Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 7 of 29
Found at i:947805 original size:18 final size:18
Alignment explanation
Indices: 947753--947808 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
947743 TTGTTTCTTT
*
947753 TTATGATTATGATTATGA
1 TTATGATTATGATTATTA
947771 TTATGATTATGATTATTA
1 TTATGATTATGATTATTA
* *
947789 TTATTATTATTATTATTA
1 TTATGATTATGATTATTA
947807 TT
1 TT
947809 TTGTGAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (18 bp):
TTATGATTATGATTATTA
Found at i:947808 original size:6 final size:6
Alignment explanation
Indices: 947753--947804 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
947743 TTGTTTCTTT
* * *
947753 TTATGA TTATGA TTATGA TTATGA TTATGA TTATTA TTATTA TTATTA
1 TTATGA TTATGA TTATGA TTATGA TTATGA TTATGA TTATGA TTATGA
947801 TTAT
1 TTAT
947805 TATTTTGTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.58
Consensus pattern (6 bp):
TTATGA
Found at i:949318 original size:18 final size:18
Alignment explanation
Indices: 949294--949334 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
949284 TTTTATTTTA
*
949294 ATTAAAAGT-TTTTAAAT
1 ATTAAAAATATTTTAAAT
*
949311 ATTAAAAATATTTTTAAT
1 ATTAAAAATATTTTAAAT
949329 ATTAAA
1 ATTAAA
949335 TAAATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
ATTAAAAATATTTTAAAT
Found at i:949975 original size:7 final size:7
Alignment explanation
Indices: 949963--949998 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
949953 AATTTGAAAT
949963 ATTATTA
1 ATTATTA
949970 ATTATT-
1 ATTATTA
949976 -TT-TTA
1 ATTATTA
949981 ATTATTA
1 ATTATTA
949988 ATTATTA
1 ATTATTA
949995 ATTA
1 ATTA
949999 AATTAACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
4 2 0.08
5 2 0.08
6 2 0.08
7 20 0.77
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
ATTATTA
Found at i:949999 original size:18 final size:18
Alignment explanation
Indices: 949963--949999 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
949953 AATTTGAAAT
**
949963 ATTATTAATTATTTTTTA
1 ATTATTAATTATTAATTA
949981 ATTATTAATTATTAATTA
1 ATTATTAATTATTAATTA
949999 A
1 A
950000 ATTAACTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTATTAATTATTAATTA
Found at i:950092 original size:24 final size:24
Alignment explanation
Indices: 950063--950119 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
950053 GATTGGTTAA
* *
950063 TTAAATTAATTAATTTTTAATTAT
1 TTAAATTAATTAAATTTAAATTAT
* *
950087 TTAAATT-TTTAAATTTAAATTTT
1 TTAAATTAATTAAATTTAAATTAT
950110 TTATAATTAA
1 TTA-AATTAA
950120 AATAAGTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTAAATTAATTAAATTTAAATTAT
Found at i:950104 original size:14 final size:15
Alignment explanation
Indices: 950074--950120 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
950064 TAAATTAATT
950074 AATTTTTAATTATTTA
1 AATTTTTAA-TATTTA
950090 AATTTTTAA-ATTTA
1 AATTTTTAATATTTA
* *
950104 AATTTTTTATAATTA
1 AATTTTTAATATTTA
950119 AA
1 AA
950121 ATAAGTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 13 0.46
15 6 0.21
16 9 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTTTTAATATTTA
Found at i:950117 original size:16 final size:16
Alignment explanation
Indices: 950074--950122 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
950064 TAAATTAATT
* *
950074 AATTTTTAATTATTTA
1 AATTTTTTATAATTTA
950090 AA-TTTTTA-AATTTA
1 AATTTTTTATAATTTA
*
950104 AATTTTTTATAATTAA
1 AATTTTTTATAATTTA
950120 AAT
1 AAT
950123 AAGTATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 7 0.25
15 11 0.39
16 10 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTTTTTATAATTTA
Found at i:950379 original size:30 final size:30
Alignment explanation
Indices: 950320--950390 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
950310 TAAAAAATTT
*
950320 TTAATTAATAAATAGATTAAAATTTTTTTA
1 TTAATTAATAAATAGATTAAAATTATTTTA
* *
950350 TTAATTGATTAATA-ATTAAATATTATTTTAA
1 TTAATTAATAAATAGATTAAA-ATTATTTT-A
*
950381 TCAATTAATA
1 TTAATTAATA
950391 TAATTAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 6 0.18
30 19 0.58
31 8 0.24
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (30 bp):
TTAATTAATAAATAGATTAAAATTATTTTA
Found at i:950584 original size:23 final size:24
Alignment explanation
Indices: 950554--950599 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
950544 ATTTAAAATT
950554 TTATTTAAA-AAAATAATATTAAA
1 TTATTTAAATAAAATAATATTAAA
* *
950577 TTATTTAAATTAACTAATATTAA
1 TTATTTAAATAAAATAATATTAA
950600 TACGATTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TTATTTAAATAAAATAATATTAAA
Found at i:951308 original size:15 final size:15
Alignment explanation
Indices: 951271--951310 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
951261 TAAAACTCAA
*
951271 TAAAAAAAATTAAAT
1 TAAAAAATATTAAAT
**
951286 TATTAAATATTAAAT
1 TAAAAAATATTAAAT
951301 TAAAAAATAT
1 TAAAAAATAT
951311 GACAAGGACG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAAAAATATTAAAT
Found at i:951849 original size:20 final size:19
Alignment explanation
Indices: 951820--951862 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
951810 ATTACAAAAT
951820 TTATATTTTTATAAT-ATAA
1 TTATATTTTT-TAATAATAA
*
951839 TTATATATTTTTTATAATAA
1 TTATAT-TTTTTAATAATAA
951859 TTAT
1 TTAT
951863 TATAACTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATATTTTTTAATAATAA
Found at i:953013 original size:28 final size:28
Alignment explanation
Indices: 952982--953036 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
952972 TATCTGTATA
952982 AATTTAAAATTAATTTTATATTT-TTTAT
1 AATTTAAAATTAA-TTTATATTTATTTAT
** *
953010 AATTTTTATTTAATTTATATTTATTTA
1 AATTTAAAATTAATTTATATTTATTTA
953037 GTTTTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
AATTTAAAATTAATTTATATTTATTTAT
Found at i:953047 original size:28 final size:27
Alignment explanation
Indices: 952991--953044 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
952981 AAATTTAAAA
952991 TTAATTTTATATTTTTTATAATTTTTAT
1 TTAATTTTATATTTTTTAT-ATTTTTAT
* *
953019 TTAA-TTTATATTTATT-TAGTTTTAT
1 TTAATTTTATATTTTTTATATTTTTAT
953044 T
1 T
953045 ATTGTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.33
26 1 0.04
27 11 0.46
28 4 0.17
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (27 bp):
TTAATTTTATATTTTTTATATTTTTAT
Found at i:953465 original size:11 final size:11
Alignment explanation
Indices: 953416--953467 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 11
953406 AAACATGATT
953416 AAATAAATAT-
1 AAATAAATATA
953426 -AATACAA-ATA
1 AAATA-AATATA
953436 AAAT-AAT-TA
1 AAATAAATATA
953445 AAATATAATATA
1 AAATA-AATATA
953457 AAATAAATATA
1 AAATAAATATA
953468 TATTTATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
9 14 0.40
10 2 0.06
11 12 0.34
12 7 0.20
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATAAATATA
Found at i:956567 original size:2 final size:2
Alignment explanation
Indices: 956560--956589 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
956550 TCAAACGCTA
956560 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
956590 TGTACTGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:958639 original size:14 final size:15
Alignment explanation
Indices: 958620--958648 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
958610 ACTTATATTC
958620 TTATTA-ATTTTTAA
1 TTATTATATTTTTAA
958634 TTATTATATTTTTAA
1 TTATTATATTTTTAA
958649 AAAAATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATTATATTTTTAA
Found at i:958640 original size:17 final size:17
Alignment explanation
Indices: 958585--958648 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
958575 AAAATATATC
*
958585 TTATTAATTTTTAATTTT
1 TTATTAATTTTTAA-TTA
** *
958603 TTATTAA-ACTTATATTC
1 TTATTAATTTTTA-ATTA
