Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold145
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: 2608604
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 28749 characters in sequence are not A, C, G, or T
File 3 of 15
Found at i:548918 original size:33 final size:32
Alignment explanation
Indices: 548850--548919 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
548840 TTAAATAATT
*
548850 TTAATAAAAATTAATTTAATATATATAATTTA
1 TTAATAAAAATTAATTTAATATATATAATTGA
* *
548882 TTAATAAAAAATTAATTTTATATAT-TTATTAGA
1 TTAAT-AAAAATTAATTTAATATATATAATT-GA
548915 TTAAT
1 TTAAT
548920 TTTTTATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 9 0.27
33 24 0.73
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
TTAATAAAAATTAATTTAATATATATAATTGA
Found at i:551322 original size:50 final size:50
Alignment explanation
Indices: 551242--551399 Score: 246
Period size: 50 Copynumber: 3.2 Consensus size: 50
551232 TTGCTTATAA
**
551242 TCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
1 TCAACAATTACGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
* *
551292 TTAATAATTACGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
1 TCAACAATTACGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
* *
551342 TCAACAATTAC-AGCCACCTCTCTCGATTGTCAAAAGTTAGTGAAGAATAG
1 TCAACAATTACGA-CCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
551392 TCAACAAT
1 TCAACAAT
551400 GATAATACTT
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
49 1 0.01
50 98 0.99
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (50 bp):
TCAACAATTACGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
Found at i:556025 original size:3 final size:3
Alignment explanation
Indices: 556017--556059 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
556007 AAAATTTTTA
* *
556017 ATT ATT ATT -TA ATAT ATT ATT ATT ATT ATT ATT ATT AGT ATT A
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT A
556060 GTGTGAAGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 1 0.03
3 31 0.91
4 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:562731 original size:2 final size:2
Alignment explanation
Indices: 562724--562752 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
562714 ACTAGTAAAT
562724 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
562753 TCTTCTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:565088 original size:19 final size:20
Alignment explanation
Indices: 565064--565106 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
565054 AGATATAAGT
* *
565064 ATTTTTA-ATTTTTAAAATA
1 ATTTTTATATATTTAAAAAA
565083 ATTTTTATATATTTAAAAAA
1 ATTTTTATATATTTAAAAAA
565103 ATTT
1 ATTT
565107 AAAAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTTATATATTTAAAAAA
Found at i:571262 original size:15 final size:16
Alignment explanation
Indices: 571242--571273 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
571232 CTTGACACAA
571242 CTGTCTC-TTGTTAGT
1 CTGTCTCTTTGTTAGT
571257 CTGTCTCTTTGTTAGT
1 CTGTCTCTTTGTTAGT
571273 C
1 C
571274 GGCCTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.06, C:0.22, G:0.19, T:0.53
Consensus pattern (16 bp):
CTGTCTCTTTGTTAGT
Found at i:578062 original size:17 final size:18
Alignment explanation
Indices: 578040--578077 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
578030 AAATATTTAA
* *
578040 ATTTAAATTTTTAAT-TT
1 ATTTAAAATTTAAATCTT
578057 ATTTAAAATTTAAATCTT
1 ATTTAAAATTTAAATCTT
578075 ATT
1 ATT
578078 ATTATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTAAAATTTAAATCTT
Found at i:578085 original size:24 final size:24
Alignment explanation
Indices: 578017--578071 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 24
578007 AAATCAAGAT
*
578017 ATTTATAATTTTTAA-ATATTT-AA
1 ATTTA-AATTTTTAATTTATTTAAA
578040 ATTTAAATTTTTAATTTATTTAAA
1 ATTTAAATTTTTAATTTATTTAAA
578064 ATTTAAAT
1 ATTTAAAT
578072 CTTATTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 9 0.31
23 10 0.34
