTTATATATTTTAAAAATT
545255 ATATTTTATAT
1 ATATTTTATAT
545266 CTATATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.21
22 12 0.43
23 10 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATATTTTATATATTTTAAAAATT
Found at i:545265 original size:21 final size:21
Alignment explanation
Indices: 545215--545265 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
545205 ATATAAATAT
* * *
545215 TTTTAAAT-TTTTTAAATTTA
1 TTTTATATATTTTAAAAATTA
545235 TTTTATATATTTTAAAAATTA
1 TTTTATATATTTTAAAAATTA
545256 TATTT-TATAT
1 T-TTTATATAT
545266 CTATATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 7 0.27
21 16 0.62
22 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTATATATTTTAAAAATTA
Found at i:545294 original size:13 final size:13
Alignment explanation
Indices: 545254--545313 Score: 61
Period size: 13 Copynumber: 4.7 Consensus size: 13
545244 TTTTAAAAAT
* *
545254 TATATTTTATATC
1 TATATTTAATATA
545267 TATATTTATATATA
1 TATATTTA-ATATA
545281 TATATTT-A-ATA
1 TATATTTAATATA
*
545292 TATATTAAATATA
1 TATATTTAATATA
*
545305 AATATTTAA
1 TATATTTAA
545314 AAGAATAAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 9 0.23
12 2 0.05
13 17 0.44
14 11 0.28
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATTTAATATA
Found at i:545309 original size:24 final size:23
Alignment explanation
Indices: 545267--545313 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
545257 ATTTTATATC
* *
545267 TATATTTATATATATATATTTAA
1 TATATTTAAATATAAATATTTAA
545290 TATATATTAAATATAAATATTTAA
1 TATAT-TTAAATATAAATATTTAA
545314 AAGAATAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATATTTAAATATAAATATTTAA
Found at i:546755 original size:3 final size:3
Alignment explanation
Indices: 546747--546779 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
546737 ATAATTACAA
546747 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
546780 AAAATAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:546909 original size:12 final size:13
Alignment explanation
Indices: 546894--546923 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
546884 ATATTTTTAA
546894 AATATTTATA-TT
1 AATATTTATATTT
546906 AATATTTATATTT
1 AATATTTATATTT
546919 AATAT
1 AATAT
546924 ATTTAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:547002 original size:15 final size:15
Alignment explanation
Indices: 546982--547020 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
546972 TTTTAAAATT
546982 TTAAATATATTTATA
1 TTAAATATATTTATA
546997 TTAAATATATATTTATA
1 TT-AA-ATATATTTATA
*
547014 TTTAATA
1 TTAAATA
547021 CACCTATCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.24
16 3 0.14
17 13 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAAATATATTTATA
Found at i:547006 original size:17 final size:17
Alignment explanation
Indices: 546986--547020 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
546976 AAAATTTTAA
546986 ATATATTTATATTAAAT
1 ATATATTTATATTAAAT
*
547003 ATATATTTATATTTAAT
1 ATATATTTATATTAAAT
547020 A
1 A
547021 CACCTATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATATTTATATTAAAT
Found at i:549655 original size:2 final size:2
Alignment explanation
Indices: 549648--549690 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
549638 GCTCACCCTC
549648 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
549690 C
1 C
549691 AAATTAACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:551301 original size:2 final size:2
Alignment explanation
Indices: 551294--551329 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
551284 CTCAGACAAA