958620 TTATTAATTTTTAATTA
1 TTATTAATTTTTAATTA
958637 TTA-T-ATTTTTAA
1 TTATTAATTTTTAA
958649 AAAAATAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
15 8 0.21
16 1 0.03
17 18 0.47
18 11 0.29
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTAATTTTTAATTA
Found at i:964857 original size:20 final size:20
Alignment explanation
Indices: 964834--964872 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
964824 ATTTTATTTT
*
964834 TTATA-ATTATATTTAAATTA
1 TTATATATT-TATATAAATTA
964854 TTATATATTTATATAAATT
1 TTATATATTTATATAAATT
964873 TTAACTGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATATATTTATATAAATTA
Found at i:965390 original size:16 final size:14
Alignment explanation
Indices: 965337--965385 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
965327 TGTTAATTAA
965337 ATTTTGTTATATTAAT
1 ATTTT-TTATA-TAAT
* *
965353 A-TATTTATATCAT
1 ATTTTTTATATAAT
965366 ATTTTTTATATAAT
1 ATTTTTTATATAAT
965380 ATTTTT
1 ATTTTT
965386 ATTATTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 4 0.14
14 21 0.75
15 2 0.07
16 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (14 bp):
ATTTTTTATATAAT
Found at i:968756 original size:16 final size:16
Alignment explanation
Indices: 968731--968767 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
968721 TAATAATTTT
968731 TTTAAAAAAAATTTAAA
1 TTTAAAAAAAA-TTAAA
*
968748 TTTAAAAAAAATTATA
1 TTTAAAAAAAATTAAA
968764 TTTA
1 TTTA
968768 TCCCTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAAAAAAAATTAAA
Found at i:968822 original size:43 final size:43
Alignment explanation
Indices: 968745--968832 Score: 99
Period size: 43 Copynumber: 2.0 Consensus size: 43
968735 AAAAAAATTT
* * *
968745 AAATTTAAAAAAAATTATATTTATCCCTATAATATTTTTTCTA
1 AAATTTAAAAAAAATTATATTTATCCCTAAAATATTATTTATA
* *
968788 AAATTTAATACAAAA-TATATTTA-CTCTTAAAATATTATTTATA
1 AAATTTAA-AAAAAATTATATTTATC-CCTAAAATATTATTTATA
968831 AA
1 AA
968833 TTAATTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
42 1 0.03
43 32 0.84
44 5 0.13
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (43 bp):
AAATTTAAAAAAAATTATATTTATCCCTAAAATATTATTTATA
Found at i:969479 original size:16 final size:16
Alignment explanation
Indices: 969444--969479 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
969434 GAAAATAACT
* *
969444 TAATAATAATTTAAGT
1 TAATAATAATTGAAGA
969460 TAATAATAATTGAAGA
1 TAATAATAATTGAAGA
969476 TAAT
1 TAAT
969480 TTTAAGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (16 bp):
TAATAATAATTGAAGA
Found at i:969638 original size:15 final size:14
Alignment explanation
Indices: 969603--969629 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
969593 TATTTAAAAT
969603 TAATTTAAAAATAA
1 TAATTTAAAAATAA
969617 TAATTTAAAAATA
1 TAATTTAAAAATA
969630 TATTTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATTTAAAAATAA
Found at i:969662 original size:25 final size:23
Alignment explanation
Indices: 969618--969689 Score: 72
Period size: 25 Copynumber: 3.0 Consensus size: 23
969608 TAAAAATAAT
* *
969618 AATTTAAAAATATATTTTTTATTA
1 AATTTAAAAATAAATATTTT-TTA
969642 AATTTAAAAAATAAATATTTTTTA
1 AATTT-AAAAATAAATATTTTTTA
* *
969666 ATGTTTAGAAATAAATATATTTTT
1 A-ATTTAAAAATAAATAT-TTTTT
969690 TAATAAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 20 0.49
25 21 0.51
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (23 bp):
AATTTAAAAATAAATATTTTTTA
Found at i:971980 original size:19 final size:19
Alignment explanation
Indices: 971928--971974 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
971918 AAATGACATA
*
971928 AAATATGATAAAAAATAATAT
1 AAATATAAT-AAAAAT-ATAT
*
971949 GAATATAATAAAAATATAT
1 AAATATAATAAAAATATAT
971968 AAATATA
1 AAATATA
971975 TCAAAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 10 0.43
20 6 0.26
21 7 0.30
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
AAATATAATAAAAATATAT
Found at i:972050 original size:20 final size:20
Alignment explanation
Indices: 972014--972054 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
972004 ATTTAAAATT
*
972014 TTTTATATAAATATATATTA
1 TTTTAAATAAATATATATTA
972034 TTTTAAATACAAT-TATATTA
1 TTTTAAATA-AATATATATTA
972054 T
1 T
972055 AAAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTAAATAAATATATATTA
Found at i:974048 original size:22 final size:22
Alignment explanation
Indices: 974020--974061 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
974010 GTTAAAGTTT
974020 TATTTTTAT-GTTAATATTTATA
1 TATTTTTATAGTT-ATATTTATA
974042 TATTTTTATAGTTATATTTA
1 TATTTTTATAGTTATATTTA
974062 AACAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (22 bp):
TATTTTTATAGTTATATTTATA
Found at i:974780 original size:12 final size:12
Alignment explanation
Indices: 974763--974787 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
974753 GAAGCTCTTT
974763 TTTTTTTTTTTC
1 TTTTTTTTTTTC
974775 TTTTTTTTTTTC
1 TTTTTTTTTTTC
974787 T
1 T
974788 CTTAGCTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:974780 original size:14 final size:14
Alignment explanation
Indices: 974761--974790 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
974751 AAGAAGCTCT
*
974761 TTTTTTTTTTTTTC
1 TTTTTTTTTTTCTC
974775 TTTTTTTTTTTCTC
1 TTTTTTTTTTTCTC
974789 TT
1 TT
974791 AGCTATCACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTTTCTC
Found at i:977799 original size:14 final size:14
Alignment explanation
Indices: 977780--977847 Score: 54
Period size: 14 Copynumber: 5.0 Consensus size: 14
977770 GTTAAAATTC
977780 TTATTAATTTTTAA
1 TTATTAATTTTTAA
* *
977794 TTATTATAATGTT-A
1 TTATTA-ATTTTTAA
*
977808 TTA-T--TTTTTAT
1 TTATTAATTTTTAA
*
977819 TTATTAATTTTTTA
1 TTATTAATTTTTAA
977833 TTATTATATTTTTAA
1 TTATTA-ATTTTTAA
977848 AAAATATATT
Statistics
Matches: 40, Mismatches: 8, Indels: 11
0.68 0.14 0.19
Matches are distributed among these distances:
10 3 0.08
11 3 0.08
12 1 0.03
13 1 0.03
14 21 0.52
15 11 0.28
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (14 bp):
TTATTAATTTTTAA
Found at i:977830 original size:15 final size:14
Alignment explanation
Indices: 977805--977845 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
977795 TATTATAATG
977805 TTATT-ATTTTTTA
1 TTATTAATTTTTTA
977818 TTTATTAATTTTTTA
1 -TTATTAATTTTTTA
977833 TTATTATATTTTT
1 TTATTA-ATTTTT
977846 AAAAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTAATTTTTTA
Found at i:977900 original size:16 final size:16
Alignment explanation
Indices: 977852--977904 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
977842 TTTTAAAAAA
*
977852 TATATTCTTATTAATT
1 TATATTCTTATTAACT
* *
977868 TTTAATT-TTTTTAAACT
1 TAT-ATTCTTATT-AACT
977885 TATATTCTTATTAACT
1 TATATTCTTATTAACT
977901 TATA
1 TATA
977905 ATGTTATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 17 0.59
17 12 0.41
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (16 bp):
TATATTCTTATTAACT
Found at i:977911 original size:16 final size:16
Alignment explanation
Indices: 977852--977913 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
977842 TTTTAAAAAA
* *
977852 TATATTCTTATTAATT
1 TATAATCTTATTAACT
* * *
977868 TTTAATTTTTTTAAACT
1 TATAATCTTATT-AACT
*
977885 TATATTCTTATTAACT
1 TATAATCTTATTAACT
*
977901 TATAATGTTATTA
1 TATAATCTTATTA
977914 TTGTTATTAA
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
16 23 0.68
17 11 0.32
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (16 bp):
TATAATCTTATTAACT
Found at i:978249 original size:14 final size:15
Alignment explanation
Indices: 978232--978260 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
978222 ATGTAAAATT
978232 TTATTA-ATTTTTAA
1 TTATTACATTTTTAA
978246 TTATTACATTTTTAA
1 TTATTACATTTTTAA
