Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold364
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: 2089110
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 10
Found at i:886541 original size:2 final size:2
Alignment explanation
Indices: 886536--886577 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
886526 ACACACACAC
*
886536 AT AT AT AT GT 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 AT AT
886578 GCTTAAAGTG
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:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:893090 original size:2 final size:2
Alignment explanation
Indices: 893083--893122 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
893073 ATTATGTAAG
893083 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
893123 ATGCTTTGAT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:893350 original size:4 final size:4
Alignment explanation
Indices: 893341--893372 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
893331 TGGAAACTCA
*
893341 TACC TACC TACC TACC TACC TACC CACC TACC
1 TACC TACC TACC TACC TACC TACC TACC TACC
893373 AAGCAGATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.25, C:0.53, G:0.00, T:0.22
Consensus pattern (4 bp):
TACC
Found at i:903367 original size:28 final size:28
Alignment explanation
Indices: 903327--903384 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
903317 GACGGTAGTT
903327 TCGCAACCACTCTCCTTTCATCAATGTA
1 TCGCAACCACTCTCCTTTCATCAATGTA
903355 TCGCAACCACTCTCCTTTCATCAATGTA
1 TCGCAACCACTCTCCTTTCATCAATGTA
903383 TC
1 TC
903385 AAAAGATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.24, C:0.36, G:0.07, T:0.33
Consensus pattern (28 bp):
TCGCAACCACTCTCCTTTCATCAATGTA
Found at i:909713 original size:22 final size:21
Alignment explanation
Indices: 909646--909713 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 21
909636 TTTTTAAATT
*
909646 TATATATAATATAAA-TTATTAA
1 TATATAT-ATAAAAATTTA-TAA
**
909668 TATAT-TA-AAAAATAAATAA
1 TATATATATAAAAATTTATAA
*
909687 AATATATGATAAAAATTTATAA
1 TATATAT-ATAAAAATTTATAA
909709 TATAT
1 TATAT
909714 CAAATCGTAC
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
19 11 0.31
20 3 0.09
21 2 0.06
22 19 0.54
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (21 bp):
TATATATATAAAAATTTATAA
Found at i:911526 original size:2 final size:2
Alignment explanation
Indices: 911519--911549 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
911509 TATATGCGTG
911519 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
911550 TCTTTAACCT
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:912184 original size:19 final size:19
Alignment explanation
Indices: 912160--912199 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
912150 AAAAAAAATT
912160 AAGATGAAAAGATCGTATA
1 AAGATGAAAAGATCGTATA
*
912179 AAGATGAAAAGATTGTATA
1 AAGATGAAAAGATCGTATA
912198 AA
1 AA
912200 ATAACATGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.03, G:0.20, T:0.23
Consensus pattern (19 bp):
AAGATGAAAAGATCGTATA
Found at i:912757 original size:2 final size:2
Alignment explanation
Indices: 912752--912777 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
912742 ATATGGGTTG
912752 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
912778 TAATCTTCTA
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:918158 original size:8 final size:8
Alignment explanation
Indices: 918145--918171 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
918135 CATAACATTT
918145 AAAAAATA
1 AAAAAATA
918153 AAAAAATA
1 AAAAAATA
918161 AAAAAATA
1 AAAAAATA
918169 AAA
1 AAA
918172 TTGATTATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAATA
Found at i:921052 original size:17 final size:17
Alignment explanation
Indices: 921032--921070 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
921022 AATCCAGAGG
921032 GGCAATATCTAAAACCT
1 GGCAATATCTAAAACCT
921049 GGCAATATCTAAAACCT
1 GGCAATATCTAAAACCT
*
921066 AGCAA
1 GGCAA
921071 AACCCCACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.23, G:0.13, T:0.21
Consensus pattern (17 bp):
GGCAATATCTAAAACCT
Found at i:929293 original size:2 final size:2
Alignment explanation
Indices: 929286--929311 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
929276 AAGTGCTTAC
929286 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
929312 TCTTTTCCTT
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:929393 original size:52 final size:52
Alignment explanation
Indices: 929315--929417 Score: 206
Period size: 52 Copynumber: 2.0 Consensus size: 52
929305 TATATATTCT
929315 TTTCCTTCTCTCGTTTCAACTTTCAACTAGCCTAGCGGGTAGTAAACATTGC
1 TTTCCTTCTCTCGTTTCAACTTTCAACTAGCCTAGCGGGTAGTAAACATTGC
929367 TTTCCTTCTCTCGTTTCAACTTTCAACTAGCCTAGCGGGTAGTAAACATTG
1 TTTCCTTCTCTCGTTTCAACTTTCAACTAGCCTAGCGGGTAGTAAACATTG
929418 TTTTTCCAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (52 bp):
TTTCCTTCTCTCGTTTCAACTTTCAACTAGCCTAGCGGGTAGTAAACATTGC
Found at i:932929 original size:18 final size:17
Alignment explanation
Indices: 932908--932971 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 17
932898 AGATCTATAT
932908 TTTTATAAATATATTAAA
1 TTTTATAAA-ATATTAAA
932926 TTTTATAAAAAAATTATTAAA
1 TTTTAT---AAAA-TATTAAA
932947 TTTTATATAAATATATAATA
1 TTTTATA-AAATAT-TAA-A
932967 TTTTA
1 TTTTA
932972 AATATGATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
18 10 0.26
19 6 0.15
20 7 0.18
21 16 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTATAAAATATTAAA
Found at i:933490 original size:25 final size:23
Alignment explanation
Indices: 933462--933516 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
933452 CAAAATTTAT
933462 ATAAATAT-AAAATATTTTAAATATA
1 ATAAATATGAAAATA--TTAAATA-A
*
933487 ATAAAATATGTAAATATTAAATAA
1 AT-AAATATGAAAATATTAAATAA
933511 ATAAAT
1 ATAAAT
933517 GAATTATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 4 0.15
24 3 0.11
25 9 0.33
26 6 0.22
27 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
ATAAATATGAAAATATTAAATAA
Found at i:935843 original size:18 final size:17
Alignment explanation
Indices: 935809--935857 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
935799 AATTTAAAAT
935809 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
935826 ATTTTAATATGTTA-AT-A
1 ATTTT-ATAT-TTATATAA
935843 A-TTTATATTTCATAT
1 ATTTTATATTT-ATAT
935858 TTGTATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 2 0.07
15 5 0.18
16 5 0.18
17 7 0.25
18 6 0.21
19 3 0.11
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:936059 original size:2 final size:2
Alignment explanation
Indices: 936052--936091 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
936042 AACTGGTGTT
936052 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
936092 AGCCAAACTT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:937152 original size:18 final size:17
Alignment explanation
Indices: 937131--937164 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
937121 TTATATTTTT
937131 AATTTTTTACATTAAATC
1 AATTTTTT-CATTAAATC
937149 AATTTTTTCATTAAAT
1 AATTTTTTCATTAAAT
937165 TTTTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTTTTCATTAAATC
Found at i:937503 original size:18 final size:17
Alignment explanation
Indices: 937471--937504 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
937461 AATAAAAGAT
*
937471 ATTAAAAATTTTATTTA
1 ATTAAAAACTTTATTTA
937488 ATTAACAAACTTTATTT
1 ATTAA-AAACTTTATTT
937505 TTTAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTAAAAACTTTATTTA
Found at i:938088 original size:19 final size:21
Alignment explanation
Indices: 938048--938092 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
938038 CATTGAAACT
938048 TTAAAGGGATAAAATTTGTAA
1 TTAAAGGGATAAAATTTGTAA
938069 TTAAAGGG-T-AAATTAT-TAA
1 TTAAAGGGATAAAATT-TGTAA
938088 TTAAA
1 TTAAA
938093 AAATATACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 13 0.57
20 2 0.09
21 8 0.35
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.36
Consensus pattern (21 bp):
TTAAAGGGATAAAATTTGTAA
Found at i:940424 original size:24 final size:25
Alignment explanation
Indices: 940357--940430 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 25
940347 CTCATAATTT
*
940357 TAAAAATAATATAA-AAATATAATA
1 TAAAAATAATTTAATAAATATAATA
* * *
940381 TAAATATAATATT-TTTAATA-AATA
1 TAAAAATAAT-TTAATAAATATAATA
*
940405 TAAAAATAATTTAATGAATATAATA
1 TAAAAATAATTTAATAAATATAATA
940430 T
1 T
940431 TATATATTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
23 2 0.05
24 27 0.69
25 10 0.26
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (25 bp):
TAAAAATAATTTAATAAATATAATA
Found at i:942786 original size:22 final size:21
Alignment explanation
Indices: 942748--942795 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
942738 AGAGAAATTA
* * *
942748 AAAAAATTAATATTTATTTTT
1 AAAAAATTAAAAATTATTATT
942769 AAAAAATTAAAAAATTATTATT
1 AAAAAATT-AAAAATTATTATT
942791 AAAAA
1 AAAAA
942796 TTTTAAAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAAATTAAAAATTATTATT
Found at i:942867 original size:15 final size:15
Alignment explanation
Indices: 942815--942866 Score: 72
Period size: 14 Copynumber: 3.6 Consensus size: 15
942805 TAAAAAATCA
* *
942815 TTTTTAACATTA-AT
1 TTTTTAAAATTATGT
942829 TTTTTAAAATTATGT
1 TTTTTAAAATTATGT
942844 TTTTTAAAATTATG-
1 TTTTTAAAATTATGT
942858 TTTTTAAAA
1 TTTTTAAAA
942867 AGTTTCAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
14 20 0.57
15 15 0.43
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (15 bp):
TTTTTAAAATTATGT
Found at i:943687 original size:7 final size:7
Alignment explanation
Indices: 943675--943707 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
943665 CACAAAAATA
943675 ATATATT
1 ATATATT
943682 ATATATT
1 ATATATT
943689 ATATATT
1 ATATATT
943696 ATATATT
1 ATATATT
943703 -TATAT
1 ATATAT
943708 AGATACAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
ATATATT
Found at i:944214 original size:21 final size:21
Alignment explanation
Indices: 944190--944230 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
944180 GTAGTAGCGG
944190 TGGCAG-TGTAGGCGGTGGTGC
1 TGGCAGTTGTA-GCGGTGGTGC
*
944211 TGGCAGTTGTAGTGGTGGTG
1 TGGCAGTTGTAGCGGTGGTG
944231 GTGGTGGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.10, C:0.10, G:0.51, T:0.29
Consensus pattern (21 bp):
TGGCAGTTGTAGCGGTGGTGC
Found at i:944228 original size:3 final size:3
Alignment explanation
Indices: 944222--944255 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
944212 GGCAGTTGTA
* *
944222 GTG GTG GTG GTG GTG GTG GTG GAG GTG GAG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG G
944256 ACCTTGTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.06, C:0.00, G:0.68, T:0.26
Consensus pattern (3 bp):
GTG
Found at i:947699 original size:2 final size:2
Alignment explanation
Indices: 947692--947717 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
947682 CATAGAATAG
947692 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
947718 GCTATTTACG
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:954107 original size:40 final size:41
Alignment explanation
Indices: 954062--954152 Score: 100
Period size: 41 Copynumber: 2.2 Consensus size: 41
954052 AAATTTTAAT
954062 AATTTAATT-AATTTAAATTA-AATTAATATA-T-AATAATAAA
1 AATTTAATTAAATTT-AATTATAA--AATATATTAAATAATAAA
*
954102 AATTTATTTAAATTTAATTATAAAATATATTAAATAATAAA
1 AATTTAATTAAATTTAATTATAAAATATATTAAATAATAAA
*
954143 ATATATAATT
1 A-ATTTAATT
954153 GATCTGATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
39 6 0.14
40 14 0.33
41 17 0.40
42 6 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (41 bp):
AATTTAATTAAATTTAATTATAAAATATATTAAATAATAAA
Found at i:964026 original size:20 final size:20
Alignment explanation
Indices: 964001--964065 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
963991 TACTCAATAG
* *
964001 TATAAATTAATATATATCGA
1 TATAAATTAATATAAATCAA
* *
964021 TATAAATAAATATAAATTAA
1 TATAAATTAATATAAATCAA
* *
964041 TATAAACTAATAT-AATTAA
1 TATAAATTAATATAAATCAA
964060 TATAAA
1 TATAAA
964066 AAATAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 12 0.31
20 27 0.69
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (20 bp):
TATAAATTAATATAAATCAA
Found at i:964033 original size:10 final size:10
Alignment explanation
Indices: 964001--964079 Score: 60
Period size: 10 Copynumber: 8.3 Consensus size: 10
963991 TACTCAATAG
*
964001 TATAAATTAA
1 TATAAATAAA
* **
964011 TATATATCGA
1 TATAAATAAA
964021 TATAAATAAA
1 TATAAATAAA
*
964031 TATAAATTAA
1 TATAAATAAA
964041 TATAAACT-AA
1 TATAAA-TAAA
*
964051 TAT-AATTAA
1 TATAAATAAA
964060 TATAAA-AAA
1 TATAAATAAA
964069 TA-AAA-AAA
1 TATAAATAAA
964077 TAT
1 TAT
964080 GATATTAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
8 9 0.16
9 11 0.19
10 36 0.63
11 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (10 bp):
TATAAATAAA
Found at i:964054 original size:30 final size:29
Alignment explanation
Indices: 964001--964065 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
963991 TACTCAATAG
* *
964001 TATAAATTAATATATATCGATATAAATAAA
1 TATAAATTAATATAAATCAATAT-AATAAA
*
964031 TATAAATTAATATAAA-CTAATATAATTAA
1 TATAAATTAATATAAATC-AATATAATAAA
964060 TATAAA
1 TATAAA
964066 AAATAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 12 0.39
30 19 0.61
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (29 bp):
TATAAATTAATATAAATCAATATAATAAA
Found at i:965961 original size:13 final size:13
Alignment explanation
Indices: 965943--965968 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
965933 CTAGTAATTC
965943 ATTTTTACTTTTT
1 ATTTTTACTTTTT
965956 ATTTTTACTTTTT
1 ATTTTTACTTTTT
965969 CAACTTATTT
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:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTTTACTTTTT
Found at i:979543 original size:24 final size:24
Alignment explanation
Indices: 979489--979537 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
979479 CCAAGCTTCA
979489 AACTTCATTAGAAATGAAAATCCC
1 AACTTCATTAGAAATGAAAATCCC
979513 AACTTCATTAGAAATGAAAATCCC
1 AACTTCATTAGAAATGAAAATCCC
979537 A
1 A
979538 GATTCAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.24
Consensus pattern (24 bp):
AACTTCATTAGAAATGAAAATCCC
Found at i:980911 original size:16 final size:17
Alignment explanation
Indices: 980886--980923 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
980876 TATTGATATA
980886 TTTATATTAT-TTTTAAT
1 TTTATATTATATTTT-AT
980903 TTTAT-TTATATTTTAT
1 TTTATATTATATTTTAT
980919 TTTAT
1 TTTAT
980924 GTTTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATATTATATTTTAT
Found at i:980928 original size:11 final size:11
Alignment explanation
Indices: 980884--980920 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
980874 TTTATTGATA
980884 TATTTATATTAT
1 TATTTATATT-T
980896 T-TTTA-ATTT
1 TATTTATATTT
980905 TATTTATATTT
1 TATTTATATTT
980916 TATTT
1 TATTT
980921 TATGTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.09