551294 AT AT AT AT 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 AT AT AT AT
551330 CTAAAGACTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:552449 original size:29 final size:29
Alignment explanation
Indices: 552391--552454 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
552381 AGAATTGTAA
*
552391 TGTGAACCAAGTTCTAATTGGAGTAGAAC
1 TGTGAACCAAGTTCTAATTGGAGGAGAAC
*
552420 TGTGGACCAAGTTCTAATTGGAGG-GAAAC
1 TGTGAACCAAGTTCTAATTGGAGGAG-AAC
552449 TGTGAA
1 TGTGAA
552455 AGTGTGAGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.27
Consensus pattern (29 bp):
TGTGAACCAAGTTCTAATTGGAGGAGAAC
Found at i:552673 original size:24 final size:26
Alignment explanation
Indices: 552620--552674 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
552610 TGTTTTTCTT
**
552620 TTTTTGGTTTTAGGGTTTTTAATTA-
1 TTTTTGGTTTTAGGGTTTTTAACAAC
*
552645 TTTTTTGTTTTA-GGTTTTTAACAAC
1 TTTTTGGTTTTAGGGTTTTTAACAAC
552670 TTTTT
1 TTTTT
552675 AATTGCACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.16, C:0.04, G:0.15, T:0.65
Consensus pattern (26 bp):
TTTTTGGTTTTAGGGTTTTTAACAAC
Found at i:552673 original size:25 final size:26
Alignment explanation
Indices: 552619--552674 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
552609 TTGTTTTTCT
**
552619 TTTTTTGGTTTTAGGGTTTTTAATTA
1 TTTTTTGGTTTTAGGGTTTTTAACAA
552645 TTTTTT-GTTTTA-GGTTTTTAACAA
1 TTTTTTGGTTTTAGGGTTTTTAACAA
*
552669 CTTTTT
1 TTTTTT
552675 AATTGCACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 15 0.56
25 6 0.22
26 6 0.22
ACGTcount: A:0.16, C:0.04, G:0.14, T:0.66
Consensus pattern (26 bp):
TTTTTTGGTTTTAGGGTTTTTAACAA
Found at i:557554 original size:2 final size:2
Alignment explanation
Indices: 557547--557578 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
557537 CCAATTGAAG
557547 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
557579 CCCGACATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:558086 original size:57 final size:57
Alignment explanation
Indices: 557984--558103 Score: 136
Period size: 57 Copynumber: 2.1 Consensus size: 57
557974 CTACTAAAAG
* * *
557984 TAAACAAAATACACCACGATAAAAAAAATATGAATGTAATAAAATT-TATAAAATTT
1 TAAAAAAAATACACCACGATAAAAAAAACATGAATATAATAAAATTATATAAAATTT
* ** * *
558040 ATAAAAAAAATACACCACGATAAAATATGCATGTAATAT-ATTAAATTATATAATATTT
1 -TAAAAAAAATACACCACGATAAAAAAAACATG-AATATAATAAAATTATATAAAATTT
558098 TAAAAA
1 TAAAAA
558104 TATAATATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
57 40 0.75
58 13 0.25
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.29
Consensus pattern (57 bp):
TAAAAAAAATACACCACGATAAAAAAAACATGAATATAATAAAATTATATAAAATTT
Found at i:558095 original size:17 final size:15
Alignment explanation
Indices: 558073--558120 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
558063 AATATGCATG
*
558073 TAATATATTAAATTATA
1 TAATAT-TTAAA-AATA
558090 TAATATTTTAAAAATA
1 TAATA-TTTAAAAATA
*
558106 TAATATTTAATAATA
1 TAATATTTAAAAATA
558121 AAAAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 9 0.32
16 8 0.29
17 10 0.36
18 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAATATTTAAAAATA
Found at i:558108 original size:16 final size:17
Alignment explanation
Indices: 558073--558113 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
558063 AATATGCATG
* *
558073 TAATATATTAAATTATA
1 TAATATTTTAAATAATA
558090 TAATATTTTAAA-AATA
1 TAATATTTTAAATAATA
558106 TAATATTT
1 TAATATTT
558114 AATAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATTTTAAATAATA
Found at i:558116 original size:23 final size:22