978261 AAAATTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTACATTTTTAA
Found at i:980733 original size:22 final size:22
Alignment explanation
Indices: 980674--980734 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 22
980664 GTCAAATTGC
*
980674 TAAATATTTAATTTCAATAAAT
1 TAAATATTTAATTTTAATAAAT
* *
980696 TAAA-A-TTACACTTTAA-AATCT
1 TAAATATTTA-ATTTTAATAA-AT
980717 TAAATATTTAATTTTAAT
1 TAAATATTTAATTTTAAT
980735 TTTTTATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
20 5 0.17
21 11 0.37
22 11 0.37
23 3 0.10
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAATATTTAATTTTAATAAAT
Found at i:982475 original size:23 final size:23
Alignment explanation
Indices: 982425--982495 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 23
982415 ACGTAAAAAT
*
982425 AACATAACATTGAAAAAATAATTAA
1 AACATAACA-TG-AAAAATAAATAA
982450 AACATAACATGAAAAATAACAT-A
1 AACATAACATGAAAAATAA-ATAA
*
982473 AACACT-ACATAAAAATATAAATA
1 AACA-TAACATGAAAA-ATAAATA
982496 TATTAAACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
23 23 0.57
24 8 0.20
25 9 0.22
ACGTcount: A:0.65, C:0.11, G:0.03, T:0.21
Consensus pattern (23 bp):
AACATAACATGAAAAATAAATAA
Found at i:983009 original size:33 final size:34
Alignment explanation
Indices: 982954--983022 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 34
982944 ATACCATAAC
* *
982954 ATAAAATTTATATAAAATATAAT-TACATAATGAT
1 ATAAAATATATATAAAATATAATATAAAT-ATGAT
982988 ATAAAATATA-AT-AAATAATAATATAAATATGAT
1 ATAAAATATATATAAAAT-ATAATATAAATATGAT
983021 AT
1 AT
983023 TAATGTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 4 0.13
33 14 0.45
34 13 0.42
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (34 bp):
ATAAAATATATATAAAATATAATATAAATATGAT
Found at i:983011 original size:22 final size:23
Alignment explanation
Indices: 982963--983014 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
982953 CATAAAATTT
* *
982963 ATATAAAATATAATTACATAATG
1 ATATAAAATATAATTAAATAATA
982986 ATATAAAATATAA-TAAATAATA
1 ATATAAAATATAATTAAATAATA
983008 ATATAAA
1 ATATAAA
983015 TATGATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
ATATAAAATATAATTAAATAATA
Found at i:983108 original size:17 final size:16
Alignment explanation
Indices: 983041--983110 Score: 56
Period size: 17 Copynumber: 4.2 Consensus size: 16
983031 ATATATATAT
983041 ATATCAAAA-TTTATAAA
1 ATAT-AAAATTTTA-AAA
983058 ATAT-AAATTATTAATAA
1 ATATAAAATT-TTAA-AA
983075 AT-TAAAATTTGTAAAA
1 ATATAAAATTT-TAAAA
*
983091 ATATAAAATATTTTAAA
1 ATATAAAAT-TTTAAAA
983108 ATA
1 ATA
983111 ATTATAAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
15 3 0.07
16 8 0.18
17 32 0.71
18 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (16 bp):
ATATAAAATTTTAAAA
Found at i:983132 original size:21 final size:21
Alignment explanation
Indices: 983108--983157 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
983098 ATATTTTAAA
*
983108 ATAATTATAAAATAAAAATAT
1 ATAAATATAAAATAAAAATAT
*
983129 ATAAATATAAAATAAATATAT
1 ATAAATATAAAATAAAAATAT
*
983150 ATGAATAT
1 ATAAATAT
983158 TAAGATTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
ATAAATATAAAATAAAAATAT
Found at i:983145 original size:11 final size:11
Alignment explanation
Indices: 983089--983148 Score: 61
Period size: 11 Copynumber: 5.6 Consensus size: 11
983079 AAATTTGTAA
983089 AAATATAAAAT
1 AAATATAAAAT
* *
983100 -ATTTTAAAAT
1 AAATATAAAAT
*
983110 AATTATAAAAT
1 AAATATAAAAT
* *
983121 AAAAAT-ATAT
1 AAATATAAAAT
983131 AAATATAAAAT
1 AAATATAAAAT
983142 AAATATA
1 AAATATA
983149 TATGAATATT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 16 0.41
11 23 0.59
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATATAAAAT
Found at i:983296 original size:10 final size:10
Alignment explanation
Indices: 983270--983299 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
983260 TCCAAAACTC
983270 TTTTTTT-TT
1 TTTTTTTGTT
983279 TTTTTTTGTT
1 TTTTTTTGTT
983289 TTTTTTTGTT
1 TTTTTTTGTT
983299 T
1 T
983300 AAAAATACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.35
10 13 0.65
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:983910 original size:13 final size:14
Alignment explanation
Indices: 983874--983911 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
983864 CTCATTTCAC
983874 TATA-TTTTATATT
1 TATATTTTTATATT
*
983887 TATATTATTAT-TT
1 TATATTTTTATATT
983900 TATATTTTTATA
1 TATATTTTTATA
983912 ATTAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATATTTTTATATT
Found at i:983915 original size:19 final size:19
Alignment explanation
Indices: 983876--983915 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
983866 CATTTCACTA
*
983876 TATTTTATATTTATATTAT
1 TATTTTATATTTATATAAT
*
983895 TATTTTATATTTTTATAAT
1 TATTTTATATTTATATAAT
983914 TA
1 TA
983916 AATTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTTATATTTATATAAT
Found at i:984960 original size:24 final size:24
Alignment explanation
Indices: 984933--984987 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
984923 AACGGATTCA
*
984933 TAAATATT-TTTATTTTAAATTTAT
1 TAAATATTATTT-TTTTAAATTAAT
984957 TAAATATTATTTTTTTAAATTAAT
1 TAAATATTATTTTTTTAAATTAAT
*
984981 TACATAT
1 TAAATAT
984988 ATTAATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TAAATATTATTTTTTTAAATTAAT
Found at i:985433 original size:11 final size:11
Alignment explanation
Indices: 985417--985451 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
985407 CACTTTATGT
985417 ATCAAGATTTA
1 ATCAAGATTTA
985428 ATCAAGATTT-
1 ATCAAGATTTA
985438 ATCAAGATTTA
1 ATCAAGATTTA
985449 ATC
1 ATC
985452 GTTACATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (11 bp):
ATCAAGATTTA
Found at i:985443 original size:10 final size:10
Alignment explanation
Indices: 985416--985448 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
985406 TCACTTTATG
985416 TATCAAGATT
1 TATCAAGATT
985426 TAATCAAGATT
1 T-ATCAAGATT
985437 TATCAAGATT
1 TATCAAGATT
985447 TA
1 TA
985449 ATCGTTACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (10 bp):
TATCAAGATT
Found at i:986168 original size:20 final size:20
Alignment explanation
Indices: 986120--986168 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
986110 AATATATATG
*
986120 TATAAATATTTTAAAATCTA
1 TATAAATATATTAAAATCTA
*
986140 TAT-AATATATTAAAATTTA
1 TATAAATATATTAAAATCTA
986159 TATAAATATA
1 TATAAATATA
986169 AAATACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAAATATATTAAAATCTA
Found at i:997120 original size:156 final size:156
Alignment explanation
Indices: 996857--997173 Score: 598
Period size: 156 Copynumber: 2.0 Consensus size: 156
996847 ATACTAGTGA
*
996857 TTTTGAAAGTGCCAACTCCCCCTGAGCAGCAGAAAGTGCAGCTATTGTGCTTTGAAGTGCTAAAT
1 TTTTGAAAGTGCCAACTCCCCCTGAGCAGCAGAAAGTGCAGCTATTGTACTTTGAAGTGCTAAAT
* *
996922 TGACCTTCTGATTTTCAGCAACCTTGTCGTAAAGGCTCTTGACTTCTTCCTTCAGGAAGGCAATC
66 GGACCTTCTGATTTTCAGCAACCTTCTCGTAAAGGCTCTTGACTTCTTCCTTCAGGAAGGCAATC
996987 TGGTTTTCCATTTCTTTTGCACTAAG
131 TGGTTTTCCATTTCTTTTGCACTAAG
*
997013 TTTTGAAAGTGCCAACTCCCCCTGAGCAGCAGAAAGTTCAGCTATTGTACTTTGAAGTGCTAAAT
1 TTTTGAAAGTGCCAACTCCCCCTGAGCAGCAGAAAGTGCAGCTATTGTACTTTGAAGTGCTAAAT
997078 GGACCTTCTGATTTTCAGCAACCTTCTCGTAAAGGCTCTTGACTTCTTCCTTCAGGAAGGCAATC
66 GGACCTTCTGATTTTCAGCAACCTTCTCGTAAAGGCTCTTGACTTCTTCCTTCAGGAAGGCAATC
997143 TGGTTTTCCATTTCTTTTGCACTAAG
131 TGGTTTTCCATTTCTTTTGCACTAAG
997169 TTTTG
1 TTTTG
997174 CAGTTTCAAG
Statistics
Matches: 157, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
156 157 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (156 bp):
TTTTGAAAGTGCCAACTCCCCCTGAGCAGCAGAAAGTGCAGCTATTGTACTTTGAAGTGCTAAAT
GGACCTTCTGATTTTCAGCAACCTTCTCGTAAAGGCTCTTGACTTCTTCCTTCAGGAAGGCAATC
TGGTTTTCCATTTCTTTTGCACTAAG