10 7 0.30
11 13 0.57
12 1 0.04
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTTATATTT
Found at i:980966 original size:30 final size:28
Alignment explanation
Indices: 980915--980973 Score: 66
Period size: 30 Copynumber: 2.0 Consensus size: 28
980905 TATTTATATT
*
980915 TTATTTTATGTTTAATAATAAATAATAAAA
1 TTATTGTATGTTTAATAATAAA-AA-AAAA
*
980945 TTATTGTAT-TTTGAATTATAAAAAAAAA
1 TTATTGTATGTTT-AATAATAAAAAAAAA
980973 T
1 T
980974 AAAGCTTGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 5 0.19
29 5 0.19
30 16 0.62
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (28 bp):
TTATTGTATGTTTAATAATAAAAAAAAA
Found at i:981996 original size:2 final size:2
Alignment explanation
Indices: 981982--982017 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
981972 CTTTCATTTC
*
981982 AT AT AT A- AC 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 A
982018 AAAGATCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:982186 original size:6 final size:6
Alignment explanation
Indices: 982172--982221 Score: 91
Period size: 6 Copynumber: 8.3 Consensus size: 6
982162 AGAATAATAG
*
982172 AAGAGA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
982220 AA
1 AA
982222 AATTACTGCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:989396 original size:19 final size:18
Alignment explanation
Indices: 989364--989401 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
989354 ATGATTAAAA
989364 TTTTACGTGTATATAATTT
1 TTTTACGTGTATAT-ATTT
989383 TTTTACGT-TAATATATTT
1 TTTTACGTGT-ATATATTT
989401 T
1 T
989402 AAATAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (18 bp):
TTTTACGTGTATATATTT
Found at i:989905 original size:15 final size:15
Alignment explanation
Indices: 989887--989918 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
989877 TTTAAAATTT
989887 AAATTAATCAAATAA
1 AAATTAATCAAATAA
*
989902 AAATTAATTAAATAA
1 AAATTAATCAAATAA
989917 AA
1 AA
989919 TTTTATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATTAATCAAATAA
Found at i:993326 original size:13 final size:13
Alignment explanation
Indices: 993308--993333 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
993298 GACAGCACTG
993308 GAAGATGTTATAT
1 GAAGATGTTATAT
993321 GAAGATGTTATAT
1 GAAGATGTTATAT
993334 AGCTCAACCA
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:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
GAAGATGTTATAT
Found at i:993477 original size:12 final size:12
Alignment explanation
Indices: 993460--993485 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
993450 TGTATTTTAC
993460 AAGAAATTGTTT
1 AAGAAATTGTTT
993472 AAGAAATTGTTT
1 AAGAAATTGTTT
993484 AA
1 AA
993486 CATGATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (12 bp):
AAGAAATTGTTT
Found at i:1002901 original size:3 final size:3
Alignment explanation
Indices: 1002893--1002934 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1002883 TGGTAGAAAT
1002893 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1002935 TAGTAGAGGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1004161 original size:22 final size:20
Alignment explanation
Indices: 1004136--1004188 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
1004126 CAAAAAGATT
*
1004136 AAAAAAATCTAAAATTTTCAAA
1 AAAAAAAT-TAAAAATTT-AAA
1004158 AAAAAAATTAAAAATTTAAA
1 AAAAAAATTAAAAATTTAAA
1004178 AATAAAAATTA
1 AA-AAAAATTA
1004189 GATAAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 5 0.17
21 16 0.55
22 8 0.28
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAAATTAAAAATTTAAA
Found at i:1004205 original size:26 final size:25
Alignment explanation
Indices: 1004166--1004240 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 25
1004156 AAAAAAAAAT
1004166 TAAAAATTTA-AAAATAAAAAT-TAG
1 TAAAAATTTATAAAATAAAAATCT-G
* *
1004190 ATAAAAATCTATAAAATTTAAAATCTG
1 -TAAAAATTTATAAAA-TAAAAATCTG
1004217 TAAAGGAATTTATAAAATAAAAAT
1 TAAA--AATTTATAAAATAAAAAT
1004241 AAAAATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
25 9 0.22
26 8 0.20
27 13 0.32
28 11 0.27
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (25 bp):
TAAAAATTTATAAAATAAAAATCTG
Found at i:1004337 original size:18 final size:17
Alignment explanation
Indices: 1004233--1004396 Score: 80
Period size: 18 Copynumber: 9.8 Consensus size: 17
1004223 AATTTATAAA
1004233 ATAAAAA-TA-AAAATT
1 ATAAAAATTATAAAATT
*
1004248 TTAAAAATTATAGAAATT
1 ATAAAAATTATA-AAATT
*
1004266 ATAAAAATTATAAAA-A
1 ATAAAAATTATAAAATT
*
1004282 ATTAAAAGTTA-AAAA-T
1 A-TAAAAATTATAAAATT
* * *
1004298 A-AAAACTCAT-ACATT
1 ATAAAAATTATAAAATT
*
1004313 TTAAAAAATCTATAAAATT
1 AT-AAAAAT-TATAAAATT
1004332 ATAAAAAAATTA-AAAATT
1 AT--AAAAATTATAAAATT
**
1004350 -TCAAAAATTATAAAAAA
1 AT-AAAAATTATAAAATT
*
1004367 AGTATAAAATTTTAAAA--
1 A-TA-AAAATTATAAAATT
1004384 ATAAAAATTATAA
1 ATAAAAATTATAA
1004397 TTTTTTGAAT
Statistics
Matches: 116, Mismatches: 18, Indels: 30
0.71 0.11 0.18
Matches are distributed among these distances:
14 8 0.07
15 16 0.14
16 18 0.16
17 23 0.20
18 25 0.22
19 19 0.16
20 7 0.06
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (17 bp):
ATAAAAATTATAAAATT
Found at i:1004346 original size:27 final size:27
Alignment explanation
Indices: 1004316--1004385 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
1004306 ATACATTTTA
*
1004316 AAAAATCT-ATAAAATTATAAAAAAATT
1 AAAAATCTCA-AAAATTATAAAAAAAGT
*
1004343 AAAAATTTCAAAAATTATAAAAAAAGT
1 AAAAATCTCAAAAATTATAAAAAAAGT
* *
1004370 ATAAAATTTTAAAAAT
1 A-AAAATCTCAAAAAT
1004386 AAAAATTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (27 bp):
AAAAATCTCAAAAATTATAAAAAAAGT
Found at i:1004396 original size:9 final size:9
Alignment explanation
Indices: 1004239--1004365 Score: 74
Period size: 9 Copynumber: 14.8 Consensus size: 9
1004229 TAAAATAAAA
1004239 ATAAAAATT
1 ATAAAAATT
*
1004248 TTAAAAATT
1 ATAAAAATT
*
1004257 ATAGAAATT
1 ATAAAAATT
1004266 ATAAAAATT
1 ATAAAAATT
1004275 ATAAAAA--
1 ATAAAAATT
* *
1004282 ATTAAAAGT
1 ATAAAAATT
1004291 -TAAAAA-T
1 ATAAAAATT
* *
1004298 A-AAAACTC
1 ATAAAAATT
* **
1004306 ATACATTTT
1 ATAAAAATT
1004315 A-AAAAATCT
1 ATAAAAAT-T
1004324 AT-AAAATT
1 ATAAAAATT
*
1004332 ATAAAAA-A
1 ATAAAAATT
1004340 ATTAAAAATT
1 A-TAAAAATT
1004350 -TCAAAAATT
1 AT-AAAAATT
1004359 ATAAAAA
1 ATAAAAA
1004366 AAGTATAAAA
Statistics
Matches: 89, Mismatches: 17, Indels: 24
0.68 0.13 0.18
Matches are distributed among these distances:
7 11 0.12
8 14 0.16
9 63 0.71
10 1 0.01
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:1004437 original size:29 final size:27
Alignment explanation
Indices: 1004391--1004593 Score: 120
Period size: 28 Copynumber: 7.4 Consensus size: 27
1004381 AAAATAAAAA
* *
1004391 TTATAATTTTTTGAATTTAATATATTT
1 TTATAATTTTATGAATTTTATATATTT
**
1004418 TTATAATTTTATTTTTATTTTATA-ATTT
1 TTATAATTTTA--TGAATTTTATATATTT
1004446 CTTATAATTTTATGAATTTTATATATTT
1 -TTATAATTTTATGAATTTTATATATTT
**
1004474 TTAATAATTTTAAAAAGTTTCTA-AT-TTT
1 TT-ATAATTTTATGAA-TTT-TATATATTT
* *
1004502 TTTTAAATTTATAGATATTTTATA-ATGTT
1 TTATAATTTTAT-GA-ATTTTATATAT-TT
* *
1004531 TT-TAATTTTAT---TTGTTAAATTTATT
1 TTATAATTTTATGAATT-TTATATAT-TT
* *
1004556 TTA-AATTTTATAGATTTTTTTATATTT
1 TTATAATTTTAT-GAATTTTATATATTT
1004583 TTAT-ATTTTAT
1 TTATAATTTTAT
1004594 TTTTTAAATT
Statistics
Matches: 137, Mismatches: 19, Indels: 40
0.70 0.10 0.20
Matches are distributed among these distances:
23 2 0.01
24 4 0.03
25 13 0.09
27 42 0.31
28 43 0.31
29 31 0.23
30 2 0.01