Alignment explanation
Indices: 558090--558155 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 22
558080 TTAAATTATA
558090 TAATATTTTAAAAATATAATATT
1 TAATATTTTAAAAATATAATA-T
* *
558113 TAATA--ATAAAAAAATAATAT
1 TAATATTTTAAAAATATAATAT
* *
558133 AAATATGATTAAAAAATATAATA
1 TAATAT--TTTAAAAATATAATA
558156 ACAAAATCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 5 0.15
21 12 0.36
23 5 0.15
24 11 0.33
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
TAATATTTTAAAAATATAATAT
Found at i:559939 original size:14 final size:13
Alignment explanation
Indices: 559904--559949 Score: 60
Period size: 14 Copynumber: 3.6 Consensus size: 13
559894 TTAATTAGAA
559904 ATTA-TTTAAT-T
1 ATTATTTTAATAT
559915 ATTATTTTAATAT
1 ATTATTTTAATAT
*
559928 TTTATGTTTAATAT
1 ATTAT-TTTAATAT
559942 ATTATTTT
1 ATTATTTT
559950 TATTAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 4 0.13
12 6 0.20
13 8 0.27
14 12 0.40
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (13 bp):
ATTATTTTAATAT
Found at i:563618 original size:15 final size:14
Alignment explanation
Indices: 563594--563623 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
563584 TTATTTACAT
563594 AAATTAATATAATA
1 AAATTAATATAATA
563608 AAATATAATATAATA
1 AAAT-TAATATAATA
563623 A
1 A
563624 TAGTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATTAATATAATA
Found at i:563734 original size:18 final size:18
Alignment explanation
Indices: 563665--563739 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 18
563655 CATATAATTA
*
563665 AATATTTTTTATT-ATTT
1 AATATTTTTTATTAATAT
* *
563682 CAAAATTTTTAATTAATA-
1 -AATATTTTTTATTAATAT
* * **
563700 AATATATATTAAAAATAT
1 AATATTTTTTATTAATAT
563718 AATATTTTTTATTAATAT
1 AATATTTTTTATTAATAT
563736 AATA
1 AATA
563740 AAATATTAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
17 11 0.26
18 29 0.69
19 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (18 bp):
AATATTTTTTATTAATAT
Found at i:563764 original size:39 final size:35
Alignment explanation
Indices: 563678--563764 Score: 93
Period size: 35 Copynumber: 2.3 Consensus size: 35
563668 ATTTTTTATT
*
563678 ATTTCAAAATTTTTAATTAATAAATATATATTAAAA
1 ATTT-AAAATTTTTAATTAATAAATAAATATTAAAA
* * *
563714 ATATAATATTTTTTATTAATATAATAAAATATTAAATTA
1 ATTTAAAATTTTTAATTAATA-AAT-AAATATTAAA--A
563753 ATTTAAAATTTT
1 ATTTAAAATTTT
563765 ATATACACAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
35 15 0.37
36 6 0.15
37 9 0.22
39 11 0.27
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (35 bp):
ATTTAAAATTTTTAATTAATAAATAAATATTAAAA
Found at i:564886 original size:117 final size:120
Alignment explanation
Indices: 564672--564910 Score: 421
Period size: 117 Copynumber: 2.0 Consensus size: 120
564662 TATTAAATAG
564672 TAGCATGAAAATATTATCTTAATAGCTTTTAATAGAGTTTCTTTTTTTAAAAAAAAAAAAATTAA
1 TAGCATGAAAATATTATCTTAATAGCTTTTAATAGAGTTTCTTTTTTT-AAAAAAAAAAAATTAA
* *
564737 ACTGAAAGAGTGTTTTATGCCCTAATTTACTCAAGAATTCATAAATTAAGTTTGTT
65 ACTAAAAGAGTGATTTATGCCCTAATTTACTCAAGAATTCATAAATTAAGTTTGTT
*
564793 TAGCATGAAAATATTATTTTAATAGCTTTTAATAGAG-TT-TTTTTTT-AAAAAAAAAAATTAAA
1 TAGCATGAAAATATTATCTTAATAGCTTTTAATAGAGTTTCTTTTTTTAAAAAAAAAAAATTAAA
564855 CTAAAAGAGTGATTTATGCCCTAATTTACTCAAGAATTCATAAATTAAGTTTGTT
66 CTAAAAGAGTGATTTATGCCCTAATTTACTCAAGAATTCATAAATTAAGTTTGTT
564910 T
1 T
564911 CAATAAACTA
Statistics
Matches: 115, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
117 70 0.61
119 7 0.06
120 2 0.02
121 36 0.31
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.40
Consensus pattern (120 bp):