Found at i:1001391 original size:33 final size:32
Alignment explanation
Indices: 1001354--1001429 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 32
1001344 ATATAACAAC
1001354 ATAATATAAA-TACATAAA-TATTTTAAAATTTAT
1 ATAATATAAATTA-ATAAAGTA--TTAAAATTTAT
1001387 ATAAT-TCAAATTAATAAAGTATTAAAATTTAT
1 ATAATAT-AAATTAATAAAGTATTAAAATTTAT
1001419 ATAAATATAAA
1 AT-AATATAAA
1001430 ATACTTTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
32 14 0.37
33 19 0.50
34 5 0.13
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (32 bp):
ATAATATAAATTAATAAAGTATTAAAATTTAT
Found at i:1001429 original size:17 final size:17
Alignment explanation
Indices: 1001377--1001431 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
1001367 ATAAATATTT
1001377 TAAAATTTATAT-AAT-
1 TAAAATTTATATAAATA
*
1001392 TCAAA-TTA-ATAAAGTA
1 TAAAATTTATATAAA-TA
1001408 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
1001426 TAAAAT
1 TAAAAT
1001432 ACTTTAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
13 2 0.06
14 5 0.16
15 5 0.16
17 10 0.31
18 5 0.16
19 5 0.16
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:1002127 original size:16 final size:16
Alignment explanation
Indices: 1002106--1002157 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
1002096 TTTTAATAAT
*
1002106 TAATTTTAAGTAAAAA
1 TAATTTTAAATAAAAA
*
1002122 TAATTTTATTTATAAATAA
1 TAATTTTA--AATAAA-AA
1002141 TAA-TTTAAATAAAAA
1 TAATTTTAAATAAAAA
1002156 TA
1 TA
1002158 TATATTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
15 4 0.13
16 13 0.43
18 8 0.27
19 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
TAATTTTAAATAAAAA
Found at i:1002348 original size:21 final size:21
Alignment explanation
Indices: 1002319--1002373 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
1002309 TATATATTCT
1002319 ATAATTAAAATTAAATAAA-A
1 ATAATTAAAATTAAATAAATA
*
1002339 ATATTATAAAATTAAATAAATA
1 ATAAT-TAAAATTAAATAAATA
1002361 ATAATTAAAATTA
1 ATAATTAAAATTA
1002374 TAAGATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 4 0.13
21 22 0.71
22 5 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAATTAAAATTAAATAAATA
Found at i:1002355 original size:15 final size:16
Alignment explanation
Indices: 1002319--1002376 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 16
1002309 TATATATTCT
1002319 ATAATTAAA-ATTA-A
1 ATAATTAAATATTATA
1002333 ATAA--AAATATTATA
1 ATAATTAAATATTATA
*
1002347 A-AATTAAATA-AATA
1 ATAATTAAATATTATA
1002361 ATAATTAAA-ATTATA
1 ATAATTAAATATTATA
1002376 A
1 A
1002377 GATATTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
12 3 0.08
13 6 0.17
14 11 0.31
15 16 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAATTAAATATTATA
Found at i:1002358 original size:25 final size:27
Alignment explanation
Indices: 1002312--1002361 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1002302 TTAATATTAT
* *
1002312 ATATTCTATAATTAAAATTAAATAAAA
1 ATATTATAAAATTAAAATTAAATAAAA
1002339 ATATTATAAAATT-AAA-TAAATAA
1 ATATTATAAAATTAAAATTAAATAA
1002362 TAATTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 3 0.14
27 11 0.52
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
ATATTATAAAATTAAAATTAAATAAAA
Found at i:1003158 original size:18 final size:19
Alignment explanation
Indices: 1003135--1003175 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1003125 TAAAAATATT
* *
1003135 TATTTTTTAAAT-TTAAAA
1 TATTTTTAAAATAATAAAA
1003153 TATTTTTAAAATAATAAAA
1 TATTTTTAAAATAATAAAA
1003172 TATT
1 TATT
1003176 AACATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTTTAAAATAATAAAA
Found at i:1003318 original size:17 final size:18
Alignment explanation
Indices: 1003296--1003331 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1003286 GAATATAATT
1003296 TATTATGTTAATAA-AAA
1 TATTATGTTAATAATAAA
*
1003313 TATTATTTTAATAATAAA
1 TATTATGTTAATAATAAA
1003331 T
1 T
1003332 TGTAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TATTATGTTAATAATAAA
Found at i:1003636 original size:16 final size:16
Alignment explanation
Indices: 1003615--1003662 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 16
1003605 CTTATCATAT
1003615 TAAATATTTAATATTA
1 TAAATATTTAATATTA
1003631 TAAATAATTTTAATATT-
1 TAAAT-A-TTTAATATTA
*
1003648 TTAATATTT-ATATTA
1 TAAATATTTAATATTA
1003663 AATTACTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 5 0.18
15 3 0.11
16 6 0.21
17 5 0.18
18 9 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TAAATATTTAATATTA
Found at i:1003772 original size:21 final size:22
Alignment explanation
Indices: 1003746--1003791 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1003736 TACATTAATA
1003746 TAAATAATAATTATAA-T-ATTT
1 TAAATAATAA-TATAATTAATTT
*
1003767 TAAATATTAATATAATTAATTT
1 TAAATAATAATATAATTAATTT
1003789 TAA
1 TAA
1003792 TAACAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAATAATAATATAATTAATTT
Found at i:1003848 original size:48 final size:49
Alignment explanation
Indices: 1003770--1003894 Score: 126
Period size: 48 Copynumber: 2.5 Consensus size: 49
1003760 AATATTTTAA
** * ** *
1003770 ATATTAATATAATTAATTTTAATAACAAATACTATTGTTTTAAGTATT-TC
1 ATATTAATATAA-T-ATTTTAATATTAAATACTATTATTAAAAATATTATC
* *
1003820 ATATTAATATAATATTTTAATATTAAATATTATTATTAAAAATATTATT
1 ATATTAATATAATATTTTAATATTAAATACTATTATTAAAAATATTATC
*
1003869 ATTTTAATATAAATATTTTTAATATT
1 ATATTAATAT-AATA-TTTTAATATT
1003895 TATATCAATA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
48 26 0.41
49 11 0.17
50 16 0.25
51 10 0.16
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (49 bp):
ATATTAATATAATATTTTAATATTAAATACTATTATTAAAAATATTATC
Found at i:1004001 original size:20 final size:21
Alignment explanation
Indices: 1003976--1004015 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1003966 TGAGCCATAA
1003976 AAAAAAACTCTAT-TTTTTTC
1 AAAAAAACTCTATATTTTTTC
* *
1003996 AAAAAATCTTTATATTTTTT
1 AAAAAAACTCTATATTTTTT
1004016 GGAAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (21 bp):
AAAAAAACTCTATATTTTTTC
Found at i:1004021 original size:22 final size:22
Alignment explanation
Indices: 1003986--1004030 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1003976 AAAAAAACTC
*
1003986 TATTTTTTTCAAAAAATCTTTA
1 TATTTTTTGCAAAAAATCTTTA
* * *
1004008 TATTTTTTGGAAAATATTTTTA
1 TATTTTTTGCAAAAAATCTTTA
1004030 T
1 T
1004031 GAAGTGAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (22 bp):
TATTTTTTGCAAAAAATCTTTA
Found at i:1004673 original size:16 final size:17
Alignment explanation
Indices: 1004630--1004674 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
1004620 TTTTAATTGA
1004630 AAAT-AAATTAAATATT
1 AAATAAAATTAAATATT
1004646 AAATAAATATTAAAT-TT
1 AAATAAA-ATTAAATATT
1004663 -AATAATAATTAA
1 AAATAA-AATTAA
1004675 TAAAAATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 14 0.54
17 5 0.19
18 7 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATAAAATTAAATATT
Found at i:1004690 original size:26 final size:28
Alignment explanation
Indices: 1004647--1004710 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 28
1004637 TTAAATATTA
*
1004647 AATAAATATTAAATTTAA-TAATAAT-T
1 AATAAAAATTAAATTTAATTAATAATAT
1004673 AATAAAAATGTAAA-TTAATTTAATAATAT
1 AATAAAAAT-TAAATTTAA-TTAATAATAT
1004702 AAGTAAAAA
1 AA-TAAAAA
1004711 AATTAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 12 0.38
27 4 0.12
28 7 0.22
29 3 0.09
30 6 0.19
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (28 bp):
AATAAAAATTAAATTTAATTAATAATAT
Found at i:1005219 original size:36 final size:38
Alignment explanation
Indices: 1005137--1005220 Score: 111
Period size: 36 Copynumber: 2.3 Consensus size: 38
1005127 AAATAATAAA
* *