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (27 bp):
TTATAATTTTATGAATTTTATATATTT
Found at i:1004482 original size:19 final size:18
Alignment explanation
Indices: 1004391--1004485 Score: 88
Period size: 19 Copynumber: 5.2 Consensus size: 18
1004381 AAAATAAAAA
1004391 TTATA-ATTTTT-TGAATT
1 TTATATATTTTTAT-AATT
*
1004408 TAATATATTTTTATAATT
1 TTATATATTTTTATAATT
* *
1004426 TTATTTTTATTTTATAATT
1 TTATATAT-TTTTATAATT
*
1004445 TCT-TATAATTTTATGAATT
1 T-TATATATTTTTAT-AATT
1004464 TTATATATTTTTAATAATT
1 TTATATATTTTT-ATAATT
1004483 TTA
1 TTA
1004486 AAAAGTTTCT
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
17 4 0.06
18 22 0.35
19 34 0.54
20 3 0.05
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (18 bp):
TTATATATTTTTATAATT
Found at i:1004483 original size:10 final size:9
Alignment explanation
Indices: 1004391--1004637 Score: 62
Period size: 10 Copynumber: 27.2 Consensus size: 9
1004381 AAAATAAAAA
1004391 TTATAATTT
1 TTATAATTT
1004400 TT-TGAA-TT
1 TTAT-AATTT
*
1004408 TAATATATTT
1 TTATA-ATTT
1004418 TTATAA-TT
1 TTATAATTT
**
1004426 TTATTTTTATT
1 TTA-TAAT-TT
1004437 TTATAATTT
1 TTATAATTT
1004446 CTTATAA-TT
1 -TTATAATTT
1004455 TTATGAA-TT
1 TTAT-AATTT
1004464 TTATATATTT
1 TTATA-ATTT
1004474 TTAATAATTT
1 TT-ATAATTT
* *
1004484 TAAAAAGTTT
1 TTATAA-TTT
* *
1004494 CTA-ATTTT
1 TTATAATTT
* *
1004502 TTTTAA-AT
1 TTATAATTT
1004510 TTATAGATATT
1 TTATA-AT-TT
1004521 TTATAATGTT
1 TTATAAT-TT
1004531 TT-TAA-TT
1 TTATAATTT
*
1004538 TTAT--TTG
1 TTATAATTT
1004545 TTA-AATTT
1 TTATAATTT
* *
1004553 ATTTTAAATT
1 -TTATAATTT
1004563 TTATAGATTT
1 TTATA-ATTT
*
1004573 TTTTATATTT
1 TTATA-ATTT
1004583 TTAT-A-TT
1 TTATAATTT
1004590 TTAT--TTT
1 TTATAATTT
1004597 TTA-AATTTTTT
1 TTATAA---TTT
*
1004608 TTATAAACTT
1 TTAT-AATTT
1004618 TTA-AATTT
1 TTATAATTT
1004626 TTAATAATTT
1 TT-ATAATTT
1004636 TT
1 TT
1004638 TTAAAATTTT
Statistics
Matches: 175, Mismatches: 29, Indels: 67
0.65 0.11 0.25
Matches are distributed among these distances:
7 19 0.11
8 34 0.19
9 37 0.21
10 63 0.36
11 20 0.11
13 2 0.01
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (9 bp):
TTATAATTT
Found at i:1004561 original size:52 final size:52
Alignment explanation
Indices: 1004496--1004610 Score: 162
Period size: 52 Copynumber: 2.2 Consensus size: 52
1004486 AAAAGTTTCT
*
1004496 AATTTTTTTTAAA-TTTATAGATATTTTATAATGTTTTTA-ATTTTATTTGTTA
1 AATTTTTTTTAAATTTTATAGAT-TTTT-TAATATTTTTATATTTTATTTGTTA
* * *
1004548 AATTTATTTTAAATTTTATAGATTTTTTTATATTTTTATATTTTATTTTTTA
1 AATTTTTTTTAAATTTTATAGATTTTTTAATATTTTTATATTTTATTTGTTA
1004600 AATTTTTTTTA
1 AATTTTTTTTA
1004611 TAAACTTTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
51 9 0.16
52 38 0.68
53 9 0.16
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (52 bp):
AATTTTTTTTAAATTTTATAGATTTTTTAATATTTTTATATTTTATTTGTTA
Found at i:1004608 original size:25 final size:25
Alignment explanation
Indices: 1004529--1004612 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 25
1004519 TTTTATAATG
*
1004529 TTTTTA-ATTTTATTTGTTAAATTT
1 TTTTTATATTTTATTTTTTAAATTT
* * ** *
1004553 ATTTTAAATTTTATAGATTTTTTTA-TA
1 TTTTTATATTTTAT---TTTTTAAATTT
1004580 TTTTTATATTTTATTTTTTAAATTT
1 TTTTTATATTTTATTTTTTAAATTT
1004605 TTTTTATA
1 TTTTTATA
1004613 AACTTTTAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
24 11 0.24
25 16 0.36
27 13 0.29
28 5 0.11
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (25 bp):
TTTTTATATTTTATTTTTTAAATTT
Found at i:1004609 original size:13 final size:14
Alignment explanation
Indices: 1004529--1004620 Score: 56
Period size: 14 Copynumber: 6.9 Consensus size: 14
1004519 TTTTATAATG
1004529 TTTTT-AATTTTAT
1 TTTTTAAATTTTAT
*
1004542 TTGTTAAA-TTTA-
1 TTTTTAAATTTTAT
1004554 -TTTTAAATTTTAT
1 TTTTTAAATTTTAT
**
1004567 AGATTT---TTTTAT
1 -TTTTTAAATTTTAT
*
1004579 ATTTTTATATTTTAT
1 -TTTTTAAATTTTAT
1004594 TTTTTAAATTTT-T
1 TTTTTAAATTTTAT
*
1004607 TTTATAAACTTTTA
1 TTTTTAAA-TTTTA
1004621 AATTTTTAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
11 6 0.10
12 14 0.23
13 16 0.26
14 17 0.27
15 9 0.15
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.68
Consensus pattern (14 bp):
TTTTTAAATTTTAT
Found at i:1004627 original size:52 final size:52
Alignment explanation
Indices: 1004496--1004637 Score: 143
Period size: 52 Copynumber: 2.7 Consensus size: 52
1004486 AAAAGTTTCT
* *
1004496 AATTTTTTTTAAA-TTTATAGATATTTTATAAT-GTTTTTAATTTTATTTGTTA
1 AATTTATTTTAAATTTTATAGAT-TTTT-TAATAATTTTTAATTTTATTTGTTA
* *
1004548 AATTTATTTTAAATTTTATAGATTTTTTTAT-ATTTTTATATTTTATTTTTTA
1 AATTTATTTTAAATTTTATAGATTTTTTAATAATTTTTA-ATTTTATTTGTTA
*
1004600 AATTTTTTTTATAAACTTTTA-A-A-TTTTTAATAATTTTT
1 AA-TTTATTT-TAAA-TTTTATAGATTTTTTAATAATTTTT
1004638 TTAAAATTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
51 9 0.12
52 37 0.47
53 22 0.28
54 5 0.06
55 5 0.06
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (52 bp):
AATTTATTTTAAATTTTATAGATTTTTTAATAATTTTTAATTTTATTTGTTA
Found at i:1004639 original size:20 final size:20
Alignment explanation
Indices: 1004548--1004648 Score: 64
Period size: 19 Copynumber: 4.8 Consensus size: 20
1004538 TTATTTGTTA
1004548 AATTTATTTTAAA-TTTT-AT
1 AATTT-TTTTAAATTTTTAAT
*
1004567 AGATTTTTTTATATTTTTATAT
1 A-ATTTTTTTAAATTTTTA-AT
** *
1004589 TTTATTTTTTAAATTTTTTTTAT
1 AAT-TTTTTTAAA--TTTTTAAT
**
1004612 AA-ACTTTTAAATTTTTAAT
1 AATTTTTTTAAATTTTTAAT
1004631 AATTTTTTTAAAATTTTT
1 AATTTTTTT-AAATTTTT
1004649 TGAGTTTAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
19 16 0.26
20 12 0.20
21 16 0.26
22 10 0.16
23 2 0.03
24 5 0.08
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (20 bp):
AATTTTTTTAAATTTTTAAT
Found at i:1004967 original size:1 final size:1
Alignment explanation
Indices: 1004961--1004985 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1004951 TCTTTTCTTT
1004961 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
1004986 TCCTTACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1009418 original size:26 final size:24
Alignment explanation
Indices: 1009361--1009420 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
1009351 TTTATCAATC
*
1009361 ATATAAATATAAAAATTTTAAAAA
1 ATATAAATATAAAAATATTAAAAA
* *
1009385 TTATTAAATATATCAAATATTAAATAA
1 ATA-TAAATATA-AAAATATTAAA-AA
1009412 ATATAAATA
1 ATATAAATA
1009421 ATATATAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 2 0.07
25 8 0.28
26 15 0.52
27 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
ATATAAATATAAAAATATTAAAAA
Found at i:1010262 original size:14 final size:14
Alignment explanation
Indices: 1010243--1010286 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1010233 TTACAATTTT
1010243 TTAAAATATAAAAA
1 TTAAAATATAAAAA
* *
1010257 TTAAAATATTAAAT
1 TTAAAATATAAAAA
*
1010271 TTAATAATAAAAAAA
1 TTAA-AATATAAAAA
1010286 T
1 T
1010287 AAATTATGCG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TTAAAATATAAAAA
Found at i:1011498 original size:3 final size:3
Alignment explanation
Indices: 1011490--1011520 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1011480 GGAAAGCCTA
*
1011490 GAG GAG GAG GAG TAG GAG GAG GAG GAG GAG G
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG G
1011521 GAGTCGGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.65, T:0.03
Consensus pattern (3 bp):
GAG
Found at i:1023460 original size:2 final size:2
Alignment explanation
Indices: 1023453--1023488 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1023443 TGCAAATGAC
* *