TAGCATGAAAATATTATCTTAATAGCTTTTAATAGAGTTTCTTTTTTTAAAAAAAAAAAATTAAA
CTAAAAGAGTGATTTATGCCCTAATTTACTCAAGAATTCATAAATTAAGTTTGTT
Found at i:566454 original size:6 final size:6
Alignment explanation
Indices: 566442--566477 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
566432 AACCCAAACC
*
566442 CCTAAT CCGAAT CCTAAT CCTAAT CCTAAT CCTAAT
1 CCTAAT CCTAAT CCTAAT CCTAAT CCTAAT CCTAAT
566478 AATAATTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.31
Consensus pattern (6 bp):
CCTAAT
Found at i:566483 original size:18 final size:18
Alignment explanation
Indices: 566444--566483 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
566434 CCCAAACCCC
**
566444 TAATCCGAATCCTAATCC
1 TAATCCGAATCCTAATAA
*
566462 TAATCCTAATCCTAATAA
1 TAATCCGAATCCTAATAA
566480 TAAT
1 TAAT
566484 TCCAATACTA
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:0.40, C:0.25, G:0.03, T:0.33
Consensus pattern (18 bp):
TAATCCGAATCCTAATAA
Found at i:571248 original size:17 final size:17
Alignment explanation
Indices: 571211--571261 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
571201 AAATATTTCG
*
571211 AATTAAAT-ATTAATA-
1 AATTAAATAAATAATAT
571226 AA-TAAATAAATAATAT
1 AATTAAATAAATAATAT
571242 AATTAAAATAAA-AATAT
1 AATT-AAATAAATAATAT
571259 AAT
1 AAT
571262 CCAATCAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
14 5 0.16
15 8 0.26
16 2 0.06
17 9 0.29
18 7 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTAAATAAATAATAT
Found at i:576647 original size:3 final size:3
Alignment explanation
Indices: 576639--576667 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
576629 TCGTCAACTG
576639 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
576668 ACTGATACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:578548 original size:28 final size:28
Alignment explanation
Indices: 578508--578562 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
578498 AGGAAAAGTA
578508 ATGTGGAATCAGCTTGGCTGCATCTATG
1 ATGTGGAATCAGCTTGGCTGCATCTATG
578536 ATGTGGAATCAGCTTGGCTGCATCTAT
1 ATGTGGAATCAGCTTGGCTGCATCTAT
578563 CAAAGTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (28 bp):
ATGTGGAATCAGCTTGGCTGCATCTATG
Found at i:585458 original size:20 final size:20
Alignment explanation
Indices: 585433--585470 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
585423 TAATTTATTT
585433 AAATT-ATTATTTAATTAATA
1 AAATTAATT-TTTAATTAATA
585453 AAATTAATTTTTAATTAA
1 AAATTAATTTTTAATTAA
585471 ATTAATCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATTAATTTTTAATTAATA
Found at i:587826 original size:2 final size:2
Alignment explanation
Indices: 587819--587853 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
587809 TGCAGGAGTG
587819 TA TA TA 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
587854 GCAAATTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:587921 original size:58 final size:58
Alignment explanation
Indices: 587825--587945 Score: 224
Period size: 58 Copynumber: 2.1 Consensus size: 58
587815 AGTGTATATA
*
587825 TATATATATATATATATATATATATATATGCAAATTGCTATTAAATAATATCGTTATC
1 TATACATATATATATATATATATATATATGCAAATTGCTATTAAATAATATCGTTATC
*
587883 TATACATATATATATATATATATATATATGCAACTTGCTATTAAATAATATCGTTATC
1 TATACATATATATATATATATATATATATGCAAATTGCTATTAAATAATATCGTTATC
587941 TATAC
1 TATAC
587946 TAATATTAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (58 bp):
TATACATATATATATATATATATATATATGCAAATTGCTATTAAATAATATCGTTATC
Found at i:596560 original size:16 final size:16
Alignment explanation