1005137 AATATAAAATAAATATACAAATATATTAAATTTTATAT
1 AATATAAAATAAATATACAAATACATTAAATTATATAT
**
1005175 AATA-AAAATAAAT-TATTAATACATTAAATTATAT-T
1 AATATAAAATAAATATACAAATACATTAAATTATATAT
1005210 AATATAAAATA
1 AATATAAAATA
1005221 TTTTAAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 5 0.12
36 23 0.56
37 9 0.22
38 4 0.10
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (38 bp):
AATATAAAATAAATATACAAATACATTAAATTATATAT
Found at i:1006137 original size:20 final size:19
Alignment explanation
Indices: 1006089--1006141 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
1006079 TTATTTTAAT
1006089 AATATATTTATATAAAATTA
1 AATATATTT-TATAAAATTA
* *
1006109 AATTTTATTTTTTAAAATATA
1 AA-TATATTTTATAAAAT-TA
1006130 AATATATTTTAT
1 AATATATTTTAT
1006142 CATATATTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AATATATTTTATAAAATTA
Found at i:1006585 original size:23 final size:24
Alignment explanation
Indices: 1006542--1006594 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
1006532 TATATAATTT
* *
1006542 TATAAATATATAAATATAATTATA
1 TATAAATAAATAAATAAAATTATA
1006566 TATAAA-AAATAAATAAAATTA-A
1 TATAAATAAATAAATAAAATTATA
1006588 TA-AAATA
1 TATAAATA
1006595 TTTTTTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 3 0.12
22 4 0.15
23 13 0.50
24 6 0.23
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
TATAAATAAATAAATAAAATTATA
Found at i:1006614 original size:17 final size:15
Alignment explanation
Indices: 1006584--1006617 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1006574 ATAAATAAAA
1006584 TTAATAAAATATTTT
1 TTAATAAAATATTTT
*
1006599 TTAATAAAATATATT
1 TTAATAAAATATTTT
1006614 TTAA
1 TTAA
1006618 ATATTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATAAAATATTTT
Found at i:1006778 original size:11 final size:12
Alignment explanation
Indices: 1006761--1006789 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1006751 ATAATAAAAA
1006761 ATAATTTTAATT
1 ATAATTTTAATT
1006773 -TAATTTTAATT
1 ATAATTTTAATT
1006784 ATAATT
1 ATAATT
1006790 AATAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATAATTTTAATT
Found at i:1006829 original size:36 final size:36
Alignment explanation
Indices: 1006746--1006831 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 36
1006736 CGAATTATTA
**
1006746 TTTAAATAATAAAAAATAATTTTAATTTAATTTTAAT
1 TTTAAATAAT-AAAAATAATTTTAATTTAATACTAAT
* *
1006783 TATAATTAATAAAAAT-ATTTTAATTTTTAATACT-AT
1 TTTAAATAATAAAAATAATTTTAA--TTTAATACTAAT
1006819 TTTAAATAATAAA
1 TTTAAATAATAAA
1006832 TTTTATTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
35 7 0.17
36 19 0.46
37 15 0.37
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (36 bp):
TTTAAATAATAAAAATAATTTTAATTTAATACTAAT
Found at i:1007087 original size:21 final size:21
Alignment explanation
Indices: 1007063--1007116 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1007053 TTTTAATTGG
* *
1007063 ATTAAAT-ATTTTTATTTATAA
1 ATTAAATAAATTTTA-TTAAAA
1007084 ATTAAATAAATTTTATTAAAA
1 ATTAAATAAATTTTATTAAAA
*
1007105 ATTAAAAAAATT
1 ATTAAATAAATT
1007117 ACAATGATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 23 0.79
22 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTAAATAAATTTTATTAAAA
Found at i:1007385 original size:21 final size:19
Alignment explanation
Indices: 1007335--1007386 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
1007325 ATATATTAAA
*
1007335 ATATTAAATAT-TATTTTT
1 ATATTAAATTTATATTTTT
*
1007353 ATATAAATATTTATATATTTT
1 ATATTAA-ATTTATAT-TTTT
1007374 ATAATTAAATTTA
1 AT-ATTAAATTTA
1007387 AATAAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 6 0.22
19 3 0.11
20 3 0.11
21 11 0.41
22 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTAAATTTATATTTTT
Found at i:1008221 original size:2 final size:2
Alignment explanation
Indices: 1008214--1008240 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1008204 AGTTAAAAAT
1008214 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
1008241 GAAAAATAGT
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:1011341 original size:17 final size:18
Alignment explanation
Indices: 1011307--1011347 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1011297 TTTTTAATAA
1011307 AATTTTTTAATTATAATT
1 AATTTTTTAATTATAATT
1011325 AATTTTATT-ATTA-AATT
1 AATTTT-TTAATTATAATT
1011342 ATATTT
1 A-ATTT
1011348 ACGTATAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.24
18 14 0.67
19 2 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTTTTAATTATAATT
Found at i:1011764 original size:18 final size:17
Alignment explanation
Indices: 1011730--1011781 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
1011720 TCATTTTAAT
* *
1011730 ATAAA-ATAATATGTTA
1 ATAAATATAAAATATTA
*
1011746 ATAAATTTTAAAATATTAA
1 ATAAA-TATAAAATATT-A
1011765 ATAAATATAAAATATTA
1 ATAAATATAAAATATTA
1011782 TACATAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 5 0.17
17 1 0.03
18 17 0.59
19 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
ATAAATATAAAATATTA
Found at i:1012048 original size:21 final size:21
Alignment explanation
Indices: 1012024--1012078 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1012014 ATGAAATTCT
*
1012024 AATCTCATTATTATAATACTC
1 AATCTCATTATTATAATAATC
* * * *
1012045 AATCTTAATATTATATTAATT
1 AATCTCATTATTATAATAATC
1012066 AATCTCATTATTA
1 AATCTCATTATTA
1012079 CTGTTGTTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (21 bp):
AATCTCATTATTATAATAATC
Found at i:1019017 original size:17 final size:17
Alignment explanation
Indices: 1018997--1019033 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1018987 AAAAAAATTG
*
1018997 ATTTAATAAATTTGAAT
1 ATTTAATAAATTTAAAT
*
1019014 ATTTAATAGATTTAAAT
1 ATTTAATAAATTTAAAT
1019031 ATT
1 ATT
1019034 CAATGAATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (17 bp):
ATTTAATAAATTTAAAT
Found at i:1021435 original size:2 final size:2
Alignment explanation
Indices: 1021428--1021468 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1021418 GTATAAATAA
1021428 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
1021469 AAGCAGCATG
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:1022806 original size:15 final size:15
Alignment explanation
Indices: 1022786--1022819 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1022776 TAAAAGACCC
*
1022786 AATGATCTATATAAG
1 AATGATCCATATAAG
1022801 AATGATCCATATAAG
1 AATGATCCATATAAG
1022816 AATG
1 AATG
1022820 TTGTTTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (15 bp):
AATGATCCATATAAG
Found at i:1034110 original size:15 final size:14
Alignment explanation
Indices: 1034073--1034114 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1034063 AATATAAGTC
1034073 ATTTTAT-TTATTTT
1 ATTTTATATT-TTTT
1034087 ATTTATATATTTTTT
1 ATTT-TATATTTTTT
1034102 AATTTTATATTTT
1 -ATTTTATATTTT
1034115 ATATATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.16
15 15 0.60
16 6 0.24
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
ATTTTATATTTTTT
Found at i:1034137 original size:54 final size:55
Alignment explanation
Indices: 1034023--1034150 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 55
1034013 ATATATTGAA
* *
1034023 ATTTA-TTTATTTATTTATATTTTTTAAATATATTTTATAAAATATAAGTCATTTT
1 ATTTATTTTATTTA-TTATATTTTTTAAATATATTTTATAAAATATAAATAATTTT
* *
1034078 ATTTATTTTATTTA-TATATTTTTTAATTTTATATTTTAT-ATATA-AAATAATTATT
1 ATTTATTTTATTTATTATATTTTTTAA--ATATATTTTATAAAATATAAATAATT-TT
1034133 -TTTATTTT-TATTATTATA
1 ATTTATTTTAT-TTATTATA
1034151 AAATTTAGAT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
53 1 0.02
54 29 0.46
55 15 0.24
56 18 0.29
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (55 bp):
ATTTATTTTATTTATTATATTTTTTAAATATATTTTATAAAATATAAATAATTTT