1023453 AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1023489 TTTTTCTAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1024332 original size:25 final size:25
Alignment explanation
Indices: 1024270--1024332 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
1024260 ATATATAATT
** *
1024270 TAAAATAAAAAATTTATTAAATTGA
1 TAAAATATTAAATTCATTAAATTGA
* *
1024295 TAAAAAATTAAATTCATTGAATTGA
1 TAAAATATTAAATTCATTAAATTGA
1024320 TAAAATATTAAAT
1 TAAAATATTAAAT
1024333 CTTAAGTGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.37
Consensus pattern (25 bp):
TAAAATATTAAATTCATTAAATTGA
Found at i:1024759 original size:35 final size:36
Alignment explanation
Indices: 1024689--1024759 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
1024679 AAAGTTTTTT
*
1024689 AAAATTTAATATTTTTTATTAAATTTTAAAATATAA
1 AAAATTTAATATATTTTATTAAATTTTAAAATATAA
*
1024725 AAAATTTAATATATTTT-TT-AATATTTAAATTATAA
1 AAAATTTAATATATTTTATTAAAT-TTTAAAATATAA
1024760 TACTACATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 3 0.09
35 13 0.41
36 16 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
AAAATTTAATATATTTTATTAAATTTTAAAATATAA
Found at i:1024955 original size:27 final size:28
Alignment explanation
Indices: 1024900--1024956 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
1024890 AAATTTTATT
** *
1024900 TTTTATTTAAATTTTTTTAACATAATAA
1 TTTTATTTAAATTCCTTTAAAATAATAA
*
1024928 TTTTATTTAAA-TCCTTTAAAATATTAA
1 TTTTATTTAAATTCCTTTAAAATAATAA
1024955 TT
1 TT
1024957 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTTATTTAAATTCCTTTAAAATAATAA
Found at i:1025000 original size:17 final size:18
Alignment explanation
Indices: 1024951--1025000 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 18
1024941 CTTTAAAATA
* *
1024951 TTAATTAAAT-TTTAAAT
1 TTAAATAAATATTTTAAT
*
1024968 TTAAATAAATAATTTAAT
1 TTAAATAAATATTTTAAT
*
1024986 TT-AATAATTATTTTA
1 TTAAATAAATATTTTA
1025001 TTTTTTATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 20 0.74
18 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTAAATAAATATTTTAAT
Found at i:1031829 original size:2 final size:2
Alignment explanation
Indices: 1031822--1031850 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1031812 GAGAAAATAG
1031822 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1031851 TCTTCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1033322 original size:4 final size:4
Alignment explanation
Indices: 1033313--1033346 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
1033303 AAAGATGTTC
1033313 AATT AATT AATT GAATT AATT GAATT AATT AATT
1 AATT AATT AATT -AATT AATT -AATT AATT AATT
1033347 TTTTAAACTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:1033331 original size:9 final size:8
Alignment explanation
Indices: 1033313--1033346 Score: 50
Period size: 9 Copynumber: 4.0 Consensus size: 8
1033303 AAAGATGTTC
1033313 AATTAATT
1 AATTAATT
1033321 AATTGAATT
1 AATT-AATT
1033330 AATTGAATT
1 AATT-AATT
1033339 AATTAATT
1 AATTAATT
1033347 TTTTAAACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (8 bp):
AATTAATT
Found at i:1033331 original size:13 final size:13
Alignment explanation
Indices: 1033313--1033346 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1033303 AAAGATGTTC
1033313 AATTAATT-AATT
1 AATTAATTGAATT
1033325 GAATTAATTGAATT
1 -AATTAATTGAATT
1033339 AATTAATT
1 AATTAATT
1033347 TTTTAAACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (13 bp):
AATTAATTGAATT
Found at i:1033482 original size:23 final size:23
Alignment explanation
Indices: 1033440--1033487 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1033430 GAATTAATCG
*
1033440 AATTTTAATTATTTATATTTTAA
1 AATTTTAATTATTTATATTTAAA
*
1033463 AATTTT-ATTTTTTATAATTTAAA
1 AATTTTAATTATTTAT-ATTTAAA
1033486 AA
1 AA
1033488 AATATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
AATTTTAATTATTTATATTTAAA
Found at i:1033483 original size:22 final size:23
Alignment explanation
Indices: 1033440--1033486 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1033430 GAATTAATCG
*
1033440 AATTTTAATTATTTATATTTTAA
1 AATTTTAATTATTTATAATTTAA
*
1033463 AATTTT-ATTTTTTATAATTTAA
1 AATTTTAATTATTTATAATTTAA
1033485 AA
1 AA
1033487 AAATATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
AATTTTAATTATTTATAATTTAA
Found at i:1035787 original size:15 final size:15
Alignment explanation
Indices: 1035767--1035819 Score: 74
Period size: 15 Copynumber: 3.6 Consensus size: 15
1035757 TAATTTTCTA
1035767 ATTATTTATATAATT
1 ATTATTTATATAATT
*
1035782 ATTATTTTTATCAA--
1 ATTATTTATAT-AATT
1035796 ATTATTTATATAATT
1 ATTATTTATATAATT
1035811 ATTATTTAT
1 ATTATTTAT
1035820 TTTTAATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 2 0.06
14 10 0.30
15 19 0.58
16 2 0.06
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTATTTATATAATT
Found at i:1035827 original size:29 final size:29
Alignment explanation
Indices: 1035759--1035827 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 29
1035749 TTTTTAAATA
1035759 ATTTTCTAATTATTTATATAATTATTATTT
1 ATTTT-TAATTATTTATATAATTATTATTT
**
1035789 -TTATCAAATTATTTATATAATTATTATTT
1 ATT-TTTAATTATTTATATAATTATTATTT
1035818 ATTTTTAATT
1 ATTTTTAATT
1035828 TAAGATGCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
29 30 0.91
30 3 0.09
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTTTTAATTATTTATATAATTATTATTT
Found at i:1035892 original size:20 final size:20
Alignment explanation
Indices: 1035858--1035916 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
1035848 CTATTTTTTT
* *
1035858 AAATAATAATTATTAATTTA
1 AAATAAAAATAATTAATTTA
* *
1035878 AAATAACAATAATT-ATGT-
1 AAATAAAAATAATTAATTTA
1035896 AAATAAAATATAATTAATTTA
1 AAATAAAA-ATAATTAATTTA
1035917 TTAATATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 7 0.23
19 9 0.29
20 15 0.48
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
AAATAAAAATAATTAATTTA
Found at i:1035902 original size:23 final size:23
Alignment explanation
Indices: 1035862--1035924 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
1035852 TTTTTTAAAT
*
1035862 AATAATTATTAATTTAAAATAAC
1 AATAATTATTAATATAAAATAAC
1035885 AATAATTATGTAA-ATAAAATATA-
1 AATAATTAT-TAATATAAAATA-AC
*
1035908 ATTAATTTATTAATATA
1 AATAA-TTATTAATATA
1035925 TTTTTAGACT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
23 23 0.68
24 11 0.32
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
AATAATTATTAATATAAAATAAC
Found at i:1036324 original size:19 final size:19
Alignment explanation
Indices: 1036300--1036355 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1036290 TAATTTATTT
*
1036300 AATAATTATAAAATTTATA
1 AATAATTATAAATTTTATA
1036319 AATAATTA-AAATTTTATTA
1 AATAATTATAAATTTTA-TA
* *
1036338 TATAATAATAAATTTTAT
1 AATAATTATAAATTTTAT
1036356 TTATTATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 7 0.22
19 17 0.53
20 8 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAATTATAAATTTTATA
Found at i:1036327 original size:26 final size:25
Alignment explanation
Indices: 1036281--1036331 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
1036271 TATATATAAA
* *
1036281 ATAAAATTTTAATTTATTTAATAATT
1 ATAAAATTTTAATATAATTAA-AATT
1036307 ATAAAATTTATAA-ATAATTAAAATT
1 ATAAAATTT-TAATATAATTAAAATT
1036332 TTATTATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.18
26 15 0.68
27 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATAAAATTTTAATATAATTAAAATT
Found at i:1036381 original size:26 final size:24