Indices: 596541--596588 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
596531 TTATTTTATA
596541 TTATAATTATATATTT
1 TTATAATTATATATTT
*
596557 TTATAATTA-ATTTTT
1 TTATAATTATATATTT
* * *
596572 TTAAAAATATTTATTT
1 TTATAATTATATATTT
596588 T
1 T
596589 AATTAAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATAATTATATATTT
Found at i:598382 original size:13 final size:12
Alignment explanation
Indices: 598364--598397 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
598354 TAGAAAAAAC
598364 TTTTATTTCTTGT
1 TTTTATTTCTT-T
598377 TTTTATTTCTTT
1 TTTTATTTCTTT
598389 TTTT-TTTCT
1 TTTTATTTCT
598398 GCCTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.24
12 5 0.24
13 11 0.52
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTTATTTCTTT
Found at i:598833 original size:2 final size:2
Alignment explanation
Indices: 598826--598872 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
598816 ACAAAAATCA
* * * *
598826 AT AT AT AT AT AT AT AT AT -T AC AT AG GT AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
598867 AT AT AT
1 AT AT AT
598873 GAACGAAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:599263 original size:2 final size:2
Alignment explanation
Indices: 599256--599298 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
599246 CCATGTAACC
599256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
599298 T
1 T
599299 TGGTTTAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:601953 original size:2 final size:2
Alignment explanation
Indices: 601946--601982 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
601936 TTAATTAGAC
601946 TA TA TA TA 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 TA T
601983 TAATTGTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:603237 original size:2 final size:2
Alignment explanation
Indices: 603230--603264 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
603220 CTTTCTTTTC
603230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
603265 CCGGTGTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:609296 original size:17 final size:15
Alignment explanation
Indices: 609273--609312 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
609263 GAAAACATTG
*
609273 GAAAAAAAGGAAAGAA
1 GAAAAAAAAGAAA-AA
609289 GAAAAAAAAGAAAAA
1 GAAAAAAAAGAAAAA
*
609304 GAGAAAAAA
1 GAAAAAAAA
609313 TTATATGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAGAAAAA
Found at i:609304 original size:18 final size:16
Alignment explanation
Indices: 609274--609312 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
609264 AAAACATTGG
*
609274 AAAAAAAGGAAAGAAGA
1 AAAAAAAGAAAAG-AGA
609291 AAAAAAAGAAAAAGAGA
1 AAAAAAAG-AAAAGAGA
609308 AAAAA
1 AAAAA
609313 TTATATGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAGAGA
Found at i:610619 original size:39 final size:38
Alignment explanation
Indices: 610558--610638 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 38
610548 TATTATAATG
*
610558 TAAATATTAAAAAATATGTTTTAAAA-TTTATAAAAAAT
1 TAAATATTAAAAAATATATTTTAAAATTTTAT-AAAAAT
* *
610596 TAAATTATTAAATATTATATTTTAAAATTTTATAAAAAT
1 TAAA-TATTAAAAAATATATTTTAAAATTTTATAAAAAT
610635 TAAA
1 TAAA
610639 AAAATATAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 4 0.11
39 29 0.76
40 5 0.13
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (38 bp):
TAAATATTAAAAAATATATTTTAAAATTTTATAAAAAT
Found at i:611797 original size:12 final size:12
Alignment explanation
Indices: 611780--611821 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
611770 AAAAAATAGT
611780 AATATAAAATTA