Found at i:1034143 original size:60 final size:55
Alignment explanation
Indices: 1034023--1034150 Score: 133
Period size: 56 Copynumber: 2.3 Consensus size: 55
1034013 ATATATTGAA
*
1034023 ATTTA-TTTATTTATTTATATTTTTTAAATATATTTTATAAAATATAAGTCATTTT
1 ATTTATTTTATTTA-TTATATTTTTTAAATATATTTTATAAAAAATAAGTCATTTT
* *
1034078 ATTTATTTTATTTA-TATATTTTTTAATTTTATATTTTATATATAAAATAA-TTATTTT
1 ATTTATTTTATTTATTATATTTTTTAA--ATATATTTTATA-A-AAAATAAGTCATTTT
*
1034135 -TAT-TTTTA-TTATTATA
1 ATTTATTTTATTTATTATA
1034151 AAATTTAGAT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
54 15 0.24
55 14 0.22
56 21 0.33
57 7 0.11
58 6 0.10
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (55 bp):
ATTTATTTTATTTATTATATTTTTTAAATATATTTTATAAAAAATAAGTCATTTT
Found at i:1034163 original size:28 final size:26
Alignment explanation
Indices: 1034099--1034169 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 26
1034089 TTATATATTT
1034099 TTTAATTTTATATTTTATATATAAAA
1 TTTAATTTTATATTTTATATATAAAA
*
1034125 TAATTATTTTTAT-TTTTATTATTATAAAA
1 T--TTAATTTTATATTTTA-TA-TATAAAA
*
1034154 TTTAGATTTTTTATTT
1 TTTA-ATTTTATATTT
1034170 CTAAAATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
26 1 0.03
27 8 0.22
28 16 0.44
29 11 0.31
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (26 bp):
TTTAATTTTATATTTTATATATAAAA
Found at i:1035821 original size:28 final size:26
Alignment explanation
Indices: 1035790--1035859 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 26
1035780 TGTTTTATAA
1035790 TATTATAATTAATTTATAAATTTTTTTT
1 TATTATAATTAATTTAT-AA-TTTTTTT
* *
1035818 TATTTTAATT-ATATATAATTTTTTT
1 TATTATAATTAATTTATAATTTTTTT
*
1035843 AATTA-AATTAATATTAT
1 TATTATAATTAAT-TTAT
1035860 TTAACTTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
24 4 0.11
25 12 0.34
26 5 0.14
27 5 0.14
28 9 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TATTATAATTAATTTATAATTTTTTT
Found at i:1035843 original size:24 final size:23
Alignment explanation
Indices: 1035812--1035861 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
1035802 TTTATAAATT
* *
1035812 TTTTTTTATTTTAATTATATATAA
1 TTTTTTTAATTAAATTA-ATATAA
*
1035836 TTTTTTTAATTAAATTAATATTA
1 TTTTTTTAATTAAATTAATATAA
1035859 TTT
1 TTT
1035862 AACTTAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTTTTAATTAAATTAATATAA
Found at i:1035848 original size:23 final size:23
Alignment explanation
Indices: 1035795--1035861 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 23
1035785 TATAATATTA
1035795 TAATTAATT-TATA-AATTTTTTTT
1 TAATTAATTATATATAA--TTTTTT
*
1035818 TATTTTAATTATATATAATTTTTT
1 TA-ATTAATTATATATAATTTTTT
*
1035842 TAATTAAATTA-ATATTATTT
1 TAATT-AATTATATATAATTT
1035862 AACTTAATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 12 0.32
24 19 0.51
25 4 0.11
26 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TAATTAATTATATATAATTTTTT
Found at i:1035862 original size:19 final size:19
Alignment explanation
Indices: 1035816--1035868 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
1035806 TAAATTTTTT
*
1035816 TTTATTTTAATTATATATAA
1 TTTA-TTTAATTAAATATAA
*
1035836 TTTTTTTAATTAAAT-TAA
1 TTTATTTAATTAAATATAA
1035854 TATTATTTAACTTAA
1 T-TTATTTAA-TTAA
1035869 TGATACTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 4 0.14
19 17 0.61
20 7 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTATTTAATTAAATATAA
Found at i:1036111 original size:12 final size:13
Alignment explanation
Indices: 1036086--1036122 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
1036076 AATAACTATC
1036086 TTTTATTATTTTA
1 TTTTATTATTTTA
1036099 TTTTATT-TTTTA
1 TTTTATTATTTTA
*
1036111 TTTTATAATTTT
1 TTTTATTATTTT
1036123 TTAATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATTATTTTA
Found at i:1038104 original size:32 final size:32
Alignment explanation
Indices: 1038020--1038107 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 32
1038010 CTTAAACTCA
* *
1038020 AAAATGATCTAAATTTAG-AATGATTTGAATTC
1 AAAATAATCGAAA-TTAGAAATGATTTGAATTC
* * *
1038052 GAAATAATCGAAACTCGAAATGATTTGAACTT-
1 AAAATAATCGAAATTAGAAATGATTTGAA-TTC
1038084 AAAATAATTCG-AATTAGAAATGAT
1 AAAATAA-TCGAAATTAGAAATGAT
1038108 CCATATCTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
31 2 0.04
32 38 0.84
33 5 0.11
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.32
Consensus pattern (32 bp):
AAAATAATCGAAATTAGAAATGATTTGAATTC
Found at i:1038249 original size:15 final size:15
Alignment explanation
Indices: 1038231--1038321 Score: 67
Period size: 15 Copynumber: 5.5 Consensus size: 15
1038221 AAGTTACTCG
*
1038231 AATTTAAATAATTTT
1 AATTTAAATAATTTA
1038246 AATTTAGAATAATTTA
1 AATTTA-AATAATTTA
* *
1038262 AATTTGAGTAATTTA
1 AATTTAAATAATTTA
1038277 AATATTAAACTTGATTGATTTA
1 AAT-TTAAA--T-A---ATTTA
1038299 AATTTAAA-ATATTTA
1 AATTTAAATA-ATTTA
1038314 AATTTAAA
1 AATTTAAA
1038322 ATAACTTGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
15 30 0.48
16 16 0.26
17 1 0.02
18 1 0.02
19 1 0.02
21 5 0.08
22 8 0.13
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.46
Consensus pattern (15 bp):
AATTTAAATAATTTA
Found at i:1038284 original size:22 final size:22
Alignment explanation
Indices: 1038245--1038306 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
1038235 TAAATAATTT
*
1038245 TAATTTAGAATAATTTAAATTTGAG
1 TAATTTA-AAT-A-TTAAACTTGAG
*
1038270 TAATTTAAATATTAAACTTGAT
1 TAATTTAAATATTAAACTTGAG
*
1038292 TGATTTAAAT-TTAAA
1 TAATTTAAATATTAAA
1038307 ATATTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.15
22 18 0.53
23 1 0.03
24 3 0.09
25 7 0.21
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (22 bp):
TAATTTAAATATTAAACTTGAG
Found at i:1039124 original size:22 final size:22
Alignment explanation
Indices: 1039098--1039148 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
1039088 TATTTTAAAA
1039098 ATTTTAAAT-ATCTT-ATTATTTT
1 ATTTTAAATAAT-TTAATT-TTTT
*
1039120 ATTTTTAATAATTTAATTTTTT
1 ATTTTAAATAATTTAATTTTTT
1039142 ATTTTAA
1 ATTTTAA
1039149 TATGGATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTTAAATAATTTAATTTTTT
Found at i:1040932 original size:2 final size:2
Alignment explanation
Indices: 1040925--1040951 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1040915 TTTCGTCCAT
1040925 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1040952 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1045207 original size:6 final size:6
Alignment explanation
Indices: 1045198--1045226 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1045188 TATGATGACG
1045198 ATGATT ATGATT ATGATT ATGATT ATGAT
1 ATGATT ATGATT ATGATT ATGATT ATGAT
1045227 GGAGAAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (6 bp):
ATGATT
Found at i:1045263 original size:18 final size:18
Alignment explanation
Indices: 1045170--1045267 Score: 58
Period size: 18 Copynumber: 5.3 Consensus size: 18
1045160 GGGTGATGAA
1045170 GATGATGAAC-AATATTAT
1 GATGATG-ACGAATATTAT
*
1045188 TATGATGACG-ATGATTAT
1 GATGATGACGAAT-ATTAT
* **
1045206 GATTATGA-TTATGATTAT
1 GATGATGACGAAT-ATTAT
* * *
1045224 GATGGAGAAGAAGAATACTAT
1 GAT---GATGACGAATATTAT
1045245 GATGATGACGAATATTAT
1 GATGATGACGAATATTAT
1045263 GATGA
1 GATGA
1045268 GAAAGACGAG
Statistics
Matches: 61, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
17 4 0.07
18 45 0.74
21 10 0.16
22 2 0.03
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.34
Consensus pattern (18 bp):
GATGATGACGAATATTAT
Found at i:1045275 original size:21 final size:20
Alignment explanation
Indices: 1045219--1045276 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 20
1045209 TATGATTATG
*
1045219 ATTATGATGGAGAAGAAGAAT
1 ATTATGATGGA-AAGACGAAT