Alignment explanation
Indices: 1036331--1036383 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 24
1036321 TAATTAAAAT
*
1036331 TTTATTATATAATAATAAATTTTA
1 TTTATTATATAATAATAAATGTTA
1036355 TTTATTATATTAAATAATCAAA-GTTA
1 TTTATTATA-T-AATAAT-AAATGTTA
1036381 TTT
1 TTT
1036384 CAAAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 9 0.36
25 1 0.04
26 12 0.48
27 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTATTATATAATAATAAATGTTA
Found at i:1036776 original size:22 final size:23
Alignment explanation
Indices: 1036728--1036775 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 23
1036718 AATTTTAATT
1036728 TATATATAATGTACAATGAATTAAAA
1 TATATATAATGTACAATG-A--AAAA
1036754 TATATATAATGTACAATGAAAA
1 TATATATAATGTACAATGAAAA
1036776 TTTTAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.14
25 1 0.05
26 18 0.82
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.33
Consensus pattern (23 bp):
TATATATAATGTACAATGAAAAA
Found at i:1037600 original size:42 final size:42
Alignment explanation
Indices: 1037541--1037642 Score: 195
Period size: 42 Copynumber: 2.4 Consensus size: 42
1037531 CCTGTCGAAA
1037541 GCAGGACTAATAATTGAAAGGAATATAAGTATATAGTAATCT
1 GCAGGACTAATAATTGAAAGGAATATAAGTATATAGTAATCT
1037583 GCAGGACTAATAATTGAAAGGAATATAAGTATATAGTAATCT
1 GCAGGACTAATAATTGAAAGGAATATAAGTATATAGTAATCT
*
1037625 GCAGGACTAACAATTGAA
1 GCAGGACTAATAATTGAA
1037643 GTGATAGGTC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.26
Consensus pattern (42 bp):
GCAGGACTAATAATTGAAAGGAATATAAGTATATAGTAATCT
Found at i:1047905 original size:22 final size:24
Alignment explanation
Indices: 1047880--1047935 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
1047870 TTTAAATGTC
**
1047880 ATAATTATTATTTA-AAAATA-AA
1 ATAATTATTATAAATAAAATATAA
1047902 ATAATTA-TATAAATAAAATATAA
1 ATAATTATTATAAATAAAATATAA
1047925 ATAATTTATTA
1 ATAA-TTATTA
1047936 ATATACTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 4 0.14
22 13 0.46
23 6 0.21
24 3 0.11
25 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATAATTATTATAAATAAAATATAA
Found at i:1048318 original size:17 final size:16
Alignment explanation
Indices: 1048294--1048334 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
1048284 GTAATCAAAA
1048294 TTTATTAAAT-TTATAT
1 TTTATTAAATATTA-AT
1048310 TTATATTAAATATTAAT
1 TT-TATTAAATATTAAT
1048327 TTTATTAA
1 TTTATTAA
1048335 TAAATAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.35
17 12 0.52
18 3 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTATTAAATATTAAT
Found at i:1055127 original size:17 final size:17
Alignment explanation
Indices: 1055096--1055135 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1055086 AACATAGTAT
*
1055096 ATAAAA-TATATTATAA
1 ATAAAATTATACTATAA
*
1055112 ATGAAATTATACTATAA
1 ATAAAATTATACTATAA
1055129 ATAAAAT
1 ATAAAAT
1055136 AAATAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (17 bp):
ATAAAATTATACTATAA
Found at i:1055132 original size:21 final size:20
Alignment explanation
Indices: 1055110--1055195 Score: 59
Period size: 20 Copynumber: 4.2 Consensus size: 20
1055100 AATATATTAT
*
1055110 AAATGAAATTATACTATAAATA
1 AAAT-AAATAATA-TATAAATA
*
1055132 AAATAAATAATATATAAACA
1 AAATAAATAATATATAAATA
*
1055152 AAA-AATATAAAATATAATATA
1 AAATAA-ATAATATATAA-ATA
** *
1055173 TTATAAATAAAAT-TCAAATA
1 AAATAAATAATATAT-AAATA
1055193 AAA
1 AAA
1055196 GTTTTCCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
19 2 0.04
20 25 0.48
21 19 0.37
22 6 0.12
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.29
Consensus pattern (20 bp):
AAATAAATAATATATAAATA
Found at i:1055214 original size:117 final size:117
Alignment explanation
Indices: 1055093--1055303 Score: 261
Period size: 117 Copynumber: 1.8 Consensus size: 117
1055083 TTTAACATAG
* *
1055093 TATATA-AAATATATTATAAAT-GAAATTATACT-ATAA-ATAAAATAAATAATATATA-AACAA
1 TATATACAAA-ATA-TATAAATAGAAATAATACTAATAATATAAAAT-AATAAGATATATAA-AA
1055153 AAAATATAAAATATAATATATTATAAATAAAATTCAAATAAAAGTTTTCCAAATATA
62 AAAATAT-AAATATAATATATTATAAATAAAATTCAAATAAAAGTTTTCCAAATATA
* * * * *
1055210 TATATACAAAATATATAAATATAAATAATATTAATAATATACAATAATAAGATATATTAAAATAA
1 TATATACAAAATATATAAATAGAAATAATACTAATAATATAAAATAATAAGATATATAAAAAAAA
**
1055275 TATTCATATAATATATTATAAATAAAATT
66 TATAAATATAATATATTATAAATAAAATT
1055304 ATACTACAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
116 7 0.09
117 41 0.51
118 25 0.31
119 7 0.09
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (117 bp):
TATATACAAAATATATAAATAGAAATAATACTAATAATATAAAATAATAAGATATATAAAAAAAA
TATAAATATAATATATTATAAATAAAATTCAAATAAAAGTTTTCCAAATATA
Found at i:1055259 original size:26 final size:23
Alignment explanation
Indices: 1055222--1055273 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 23
1055212 TATACAAAAT
1055222 ATATAAATATAA-ATAATATTAATA
1 ATATAAATATAAGAT-ATATTAA-A
1055246 ATATACAATAATAAGATATATTAAA
1 ATATA-AAT-ATAAGATATATTAAA
1055271 ATA
1 ATA
1055274 ATATTCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 5 0.20
25 7 0.28
26 11 0.44
27 2 0.08
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
ATATAAATATAAGATATATTAAA
Found at i:1065751 original size:12 final size:12
Alignment explanation
Indices: 1065733--1065766 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1065723 ATCTATATAT
*
1065733 ATATATGTATGT
1 ATATATGTATGC
*
1065745 ATGTATGTATGC
1 ATATATGTATGC
1065757 ATATATGTAT
1 ATATATGTAT
1065767 CATTTTCACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (12 bp):
ATATATGTATGC
Found at i:1070560 original size:2 final size:2
Alignment explanation
Indices: 1070553--1070579 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1070543 ATTTTCAGGT
1070553 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1070580 CAGTCAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1073094 original size:22 final size:21
Alignment explanation
Indices: 1073066--1073119 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1073056 TTAAAAAATT
1073066 ATATTAATAAAAATAATTAATA
1 ATATTAATAAAAATAATTAA-A
* *
1073088 ATATTAA-AAAAATTATTTAA
1 ATATTAATAAAAATAATTAAA
*
1073108 ATAATAATAAAA
1 ATATTAATAAAA
1073120 TTTTAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.25
21 14 0.50
22 7 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATATTAATAAAAATAATTAAA
Found at i:1076122 original size:18 final size:19
Alignment explanation
Indices: 1076091--1076133 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
1076081 TAATTAAAAA
1076091 TTAATTTAATTATTTTTAT
1 TTAATTTAATTATTTTTAT
1076110 TTAATTT-ATTATTTTTAT
1 TTAATTTAATTATTTTTAT
*
1076128 TAAATT
1 TTAATT
1076134 AAAAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTAATTTAATTATTTTTAT
Found at i:1076367 original size:23 final size:21
Alignment explanation
Indices: 1076337--1076385 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
1076327 ATTATATAAA
1076337 TTTT-TTTAAAAAAATTATGATT
1 TTTTATTTAAAAAAATTAT--TT
*
1076359 TTTTATTTAGAAAAATTATTT
1 TTTTATTTAAAAAAATTATTT
1076380 TTTTAT
1 TTTTAT
1076386 AAAAATATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 8 0.32
22 4 0.16
23 13 0.52
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
TTTTATTTAAAAAAATTATTT
Found at i:1078729 original size:38 final size:41
Alignment explanation
Indices: 1078687--1078764 Score: 99
Period size: 38 Copynumber: 2.0 Consensus size: 41
1078677 AGATTATTTG
*
1078687 TATTTTAAATTTTAT-AGAAAGA-ATAAA-ATAAATAAATA
1 TATTTTAAATTTTATAAAAAAGATATAAATATAAATAAATA