1 AATATAAAATTA
611792 AATATATAAA-TA
1 AATATA-AAATTA
*
611804 AATATTAAATTTA
1 AATA-TAAAATTA
611817 AATAT
1 AATAT
611822 TTAAATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATAAAATTA
Found at i:611812 original size:25 final size:24
Alignment explanation
Indices: 611780--611827 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
611770 AAAAAATAGT
611780 AATATAAAATTAAATATATAAATA
1 AATATAAAATTAAATATATAAATA
* *
611804 AATATTAAATTTAAATATTTAAAT
1 AATA-TAAAATTAAATATATAAAT
611828 TTATTATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AATATAAAATTAAATATATAAATA
Found at i:612867 original size:15 final size:15
Alignment explanation
Indices: 612847--612877 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
612837 CATCTTCAAC
612847 TGGATCTGTTTTAAA
1 TGGATCTGTTTTAAA
612862 TGGATCTGTTTTAAA
1 TGGATCTGTTTTAAA
612877 T
1 T
612878 AAGATACGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (15 bp):
TGGATCTGTTTTAAA
Found at i:613978 original size:51 final size:51
Alignment explanation
Indices: 613919--614030 Score: 140
Period size: 51 Copynumber: 2.2 Consensus size: 51
613909 AACATAATTT
*
613919 TTTTTAATTTAAA-TCAATTAGATTAA-A-ATAAATATTTAATAATAAAAATAA
1 TTTTTAATTTAAATTCAATTAGA-AAATATATAAAT-TTTAAT-ATAAAAATAA
* *
613970 TTTTTAATTTAAATTTAATTATAAAATATATAAATTTTAATATAAAAATAA
1 TTTTTAATTTAAATTCAATTAGAAAATATATAAATTTTAATATAAAAATAA
*
614021 TTTTTTATTT
1 TTTTTAATTT
614031 TTATTAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
51 34 0.63
52 14 0.26
53 6 0.11
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
TTTTTAATTTAAATTCAATTAGAAAATATATAAATTTTAATATAAAAATAA
Found at i:616265 original size:54 final size:54
Alignment explanation
Indices: 616183--616290 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
616173 GTGTGTATGA
*
616183 GATGTGCAATTAAAATCTAAGCTTTGAATGTTTTGCCATGGCACTTGTGAGCAC
1 GATGTGCAATTAAAACCTAAGCTTTGAATGTTTTGCCATGGCACTTGTGAGCAC
*
616237 GATGTGCAATTAAAACCTAAGCTTTGAATGTTTTGCCATGGCATTTGTGAGCAC
1 GATGTGCAATTAAAACCTAAGCTTTGAATGTTTTGCCATGGCACTTGTGAGCAC
616291 AGTTAAAGTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (54 bp):
GATGTGCAATTAAAACCTAAGCTTTGAATGTTTTGCCATGGCACTTGTGAGCAC
Found at i:617339 original size:36 final size:36
Alignment explanation
Indices: 617271--617339 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
617261 ATTAATAAAA
* * *
617271 AAATATTTTTATTGTATATTTTATTATAAAAATATT
1 AAATAATTTTATTATATATTTTAATATAAAAATATT
*
617307 AAATAATTTT-TTATATATTTTAAATATTAAAAT
1 AAATAATTTTATTATATATTTT-AATATAAAAAT
617340 GATTTTCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 10 0.36
36 18 0.64
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (36 bp):
AAATAATTTTATTATATATTTTAATATAAAAATATT
Found at i:623389 original size:3 final size:3
Alignment explanation
Indices: 623383--623407 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
623373 TTATGTCTAG
623383 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
623408 AAAAATTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:627703 original size:22 final size:22
Alignment explanation
Indices: 627678--627721 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
627668 GCCATCAACC
*
627678 CTGCCCCCAATAGAAAGCAAAT
1 CTGCCCCCAAAAGAAAGCAAAT
*
627700 CTGCCCCCAAAAGAGAGCAAAT
1 CTGCCCCCAAAAGAAAGCAAAT
627722 GAATAAGGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.32, G:0.16, T:0.11
Consensus pattern (22 bp):
CTGCCCCCAAAAGAAAGCAAAT
Found at i:629341 original size:2 final size:2
Alignment explanation