* *
1045240 ACTATGAT-G-ATGACGAAT
1 ATTATGATGGAAAGACGAAT
1045258 ATTATGATGAGAAAGACGA
1 ATTATGATG-GAAAGACGA
1045277 GAAAAATGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 14 0.48
20 2 0.07
21 13 0.45
ACGTcount: A:0.45, C:0.05, G:0.26, T:0.24
Consensus pattern (20 bp):
ATTATGATGGAAAGACGAAT
Found at i:1046090 original size:13 final size:14
Alignment explanation
Indices: 1046065--1046093 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1046055 TTTTGATAGA
1046065 TATTATCTTACCAT
1 TATTATCTTACCAT
1046079 TATTAT-TTACCAT
1 TATTATCTTACCAT
1046092 TA
1 TA
1046094 AATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTATCTTACCAT
Found at i:1046102 original size:2 final size:2
Alignment explanation
Indices: 1046095--1046137 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1046085 TTACCATTAA
1046095 AT AT 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 AT AT
1046137 A
1 A
1046138 ACTTTCCAGC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1046250 original size:16 final size:18
Alignment explanation
Indices: 1046228--1046268 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
1046218 TTGAGTTTTG
1046228 ATAAATTTA-ACTTGTAT
1 ATAAATTTAGACTTGTAT
*
1046245 -TAAA-TTAGATTTGTAT
1 ATAAATTTAGACTTGTAT
1046261 ATAAATTT
1 ATAAATTT
1046269 TTTATGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
15 3 0.15
16 11 0.55
17 4 0.20
18 2 0.10
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (18 bp):
ATAAATTTAGACTTGTAT
Found at i:1046926 original size:16 final size:17
Alignment explanation
Indices: 1046905--1046937 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1046895 AAATAAATAT
1046905 TTATATTGTAT-TTATA
1 TTATATTGTATGTTATA
*
1046921 TTATATTTTATGTTATA
1 TTATATTGTATGTTATA
1046938 ATCATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (17 bp):
TTATATTGTATGTTATA
Found at i:1047372 original size:18 final size:18
Alignment explanation
Indices: 1047312--1047372 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
1047302 CAAAATTTAT
1047312 TATTAAAATAATAATATTA
1 TATTAAAATAAT-ATATTA
*
1047331 T-TGTACTAAATAAT-T-TTT
1 TAT-TA--AAATAATATATTA
1047349 TATTAAAATAATATATTA
1 TATTAAAATAATATATTA
1047367 TATTAA
1 TATTAA
1047373 TTTTTCGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
16 7 0.21
17 1 0.03
18 14 0.41
19 5 0.15
21 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
TATTAAAATAATATATTA
Found at i:1052283 original size:12 final size:12
Alignment explanation
Indices: 1052264--1052296 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1052254 CATAAAAAAT
1052264 AATA-TAATTTA
1 AATATTAATTTA
1052275 AATATTAATTTA
1 AATATTAATTTA
*
1052287 TATATTAATT
1 AATATTAATT
1052297 AAAAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AATATTAATTTA
Found at i:1054011 original size:27 final size:27
Alignment explanation
Indices: 1053974--1054060 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
1053964 ACGGCAAGGG
*
1053974 TGATGAAGATGATGAAGAATATTATTA
1 TGATGACGATGATGAAGAATATTATTA
* * * *
1054001 TGATGACGATGATTATGATTATGATTA
1 TGATGACGATGATGAAGAATATTATTA
* * *
1054028 TGATGA--A-GAAGAAGAATACTATGA
1 TGATGACGATGATGAAGAATATTATTA
1054052 TGATGACGA
1 TGATGACGA
1054061 ATATTATGAT
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
24 16 0.35
25 1 0.02
26 1 0.02
27 28 0.61
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (27 bp):
TGATGACGATGATGAAGAATATTATTA
Found at i:1055035 original size:16 final size:18
Alignment explanation
Indices: 1055013--1055053 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
1055003 TTGAGTTTTG
1055013 ATAAATTTA-ACTTGTAT
1 ATAAATTTAGACTTGTAT
*
1055030 -TAAA-TTAGATTTGTAT
1 ATAAATTTAGACTTGTAT
1055046 ATAAATTT
1 ATAAATTT
1055054 TTTATGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
15 3 0.15
16 11 0.55
17 4 0.20
18 2 0.10
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (18 bp):
ATAAATTTAGACTTGTAT
Found at i:1061005 original size:12 final size:12
Alignment explanation
Indices: 1060986--1061018 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1060976 CATAAAAAAT
1060986 AATA-TAATTTA
1 AATATTAATTTA
1060997 AATATTAATTTA
1 AATATTAATTTA
*
1061009 TATATTAATT
1 AATATTAATT
1061019 AAAAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AATATTAATTTA
Found at i:1062734 original size:27 final size:27
Alignment explanation
Indices: 1062697--1062783 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
1062687 ACGGCAAGGG
*
1062697 TGATGAAGATGATGAAGAATATTATTA
1 TGATGACGATGATGAAGAATATTATTA
* * * *
1062724 TGATGACGATGATTATGATTATGATTA
1 TGATGACGATGATGAAGAATATTATTA
* * *
1062751 TGATGA--A-GAAGAAGAATACTATGA
1 TGATGACGATGATGAAGAATATTATTA
1062775 TGATGACGA
1 TGATGACGA
1062784 ATATTATGAT
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
24 16 0.35
25 1 0.02
26 1 0.02
27 28 0.61
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (27 bp):
TGATGACGATGATGAAGAATATTATTA
Found at i:1063759 original size:16 final size:18
Alignment explanation
Indices: 1063737--1063777 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
1063727 TTGAGTTTTG
1063737 ATAAATTTA-ACTTGTAT
1 ATAAATTTAGACTTGTAT
*
1063754 -TAAA-TTAGATTTGTAT
1 ATAAATTTAGACTTGTAT
1063770 ATAAATTT
1 ATAAATTT
1063778 TTTATGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
15 3 0.15
16 11 0.55
17 4 0.20
18 2 0.10
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (18 bp):
ATAAATTTAGACTTGTAT
Found at i:1064598 original size:28 final size:27
Alignment explanation
Indices: 1064558--1064615 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
1064548 TTTAATACTA
*
1064558 AAAATATTATA-TTAATACTAAATACAT
1 AAAATAATATATTTAATACTAAA-ACAT
*
1064585 AAAATAATACTATTTAATATTAAAACAT
1 AAAATAATA-TATTTAATACTAAAACAT
1064613 AAA
1 AAA
1064616 TTATATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 8 0.30
28 9 0.33
29 10 0.37
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (27 bp):
AAAATAATATATTTAATACTAAAACAT
Found at i:1064745 original size:27 final size:27
Alignment explanation
Indices: 1064715--1064829 Score: 92
Period size: 27 Copynumber: 4.1 Consensus size: 27
1064705 AAGTATAATT
*
1064715 TATATAAATTTATTATTAAAATAGTAA
1 TATATAAATTTATTATTAAAATAATAA
* *
1064742 TATATAAATTTTTTAATAAAATAATAA
1 TATATAAATTTATTATTAAAATAATAA
* **
1064769 -A-AGTACTATTTAAAATTTAAAAT-ATCAA
1 TATA-TA-AATTTATTA-TTAAAATAAT-AA
1064797 TAATATCAAAATTTATTATTAAAATAATAA
1 T-ATAT--AAATTTATTATTAAAATAATAA
1064827 TAT
1 TAT
1064830 TATTGTACTA
Statistics
Matches: 67, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
25 1 0.01
26 3 0.04
27 31 0.46
28 8 0.12
29 2 0.03
30 12 0.18
31 9 0.13
32 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (27 bp):
TATATAAATTTATTATTAAAATAATAA
Found at i:1070131 original size:29 final size:28
Alignment explanation
Indices: 1070063--1070132 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
1070053 TTTAAAAAAT
*
1070063 AATTATTTTAATTTTTTAAATATTTCAA
1 AATTATTTTAATATTTTAAATATTTCAA
* * *
1070091 AATAAATATTAATGATTTTAAA-ATTTTAA
1 AAT-TATTTTAAT-ATTTTAAATATTTCAA
1070120 AATTGATTTTAAT
1 AATT-ATTTTAAT
1070133 TTCATAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
28 3 0.09
29 23 0.70
30 7 0.21
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATTTTAATATTTTAAATATTTCAA
Found at i:1070223 original size:51 final size:50
Alignment explanation
Indices: 1070161--1070268 Score: 128
Period size: 49 Copynumber: 2.1 Consensus size: 50
1070151 AATTTTTAAT
* * * *
1070161 TTTTTTAAAAAATCACATATTAATGATTTTAAAATTTTTATATTTTAAAACA
1 TTTTTTAAAAAATCACATA-CAAT-ATTTTAAAAATTTTATATTTCAAAAAA
* *
1070213 TTTTTT-AAAAATTAGATACAATATTTTAAAAATTTTATATTTCAAAAAA