24 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTAAATTTTTAATTTATTTAAA
Found at i:583321 original size:30 final size:30
Alignment explanation
Indices: 583285--583346 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
583275 ACTTGAAGCT
583285 AATTAATTTGTGGTCTAATTTCTTCTTAAA
1 AATTAATTTGTGGTCTAATTTCTTCTTAAA
583315 AATTAATTTGTGGTCTAATTTCTTCTTAAA
1 AATTAATTTGTGGTCTAATTTCTTCTTAAA
583345 AA
1 AA
583347 ATAAACTTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (30 bp):
AATTAATTTGTGGTCTAATTTCTTCTTAAA
Found at i:584239 original size:2 final size:2
Alignment explanation
Indices: 584232--584259 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
584222 CTTTGTTTCA
584232 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
584260 CATTAGAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:584800 original size:2 final size:2
Alignment explanation
Indices: 584793--584836 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
584783 ATAAACCCTC
* *
584793 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT TT 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
584835 AT
1 AT
584837 GACATAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:585933 original size:18 final size:18
Alignment explanation
Indices: 585910--585961 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
585900 ATATTTATAT
585910 TAAATTATTTATATAATA
1 TAAATTATTTATATAATA
*
585928 TAAATTATTAATA-AAT-
1 TAAATTATTTATATAATA
585944 TAAA--ATTTATATTAATA
1 TAAATTATTTATA-TAATA
585961 T
1 T
585962 TTAATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 6 0.21
16 7 0.24
17 4 0.14
18 12 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTATTTATATAATA
Found at i:585942 original size:29 final size:27
Alignment explanation
Indices: 585892--585945 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
585882 AAATAATAAA
* *
585892 TATATAATATATTTATATTAAATTATT
1 TATATAATATAATTATAATAAATTATT
585919 TATATAATATAAATTATTAATAAATTA
1 TATATAATAT-AATTA-TAATAAATTA
585946 AAATTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 10 0.43
28 4 0.17
29 9 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TATATAATATAATTATAATAAATTATT
Found at i:585975 original size:32 final size:31
Alignment explanation
Indices: 585890--585981 Score: 78
Period size: 34 Copynumber: 2.8 Consensus size: 31
585880 AAAAATAATA
* *
585890 AATATATAATATATTTATATTAAATTATTTATAT
1 AATATTTAATAT-TTTAAATTAAA--ATTTATAT
* *
585924 AATA-TAAATTATTAATAAATTAAAATTTATATT
1 AATATTTAA-TATT-TTAAATTAAAATTTATA-T
585957 AATATTTAATATTTTAAATATAAAA
1 AATATTTAATATTTTAAAT-TAAAA
585982 AATAATATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
32 12 0.26
33 17 0.36
34 18 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
AATATTTAATATTTTAAATTAAAATTTATAT
Found at i:586231 original size:3 final size:3
Alignment explanation
Indices: 586223--586256 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
586213 AATATTAATT
586223 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
586257 CAGCAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:586834 original size:18 final size:17
Alignment explanation
Indices: 586808--586875 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 17
586798 TTTATAAAAA
586808 TTTTAATATATTAATAAT
1 TTTTAATATATT-ATAAT
586826 TTATT-ATATA-TATAAT
1 TT-TTAATATATTATAAT
586842 TTTTAATATATT-T-AT
1 TTTTAATATATTATAAT
* *
586857 TTATATTATATTAT-AT
1 TTTTAATATATTATAAT
586873 TTT
1 TTT
586876 AATTTTTCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
15 14 0.33
16 18 0.42
17 2 0.05
18 7 0.16
19 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAATATATTATAAT
Found at i:586872 original size:34 final size:34
Alignment explanation
Indices: 586794--586872 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 34
586784 TTTAAAATAA
*
586794 TATATTTATAAAAATTTTAATATATTAATAATTTAT
1 TATA-TTATATAAATTTTAATATATT-ATAATTTAT
* *
586830 TATA-TATATAATTTTTAATATATT-TATTTATAT
1 TATATTATATAAATTTTAATATATTATAATT-TAT
586863 TATATTATAT
1 TATATTATAT