Indices: 629334--629360 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
629324 ATACTTTCTT
629334 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
629361 GGACAAAAAA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:637384 original size:22 final size:22
Alignment explanation
Indices: 637359--637402 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
637349 GCCATCAACC
*
637359 CTGCCCCCAATAGAAAGCAAAT
1 CTGCCCCCAAAAGAAAGCAAAT
*
637381 CTGCCCCCAAAAGAGAGCAAAT
1 CTGCCCCCAAAAGAAAGCAAAT
637403 GAATAAGGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.32, G:0.16, T:0.11
Consensus pattern (22 bp):
CTGCCCCCAAAAGAAAGCAAAT
Found at i:639023 original size:2 final size:2
Alignment explanation
Indices: 639016--639044 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
639006 ATACTTTCTT
639016 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
639045 GGACAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:642902 original size:2 final size:2
Alignment explanation
Indices: 642895--642934 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
642885 AACGCCCGCA
642895 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
642935 GGTAAAAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:644375 original size:23 final size:25
Alignment explanation
Indices: 644344--644389 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
644334 GGGTCTATAG
*
644344 TAGAATTCA-GTT-TTTGGGTATTT
1 TAGAATTCATGTTATTTAGGTATTT
*
644367 TAGATTTCATGTTATTTAGGTAT
1 TAGAATTCATGTTATTTAGGTAT
644390 ATATTTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 3 0.16
25 8 0.42
ACGTcount: A:0.24, C:0.04, G:0.20, T:0.52
Consensus pattern (25 bp):
TAGAATTCATGTTATTTAGGTATTT
Found at i:645506 original size:13 final size:13
Alignment explanation
Indices: 645473--645498 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
645463 GAATTTGTTA
645473 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
645486 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
645499 TTTCTTCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
CTTTTTCTTTTTT
Found at i:650275 original size:17 final size:16
Alignment explanation
Indices: 650236--650275 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
650226 AAAATAATTT
*
650236 TATTTTTAAAAATATA
1 TATTTTTAAAAAAATA
650252 T-TTTTTAAAAAAATAA
1 TATTTTTAAAAAAAT-A
650268 TATTTTTA
1 TATTTTTA
650276 TTTCATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 12 0.57
16 3 0.14
17 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTTTTAAAAAAATA
Found at i:650407 original size:2 final size:2
Alignment explanation
Indices: 650402--650426 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
650392 TTTTGACAAG
650402 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 T
650427 GTACCAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:655948 original size:2 final size:2
Alignment explanation
Indices: 655941--655978 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
655931 ATTTGCGTTG
655941 AT AT AT AT AT 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 AT AT AT AT AT
655979 GTATGTATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:657627 original size:17 final size:16
Alignment explanation
Indices: 657602--657635 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
657592 GGACCTTACT
*
657602 GAAACAAGCAAGATAAA
1 GAAAAAAGCAAGA-AAA
657619 GAAAAAAGCAAGAAAA
1 GAAAAAAGCAAGAAAA
657635 G
1 G
657636 TGTAGACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.68, C:0.09, G:0.21, T:0.03
Consensus pattern (16 bp):