1 TTTTTTAAAAAATCACATACAATATTTTAAAAATTTTATATTTCAAAAAA
1070262 TATTTTT
1 T-TTTTT
1070269 TCTTTATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
49 25 0.51
50 8 0.16
51 10 0.20
52 6 0.12
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (50 bp):
TTTTTTAAAAAATCACATACAATATTTTAAAAATTTTATATTTCAAAAAA
Found at i:1070851 original size:12 final size:11
Alignment explanation
Indices: 1070805--1070839 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1070795 TTTAATTTTT
*
1070805 ATTTTAAATTG
1 ATTTTAAATTA
1070816 ATTTTAAATTA
1 ATTTTAAATTA
1070827 ATTTTAAAATTA
1 ATTTT-AAATTA
1070839 A
1 A
1070840 ATTAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 15 0.68
12 7 0.32
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:1071154 original size:21 final size:18
Alignment explanation
Indices: 1071129--1071178 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 18
1071119 ATAGTTATTT
1071129 TTTTTTACTTTTTTTCATCAA
1 TTTTTTA-TTTTTTT-AT-AA
1071150 TTTTTTATTTTTTTATAA
1 TTTTTTATTTTTTTATAA
1071168 TTTTTTTATTT
1 -TTTTTTATTT
1071179 GTTTGTTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 2 0.07
19 12 0.43
20 7 0.25
21 7 0.25
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTATTTTTTTATAA
Found at i:1072194 original size:21 final size:20
Alignment explanation
Indices: 1072147--1072194 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
1072137 AAAAATATAC
*
1072147 TTTTTTGTTAGTGTTTTTTT
1 TTTTTTGATAGTGTTTTTTT
1072167 TTGTTTTGATAGT-TCTTTTTT
1 TT-TTTTGATAGTGT-TTTTTT
1072188 GTTTTTT
1 -TTTTTT
1072195 TATTCTTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 3 0.12
21 19 0.79
22 2 0.08
ACGTcount: A:0.06, C:0.02, G:0.15, T:0.77
Consensus pattern (20 bp):
TTTTTTGATAGTGTTTTTTT
Found at i:1074112 original size:79 final size:80
Alignment explanation
Indices: 1073975--1074127 Score: 177
Period size: 79 Copynumber: 1.9 Consensus size: 80
1073965 GTACATCCCC
* * * * * *
1073975 GATGAAAAATTTGATATTTTAGAGATAAAATCGGGGTTGAAGTATTCTTTAAAAAATAATAGGGT
1 GATGAAAAATTTAATATTTTAGAAATAAAACCGAGATTGAAGTATTCTTTAAAAAATAACAGGGT
1074040 TAGAGTATCCCTAAT
66 TAGAGTATCCCTAAT
* * *
1074055 GATGAAAAA-TTAATATTTT-GAAAATAAAACCGAGATTGGAGTATCTCTTT-AAGAATAACGGG
1 GATGAAAAATTTAATATTTTAG-AAATAAAACCGAGATTGAAGTAT-TCTTTAAAAAATAACAGG
*
1074117 GTTGGAGTATC
64 GTTAGAGTATC
1074128 GTCGAGATAA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
78 1 0.02
79 46 0.75
80 14 0.23
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (80 bp):
GATGAAAAATTTAATATTTTAGAAATAAAACCGAGATTGAAGTATTCTTTAAAAAATAACAGGGT
TAGAGTATCCCTAAT
Found at i:1074259 original size:79 final size:78
Alignment explanation
Indices: 1074169--1074548 Score: 370
Period size: 79 Copynumber: 4.8 Consensus size: 78
1074159 GTGAAAACAA
* * * * * * *
1074169 GGTTGGAGTATCCCCGATGATAAAAAAT-TGATATTTTATAAATAAAATCGGGATTAGAGTATCC
1 GGTTGGAGTATCCCCGATGGTGAAAAATCAG-TGTTTTAGAAATAAAACCGGG-TTGGAGTATCC
*
1074233 TCTCAGAAATAACGG
64 TCTCAAAAATAACGG
* * *
1074248 GGTTGGAGTATCCCCAACGGTGAAAAATCAGTGCTTTAGAAATAAAACCAGGGTTGGAGTATCCT
1 GGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTAGAAATAAAACC-GGGTTGGAGTATCCT
*
1074313 -TGCAAAAATAACGA
65 CT-CAAAAATAACGG
*** * * *
1074327 GGTTGGAGTATAGTCGATGGTGGAAAATCAGTGTTTTAGAAATAAAACCGGGATTAGAGTATCCC
1 GGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTAGAAATAAAACCGGG-TTGGAGTATCCT
*
1074392 CTAAAAAATAACGG
65 CTCAAAAATAACGG
* * * *
1074406 GATTGGAGTATCTCCGATTGTGAAAAATCAGTGTTGTAGAAATAAAACCGAGGTTGGAGTATCC-
1 GGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTAGAAATAAAACCG-GGTTGGAGTATCCT
* *
1074470 CTTCGAAAATAATGG
65 C-TCAAAAATAACGG
* *** * ** *
1074485 GGTTAGAGTATCCTTAATGGTAAAAAATTGGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTAGAAATAAAA-CCGGGTTGGAGTATCC
1074549 CGGATGGTGG
Statistics
Matches: 247, Mismatches: 46, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
78 5 0.02
79 233 0.94
80 9 0.04
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (78 bp):
GGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTAGAAATAAAACCGGGTTGGAGTATCCTC
TCAAAAATAACGG
Found at i:1074325 original size:211 final size:210
Alignment explanation
Indices: 1073960--1074343 Score: 463
Period size: 211 Copynumber: 1.8 Consensus size: 210
1073950 GGGTATGCGA
* * * * *
1073960 TTGGAGTACATCCCCGATGAAAAATTTGATATTTTAGAGATAAAATCGGGGTTGAAGTATTCTTT
1 TTGGAGTA-ATCCCCGATGAAAAAATTGATATTTTAGAAATAAAATCGGGATTGAAGTATCCTCT
* * * * *
1074025 AAAAAATAATAGGGTTAGAGTATCCCTAATGATGAAAAATTAATATTTTGAAAATAAAACCGAGA
65 AAAAAATAACAGGGTTAGAGTATCCCCAACGATGAAAAATCAATATTTAGAAAATAAAACCGAGA
* * * *
1074090 TTGGAGTATCTCTTTAAGAATAACGGGGTTGGAGTATCGTCGAGATAAAAAAATTTTAATATTTT
130 TTGGAGTATCTCTTCAAAAATAACGAGGTTGGAGTATAGTCGAGATAAAAAAATTTTAATATTTT
1074155 GAAAGTGAAAACAAGG
195 GAAAGTGAAAACAAGG
*
1074171 TTGGAGT-ATCCCCGATGATAAAAAATTGATATTTTATAAATAAAATCGGGATT-AGAGTATCCT
1 TTGGAGTAATCCCCGATG--AAAAAATTGATATTTTAGAAATAAAATCGGGATTGA-AGTATCCT
* * * * * * *
1074234 CTCAGAAATAACGGGGTTGGAGTATCCCCAACGGTGAAAAATCAGTGCTTTAG-AAATAAAACC-
63 CTAAAAAATAACAGGGTTAGAGTATCCCCAACGATGAAAAATCAAT-ATTTAGAAAATAAAACCG
*
1074297 AGGGTTGGAGTATC-CTTGCAAAAATAACGAGGTTGGAGTATAGTCGA
127 A-GATTGGAGTATCTCTT-CAAAAATAACGAGGTTGGAGTATAGTCGA
1074344 TGGTGGAAAA
Statistics
Matches: 144, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
209 10 0.07
210 5 0.03
211 125 0.87
212 4 0.03
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.29
Consensus pattern (210 bp):
TTGGAGTAATCCCCGATGAAAAAATTGATATTTTAGAAATAAAATCGGGATTGAAGTATCCTCTA
AAAAATAACAGGGTTAGAGTATCCCCAACGATGAAAAATCAATATTTAGAAAATAAAACCGAGAT
TGGAGTATCTCTTCAAAAATAACGAGGTTGGAGTATAGTCGAGATAAAAAAATTTTAATATTTTG
AAAGTGAAAACAAGG
Found at i:1074461 original size:158 final size:158
Alignment explanation
Indices: 1074202--1074549 Score: 432
Period size: 158 Copynumber: 2.2 Consensus size: 158
1074192 AAAATTGATA
* * * * *
1074202 TTTTATAAATAAAATCGGGATTAGAGTATCCTCTCAGAAATAACGGGGTTGGAGTATCCCCAACG
1 TTTTAGAAATAAAATCGGGATTAGAGTATCCCCTAAAAAATAACGGGATTGGAGTATCCCCAACG
1074267 GTGAAAAATCAGTGCTTTAGAAATAAAACCAGGGTTGGAGTAT-CCTTGCAAAAATAACGAGGTT
66 GTGAAAAATCAGTGCTTTAGAAATAAAACCAGGGTTGGAGTATCCCTT-CAAAAATAACGAGGTT
* * * **
1074331 GGAGTATAGTCGATGGTGGAAAATCAGTG
130 AGAGTATACTCAATGGTAAAAAATCAGTG
* * * **
1074360 TTTTAGAAATAAAACCGGGATTAGAGTATCCCCTAAAAAATAACGGGATTGGAGTATCTCCGATT
1 TTTTAGAAATAAAATCGGGATTAGAGTATCCCCTAAAAAATAACGGGATTGGAGTATCCCCAACG
* * *
1074425 GTGAAAAATCAGTG-TTGTAGAAATAAAACC-GAGGTTGGAGTATCCCTTCGAAAATAATGGGGT
66 GTGAAAAATCAGTGCTT-TAGAAATAAAACCAG-GGTTGGAGTATCCCTTCAAAAATAACGAGGT
* * **
1074488 TAGAGTATCCTTAATGGTAAAAAATTGGTG
129 TAGAGTATACTCAATGGTAAAAAATCAGTG
* *
1074518 TTTTAGAAATAAAATCGGGGTTGGAGTATCCC
1 TTTTAGAAATAAAATCGGGATTAGAGTATCCC
1074550 GGATGGTGGA
Statistics
Matches: 162, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
157 3 0.02
158 155 0.96
159 4 0.02
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (158 bp):
TTTTAGAAATAAAATCGGGATTAGAGTATCCCCTAAAAAATAACGGGATTGGAGTATCCCCAACG
GTGAAAAATCAGTGCTTTAGAAATAAAACCAGGGTTGGAGTATCCCTTCAAAAATAACGAGGTTA
GAGTATACTCAATGGTAAAAAATCAGTG
Found at i:1077029 original size:20 final size:20
Alignment explanation
Indices: 1076983--1077060 Score: 111
Period size: 20 Copynumber: 3.8 Consensus size: 20
1076973 AAAACCTATA
**
1076983 ATGTATCGATACAATTATAAGT
1 ATGTATCGATAC-ATT-TACTT
*
1077005 ATGTATCAATACATTTACTT
1 ATGTATCGATACATTTACTT
1077025 ATGTATCGATACATTTACTT
1 ATGTATCGATACATTTACTT
1077045 ATGTATCGATACATTT
1 ATGTATCGATACATTT
1077061 CTTTGGCAGT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 38 0.73
21 3 0.06
22 11 0.21
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTACTT
Done.