* * *
1078725 TATTTTTAATTTTTTAAAAAATATATAAATATAAATAAAT
1 TATTTTAAATTTTATAAAAAAGATATAAATATAAATAAAT
1078765 CTGAACTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 13 0.39
39 5 0.15
40 5 0.15
41 10 0.30
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (41 bp):
TATTTTAAATTTTATAAAAAAGATATAAATATAAATAAATA
Found at i:1079302 original size:7 final size:7
Alignment explanation
Indices: 1079285--1079356 Score: 54
Period size: 8 Copynumber: 9.3 Consensus size: 7
1079275 TTAAGTATTG
1079285 ATAAAATT
1 ATAAAA-T
1079293 ATAAAAT
1 ATAAAAT
1079300 ATAAAAAT
1 AT-AAAAT
*
1079308 AATAAAAA
1 -ATAAAAT
**
1079316 ATAATGT
1 ATAAAAT
1079323 ATAAAAT
1 ATAAAAT
1079330 ATAATATAAT
1 AT-A-A-AAT
1079340 ATAAAAT
1 ATAAAAT
1079347 ATATAAAT
1 ATA-AAAT
1079355 AT
1 AT
1079357 TTTAAAATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
7 20 0.38
8 23 0.44
9 4 0.08
10 5 0.10
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (7 bp):
ATAAAAT
Found at i:1079306 original size:16 final size:16
Alignment explanation
Indices: 1079287--1079420 Score: 71
Period size: 18 Copynumber: 8.1 Consensus size: 16
1079277 AAGTATTGAT
1079287 AAAATTATAAAATATA
1 AAAATTATAAAATATA
*
1079303 AAAATAAT-AAA-A-A
1 AAAATTATAAAATATA
*
1079316 ATAATGTATAAAATATA
1 AAAAT-TATAAAATATA
1079333 ATATAA-TATAAAATATA
1 A-A-AATTATAAAATATA
*
1079350 TAAATATTTTAAAATATA
1 -AAA-ATTATAAAATATA
** *
1079368 TATTATTATTAACATATA
1 -AAAATTA-TAAAATATA
*
1079386 AAAATTTAAATAAATATA
1 AAAA-TTATA-AAATATA
*
1079404 AAATATT-TTAAATATA
1 AAA-ATTATAAAATATA
1079420 A
1 A
1079421 TTATAATAAA
Statistics
Matches: 90, Mismatches: 15, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
13 5 0.06
14 3 0.03
15 6 0.07
16 17 0.19
17 21 0.23
18 35 0.39
19 3 0.03
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.37
Consensus pattern (16 bp):
AAAATTATAAAATATA
Found at i:1079317 original size:10 final size:11
Alignment explanation
Indices: 1079297--1079338 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 11
1079287 AAAATTATAA
1079297 AATATAAAAAT
1 AATATAAAAAT
1079308 AATA-AAAAAT
1 AATATAAAAAT
1079318 AATGTATAAAATAT
1 AA--TATAAAA-AT
1079332 AATATAA
1 AATATAA
1079339 TATAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 8 0.30
11 4 0.15
12 7 0.26
13 4 0.15
14 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:1080204 original size:27 final size:27
Alignment explanation
Indices: 1080174--1080268 Score: 92
Period size: 26 Copynumber: 3.6 Consensus size: 27
1080164 TAATATTTAA
*
1080174 ATATAATAATTTTAAATTTATATAATT
1 ATATAATAATATTAAATTTATATAATT
* * *
1080201 ATATAA-AAAATTATA-TGATATAAATT
1 ATATAATAATATTAAATTTATAT-AATT
*
1080227 AT-TAAT-ATATTAATATTTATATAAAT
1 ATATAATAATATTAA-ATTTATATAATT
1080253 ATATAATAAT-TTAAAT
1 ATATAATAATATTAAAT
1080269 ATAATTATAA
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
25 13 0.24
26 20 0.37
27 19 0.35
28 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (27 bp):
ATATAATAATATTAAATTTATATAATT
Found at i:1080245 original size:52 final size:48
Alignment explanation
Indices: 1080157--1080281 Score: 137
Period size: 52 Copynumber: 2.5 Consensus size: 48
1080147 ACCGGAAAGA
* * *
1080157 AAAAAATTAATATTTAAATATAATAATTTTAAATTTATATAATTATAT
1 AAAAAATTAATATATAAATATAATAATATTAAATTTATATAAATATAT
1080205 AAAAAATTATATGATATAAATTATTAAT-ATATTAATATTTATATAAATATAT
1 AAAAAATTA-AT-ATATAAA-TA-TAATAATATTAA-ATTTATATAAATATAT
* * *
1080257 AATAATTTAA-ATATAATTATAATAA
1 AAAAAATTAATATATAAATATAATAA
1080282 AAAATAATTC
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
47 4 0.06
48 12 0.18
49 8 0.12
50 6 0.09
51 9 0.14
52 26 0.40
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (48 bp):
AAAAAATTAATATATAAATATAATAATATTAAATTTATATAAATATAT
Found at i:1080277 original size:20 final size:20
Alignment explanation
Indices: 1080230--1080281 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1080220 ATAAATTATT
*
1080230 AATATATTAAT-ATTTATATA
1 AATATA-TAATAATTTAAATA
1080250 AATATATAATAATTTAAATA
1 AATATATAATAATTTAAATA
1080270 TAAT-TATAATAA
1 -AATATATAATAA
1080282 AAAATAATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 4 0.14
20 22 0.76
21 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATATAATAATTTAAATA
Found at i:1080939 original size:21 final size:21
Alignment explanation
Indices: 1080905--1080973 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
1080895 ATTTAACTGT
1080905 TTATA-TAT-TTATATTTATA
1 TTATATTATATTATATTTATA
* *
1080924 TTATATTATATTATATATAAA
1 TTATATTATATTATATTTATA
* **
1080945 TTTTAAAATATTAATAATTTATA
1 TTATATTATATT-AT-ATTTATA
1080968 TTATAT
1 TTATAT
1080974 AAATTTTTAT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
19 5 0.14
20 3 0.08
21 18 0.49
22 2 0.05
23 9 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATATTATATTATATTTATA
Found at i:1081538 original size:20 final size:22
Alignment explanation
Indices: 1081513--1081554 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1081503 AAAAATTTAT
*
1081513 TTAAAA-ATTTTATTT-TATTA
1 TTAAAATATTATATTTATATTA
1081533 TTAAAATATTATATTTATATTA
1 TTAAAATATTATATTTATATTA
1081555 ATATATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTAAAATATTATATTTATATTA
Found at i:1081544 original size:19 final size:19
Alignment explanation
Indices: 1081507--1081561 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1081497 GGTTTAAAAA
*
1081507 ATTTAT-TTAAAA-ATTTT
1 ATTTATATTAAAATATTAT
1081524 ATTTTATTATTAAAATATTAT
1 A-TTTA-TATTAAAATATTAT
*
1081545 ATTTATATTAATATATT
1 ATTTATATTAAAATATT
1081562 TATAATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 1 0.03
18 4 0.12
19 12 0.38
20 10 0.31
21 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTATATTAAAATATTAT
Found at i:1081559 original size:14 final size:15
Alignment explanation
Indices: 1081542--1081570 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1081532 ATTAAAATAT
1081542 TATATTTAT-ATTAA
1 TATATTTATAATTAA
1081556 TATATTTATAATTAA
1 TATATTTATAATTAA
1081571 ATTTAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATTTATAATTAA
Found at i:1081611 original size:16 final size:15
Alignment explanation
Indices: 1081590--1081623 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1081580 AATTTTTATT
1081590 ATTAAATAATAATTAA
1 ATTAAATAA-AATTAA
*
1081606 ATTAAATAAATTTAA
1 ATTAAATAAAATTAA
1081621 ATT
1 ATT
1081624 TATAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAAATAAAATTAA
Found at i:1094655 original size:19 final size:19
Alignment explanation
Indices: 1094592--1094655 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
1094582 AGTCGTCAAA
*
1094592 AGTTGAGTCGAGAAAATAT
1 AGTTGAGTGGAGAAAATAT
*
1094611 AGTT-ATGTTGGA-AAAATAAA
1 AGTTGA-G-TGGAGAAAAT-AT
1094631 AG--GAGTGGAGAAAATAT
1 AGTTGAGTGGAGAAAATAT
1094648 AGTTGAGT
1 AGTTGAGT
1094656 CATCAAAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
17 7 0.20
18 7 0.20
19 15 0.43
20 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.28, T:0.27
Consensus pattern (19 bp):
AGTTGAGTGGAGAAAATAT
Found at i:1097998 original size:50 final size:50
Alignment explanation
Indices: 1097923--1098028 Score: 131
Period size: 50 Copynumber: 2.1 Consensus size: 50
1097913 GCAAAGTGAT
* ** * * * * *
1097923 TTGACTATTCTTCATCAGTCTTTGACAATCGAGAGAGGTGACTGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATAGAAAAAGATGACCGTAATTG
*
1097973 TTGACTATTTTTCACCAACCTTTGACAATAGAAAAAGATGACCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATAGAAAAAGATGACCGTAATTG
1098023 TTGACT
1 TTGACT
1098029 CTAAGCATCT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACCTTTGACAATAGAAAAAGATGACCGTAATTG
Found at i:1100742 original size:3 final size:3
Alignment explanation
Indices: 1100734--1100762 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1100724 TTGGACTGAG
1100734 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1100763 TTAATTGATT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1101562 original size:32 final size:32
Alignment explanation
Indices: 1101523--1101635 Score: 210
Period size: 32 Copynumber: 3.5 Consensus size: 32
1101513 ATGAGAACAT
1101523 TTTATTGACAAAATTCATGGCATGTGCAATTG
1 TTTATTGACAAAATTCATGGCATGTGCAATTG
1101555 TTTATTGACAAAATTCATGGCATGTGCAATTG
1 TTTATTGACAAAATTCATGGCATGTGCAATTG
1101587 TTTATTGACAAAATTCATGGCATGTGCAATTG
1 TTTATTGACAAAATTCATGGCATGTGCAATTG
1101619 TTTATT-ACCAAAATTCA
1 TTTATTGA-CAAAATTCA
1101636 ATGTTTATGA
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
31 1 0.01
32 79 0.99
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (32 bp):
TTTATTGACAAAATTCATGGCATGTGCAATTG
Found at i:1103402 original size:17 final size:18
Alignment explanation
Indices: 1103370--1103406 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1103360 TCCATAAATC
1103370 AAAAGAAATTAAAAAAAA
1 AAAAGAAATTAAAAAAAA
1103388 AAAAGAAA-TAGAAAAAAA
1 AAAAGAAATTA-AAAAAAA
1103406 A
1 A
1103407 CCAGGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (18 bp):
AAAAGAAATTAAAAAAAA
Found at i:1106352 original size:16 final size:18
Alignment explanation
Indices: 1106331--1106383 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 18
1106321 TTAATAAAAT
1106331 ATATTAAA-AAAT-TTTA
1 ATATTAAATAAATATTTA
1106347 ATATTAAATAAATATTTA
1 ATATTAAATAAATATTTA
* *
1106365 ATA-AAAATATATATTTA
1 ATATTAAATAAATATTTA
1106382 AT
1 AT
1106384 TAAATAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
16 8 0.24
17 18 0.55
18 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATTAAATAAATATTTA
Found at i:1106393 original size:17 final size:17
Alignment explanation
Indices: 1106349--1106394 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1106339 AAATTTTAAT
1106349 ATTAAATAA-ATATTTA
1 ATTAAATAATATATTTA
*
1106365 A-TAAAAATATATATTTA
1 ATTAAATA-ATATATTTA
1106382 ATTAAATAATATA
1 ATTAAATAATATA
1106395 ATTTTTATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 5 0.20
16 2 0.08
17 13 0.52
18 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAAATAATATATTTA
Found at i:1110276 original size:24 final size:24
Alignment explanation
Indices: 1110218--1110280 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
1110208 TAATTTATTT
1110218 TTAA-ATAAAAATAACATAATATA
1 TTAATATAAAAATAACATAATATA
*
1110241 TTAATATCAAAATTAACAT-ATATAA
1 TTAATAT-AAAAATAACATAATAT-A
1110266 TTGAAT-TAAAAATAA
1 TT-AATATAAAAATAA
1110281 GTTTAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
23 4 0.12
24 13 0.38
25 14 0.41
26 3 0.09
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (24 bp):
TTAATATAAAAATAACATAATATA
Found at i:1111700 original size:3 final size:3
Alignment explanation
Indices: 1111692--1111719 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1111682 ACTTCGTTTG
1111692 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1111720 CAAGGACATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1113733 original size:26 final size:26
Alignment explanation
Indices: 1113697--1113748 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1113687 GGCTATCGGA
*
1113697 CAAATTGGGCCTAACATTGTCCCAAT
1 CAAATTGGGCCTAACATCGTCCCAAT
*
1113723 CAAATTGGGCCTATCATCGTCCCAAT
1 CAAATTGGGCCTAACATCGTCCCAAT
1113749 TAAGTGGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (26 bp):
CAAATTGGGCCTAACATCGTCCCAAT
Found at i:1114487 original size:14 final size:14
Alignment explanation
Indices: 1114465--1114500 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1114455 TTGTAAAGAA
*
1114465 ATATATATATATAT
1 ATATGTATATATAT
1114479 ATATGTATATATAT
1 ATATGTATATATAT
*
1114493 GTATGTAT
1 ATATGTAT
1114501 GTATGTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (14 bp):
ATATGTATATATAT
Found at i:1114493 original size:10 final size:10
Alignment explanation
Indices: 1114465--1114496 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1114455 TTGTAAAGAA
*
1114465 ATATATATAT
1 ATATATATGT
1114475 ATATATATGT
1 ATATATATGT
1114485 ATATATATGT
1 ATATATATGT
1114495 AT
1 AT
1114497 GTATGTATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (10 bp):
ATATATATGT
Found at i:1122982 original size:3 final size:3
Alignment explanation
Indices: 1122974--1123000 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1122964 TTAACCTTCC
1122974 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1123001 CAAACAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1123391 original size:13 final size:15
Alignment explanation
Indices: 1123373--1123428 Score: 53
Period size: 19 Copynumber: 3.6 Consensus size: 15
1123363 AAATTATAAG
1123373 ATATTA-ATA-ATTT
1 ATATTATATATATTT
1123386 ATATTATATATATTT
1 ATATTATATATATTT
*
1123401 AAAATATTTATATATTTTT
1 ---ATA-TTATATATATTT
1123420 ATATTATAT
1 ATATTATAT
1123429 TTAAAAATTC
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 6 0.17
14 3 0.08
15 10 0.28
16 3 0.08
18 3 0.08
19 11 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATTATATATATTT
Found at i:1123391 original size:32 final size:34
Alignment explanation
Indices: 1123354--1123428 Score: 93
Period size: 32 Copynumber: 2.3 Consensus size: 34
1123344 ATAGTATAAA
*
1123354 ATATTATATAAATTATAAGATA-TTA-ATA-ATTT
1 ATATTATATAAATT-TAAAATATTTATATATATTT
* *
1123386 ATATTATATATATTTAAAATATTTATATATTTTT
1 ATATTATATAAATTTAAAATATTTATATATATTT
1123420 ATATTATAT
1 ATATTATAT
1123429 TTAAAAATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 6 0.16
32 16 0.43
33 3 0.08
34 12 0.32
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (34 bp):
ATATTATATAAATTTAAAATATTTATATATATTT
Found at i:1123394 original size:18 final size:19
Alignment explanation
Indices: 1123348--1123388 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1123338 TTTTTTATAG
*
1123348 TATAAAATATTATATAAAT
1 TATAAGATATTATATAAAT
*
1123367 TATAAGATATTA-ATAATT
1 TATAAGATATTATATAAAT
1123385 TATA
1 TATA
1123389 TTATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
TATAAGATATTATATAAAT
Found at i:1127026 original size:16 final size:17
Alignment explanation
Indices: 1126986--1127019 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1126976 AGAATATTTT
1126986 TTTATTTAAAAAAGTTA
1 TTTATTTAAAAAAGTTA
1127003 TTTATTTAAAAAA-TTA
1 TTTATTTAAAAAAGTTA
1127019 T
1 T
1127020 ATTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTATTTAAAAAAGTTA
Found at i:1127074 original size:12 final size:12
Alignment explanation
Indices: 1127040--1127124 Score: 59
Period size: 12 Copynumber: 7.1 Consensus size: 12
1127030 ATTTATAATC
*
1127040 AAATATGTATA-
1 AAATATATATAT
*
1127051 AAATACATATAT
1 AAATATATATAT
*
1127063 AAATATAAATATT
1 AAATATATATA-T
* * *
1127076 AAAATAAAAATTT
1 -AAATATATATAT
1127089 AAATA-ATATA-
1 AAATATATATAT
1127099 AAATTATATATAT
1 AAA-TATATATAT
*
1127112 ATATATATATAT
1 AAATATATATAT
1127124 A
1 A
1127125 TTTTGGAAAG
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
10 3 0.05
11 14 0.24
12 29 0.49
13 4 0.07
14 9 0.15
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (12 bp):
AAATATATATAT
Done.