GAAAAAAGCAAGAAAA
Found at i:660409 original size:89 final size:89
Alignment explanation
Indices: 660258--660436 Score: 304
Period size: 89 Copynumber: 2.0 Consensus size: 89
660248 TTGTTTTTTT
* * *
660258 CTTTTCTCGTCCTATATACCTTGCATTCATGAACCCAGAAGTCCTCACAACAGAAACTGCAATCT
1 CTTTTCTCATCCAATATACCTTGCATTCATGAACCCAGAAGACCTCACAACAGAAACTGCAATCT
*
660323 AATAGTTTACATTTTTGATGTGAA
66 AATAGTTCACATTTTTGATGTGAA
*
660347 CTTTTCTCATCCAATATACCTTGCATTCATGAACCCAGAAGACCTGACAACAGAAACTGCAATCT
1 CTTTTCTCATCCAATATACCTTGCATTCATGAACCCAGAAGACCTCACAACAGAAACTGCAATCT
*
660412 AATAGTTCACATTTTTTATGTGAA
66 AATAGTTCACATTTTTGATGTGAA
660436 C
1 C
660437 AAAAAACAAC
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (89 bp):
CTTTTCTCATCCAATATACCTTGCATTCATGAACCCAGAAGACCTCACAACAGAAACTGCAATCT
AATAGTTCACATTTTTGATGTGAA
Found at i:668069 original size:36 final size:36
Alignment explanation
Indices: 668029--668101 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
668019 TTGCCCAAAG
*
668029 TGTTGTGTTGTGATTAGTTTGTGTTTCCTCCTAGTT
1 TGTTGTGTTGTGATTAGTTTGCGTTTCCTCCTAGTT
668065 TGTTGTGTTGTGATTAGTTTGCGTTTCCTCCTAGTT
1 TGTTGTGTTGTGATTAGTTTGCGTTTCCTCCTAGTT
668101 T
1 T
668102 TTCTTCTGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.08, C:0.12, G:0.25, T:0.55
Consensus pattern (36 bp):
TGTTGTGTTGTGATTAGTTTGCGTTTCCTCCTAGTT
Found at i:669775 original size:17 final size:18
Alignment explanation
Indices: 669743--669781 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
669733 TATATAAATA
*
669743 TTAATAAAAAATATTTTT
1 TTAATAAAAAATATTTAT
*
669761 TTAATAAAATA-ATTTAT
1 TTAATAAAAAATATTTAT
669778 TTAA
1 TTAA
669782 GTTTATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAATAAAAAATATTTAT
Found at i:669825 original size:7 final size:6
Alignment explanation
Indices: 669796--669821 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
669786 ATTAATTGAG
669796 TTAAAT TTAAAT TTAAAT TTAAAT TT
1 TTAAAT TTAAAT TTAAAT TTAAAT TT
669822 TAAAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:675035 original size:145 final size:145
Alignment explanation
Indices: 674772--675069 Score: 544
Period size: 145 Copynumber: 2.1 Consensus size: 145
674762 CCTAATGTAA
*
674772 TCCTATATAACTTGGACTTAGGTGTGAGTGTCGGATAAGGGTATAGGTCCTACATGGGTATGTTT
1 TCCTATATAACTTGGACTTAGGTGTGAGTGTCAGATAAGGGTATAGGTCCTACATGGGTATGTTT
674837 ATCTTTTTAGAAGTTTTTTCATATATTTGAAGGGTGATAGCCTAATACTCATGTCAAAAGGTGTT
66 ATCTTTTTAGAAGTTTTTTCATATATTTGAAGGGTGATAGCCTAATACTCATGTCAAAAGGTGTT
674902 GGATACAGCTATGGT
131 GGATACAGCTATGGT
*
674917 TCCTATTTAACTTGGA-TTCAGGTGTGAGTGTCAGATAAGGGTATAGGTCCTACATGGGTATGTT
1 TCCTATATAACTTGGACTT-AGGTGTGAGTGTCAGATAAGGGTATAGGTCCTACATGGGTATGTT
* *
674981 TATTTTTTTAGAAGTTTTTTCATATATTTGAAGGGTGATAGCCTCATACTCATGTCAAAAGGTGT
65 TATCTTTTTAGAAGTTTTTTCATATATTTGAAGGGTGATAGCCTAATACTCATGTCAAAAGGTGT
675046 TGGATACAGCTATGGT
130 TGGATACAGCTATGGT
675062 TCCTATAT
1 TCCTATAT
675070 GGGTATATTT
Statistics
Matches: 147, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
144 2 0.01
145 145 0.99
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (145 bp):
TCCTATATAACTTGGACTTAGGTGTGAGTGTCAGATAAGGGTATAGGTCCTACATGGGTATGTTT
ATCTTTTTAGAAGTTTTTTCATATATTTGAAGGGTGATAGCCTAATACTCATGTCAAAAGGTGTT
GGATACAGCTATGGT
Found at i:680035 original size:2 final size:2
Alignment explanation
Indices: 680028--680059 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
680018 CTGCCAGACG
680028 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
680060 CAACACCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.