586873 TTTAATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
32 4 0.11
33 7 0.18
34 23 0.61
36 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (34 bp):
TATATTATATAAATTTTAATATATTATAATTTAT
Found at i:587147 original size:2 final size:2
Alignment explanation
Indices: 587140--587164 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
587130 TATAATCATT
587140 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
587165 TTGTCTCGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:587483 original size:25 final size:25
Alignment explanation
Indices: 587446--587511 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
587436 TCCTATGATA
587446 ATAATCAAATATAATAAATATTTTT
1 ATAATCAAATATAATAAATATTTTT
* * *
587471 ATAATTAATTATAATAAATATTTATA
1 ATAATCAAATATAATAAATATTT-TT
587497 ATAAT-AAA-ATAATAA
1 ATAATCAAATATAATAA
587512 TTTTAATATC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 7 0.19
25 23 0.64
26 6 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAATCAAATATAATAAATATTTTT
Found at i:587495 original size:13 final size:13
Alignment explanation
Indices: 587455--587500 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
587445 AATAATCAAA
587455 TATAATAAATATT
1 TATAATAAATATT
* * *
587468 T-TTATAATTAAT
1 TATAATAAATATT
587480 TATAATAAATATT
1 TATAATAAATATT
587493 TATAATAA
1 TATAATAA
587501 TAAAATAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
12 9 0.35
13 17 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATAAATATT
Found at i:588386 original size:2 final size:2
Alignment explanation
Indices: 588379--588414 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
588369 TCCTCTCCCC
588379 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
588415 TCTGAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:591414 original size:23 final size:21
Alignment explanation
Indices: 591384--591430 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
591374 TATGAAAATA
591384 TAATATTTAATAATTTTAAATTT
1 TAATATTTAA-AATTTT-AATTT
*
591407 TAATATTTAAAATTTTTATTT
1 TAATATTTAAAATTTTAATTT
591428 TAA
1 TAA
591431 AAATATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.30
22 6 0.26
23 10 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATATTTAAAATTTTAATTT
Found at i:591432 original size:14 final size:14
Alignment explanation
Indices: 591394--591432 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
591384 TAATATTTAA
591394 TAATTTT-AAATTT
1 TAATTTTAAAATTT
591407 TAATATTTAAAATTT
1 TAAT-TTTAAAATTT
*
591422 TTATTTTAAAA
1 TAATTTTAAAA
591433 ATATAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 10 0.43
15 9 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATTTTAAAATTT
Found at i:591434 original size:15 final size:15
Alignment explanation
Indices: 591389--591432 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
591379 AAATATAATA
*
591389 TTTAATAATTTTAAAT
1 TTTAAT-ATTTAAAAT
591405 TTTAATATTTAAAAT
1 TTTAATATTTAAAAT
*
591420 TTTTAT-TTTAAAA
1 TTTAATATTTAAAA
591433 ATATAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 7 0.27
15 13 0.50
16 6 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAATATTTAAAAT
Found at i:591444 original size:18 final size:18
Alignment explanation
Indices: 591421--591461 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
591411 ATTTAAAATT
591421 TTTATTTTA-AAAATATAA
1 TTTATTTTATAAAA-ATAA
591439 TTTATTTTATAAAAATAA
1 TTTATTTTATAAAAATAA
591457 TTTAT
1 TTTAT
591462 AATTTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTATTTTATAAAAATAA
Found at i:591587 original size:15 final size:17
Alignment explanation
Indices: 591557--591607 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 17
591547 TTGATATTTT
591557 TTAATATTTATTTTATA
1 TTAATATTTATTTTATA
*
591574 TTAATA-TT-TTTTATT
1 TTAATATTTATTTTATA
591589 TTAA-ATTATATTTTA-A
1 TTAATATT-TATTTTATA
591605 TTA
1 TTA
591608 TTTTAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 1 0.03
15 11 0.38
16 6 0.21
17 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAATATTTATTTTATA
Found at i:591588 original size:20 final size:18
Alignment explanation
Indices: 591563--591620 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 18
591553 TTTTTTAATA
591563 TTTATTTTATATTAATATTT
1 TTTATTTTA-ATT-ATATTT
591583 TTTATTTTAAATTATATTT
1 TTTATTTT-AATTATATTT
591602 TAATTATTTTAATTATATT
1 T--TTATTTTAATTATATT
591621 ATATAGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.20
20 20 0.57
21 8 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTTTAATTATATTT
Found at i:591591 original size:25 final size:27
Alignment explanation
Indices: 591550--591600 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
591540 TAATATTTTG
**
591550 ATATTTTTTAATATTTATTTTATATTA
1 ATATTTTTTAATATTTAAATTATATTA
591577 ATATTTTTT-AT-TTTAAATTATATT
1 ATATTTTTTAATATTTAAATTATATT
591601 TTAATTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
26 2 0.09
27 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
ATATTTTTTAATATTTAAATTATATTA
Found at i:591604 original size:27 final size:27
Alignment explanation
Indices: 591517--591633 Score: 75
Period size: 27 Copynumber: 4.4 Consensus size: 27
591507 CATATTTAAA
* *
591517 ATTTTATATATTTATATAAAATTTA--AT
1 ATTTTA-ATATTT-TTTAATATTTATTAT
* *
591544 ATTTTGATATTTTTTAATATTTATTTT
1 ATTTTAATATTTTTTAATATTTATTAT
*
591571 ATATTAATATTTTTT-AT-TTTAAATTAT
1 ATTTTAATATTTTTTAATATTT--ATTAT
* *
591598 ATTTTAAT-TATTTTAAT-TATATTAT
1 ATTTTAATATTTTTTAATATTTATTAT
**
591623 ATAGTAATATT
1 ATTTTAATATT
591634 GTATTCGAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 13
0.73 0.13 0.13
Matches are distributed among these distances:
25 23 0.32
26 14 0.20
27 34 0.48
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
ATTTTAATATTTTTTAATATTTATTAT
Found at i:597899 original size:11 final size:11
Alignment explanation
Indices: 597869--597929 Score: 61
Period size: 11 Copynumber: 5.4 Consensus size: 11
597859 TGGTAGAAAA
597869 ATAAT-TAATAT
1 ATAATATAA-AT
* *
597880 ATGATATAAAA
1 ATAATATAAAT
597891 ATAATATAAAT
1 ATAATATAAAT
*
597902 ATATTATAAAT
1 ATAATATAAAT
597913 ATATATATAAATT
1 ATA-ATATAAA-T
597926 ATAA
1 ATAA
597930 ATTATTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
11 27 0.66
12 10 0.24
13 4 0.10
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:597909 original size:22 final size:23
Alignment explanation
Indices: 597865--597928 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 23
597855 TGGGTGGTAG
597865 AAAAATAAT-T-AATATATGATAT
1 AAAAATAATATAAATATAT-ATAT
597887 AAAAATAATATAAATATAT-TAT
1 AAAAATAATATAAATATATATAT
*
597909 AAATATATATATAAAT-TATA
1 AAAAATA-ATATAAATATATA
597929 AATTATTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 21 0.57
23 9 0.24
24 7 0.19
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAAATAATATAAATATATATAT
Found at i:597916 original size:19 final size:20
Alignment explanation
Indices: 597889--597931 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
597879 TATGATATAA
*
597889 AAATAATATAAATATATTAT
1 AAATAATATAAATAAATTAT
*
597909 AAAT-ATATATATAAATTAT
1 AAATAATATAAATAAATTAT
597928 AAAT
1 AAAT
597932 TATTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATAATATAAATAAATTAT
Found at i:598718 original size:6 final size:6
Alignment explanation
Indices: 598704--598804 Score: 66
Period size: 6 Copynumber: 16.8 Consensus size: 6
598694 GCAACTAGAA
* *
598704 GAAGTG GAAGAG GAAGTA- GAAGTA- GAAGAA GAAGTA- GAAGTA- GAAGAG
1 GAAGAG GAAGAG GAAG-AG GAAG-AG GAAGAG GAAG-AG GAAG-AG GAAGAG
** * * * *
598752 GAAGTT GAAGAA GAAGAT GAAGAG GAAGAG GAAGAG GAAGAA GAGGAG
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG
598800 GAAGA
1 GAAGA
598805 AGGATACGAT
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
5 2 0.03
6 76 0.95
7 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.42, T:0.08
Consensus pattern (6 bp):
GAAGAG
Found at i:598726 original size:18 final size:18
Alignment explanation
Indices: 598703--598791 Score: 101
Period size: 18 Copynumber: 4.9 Consensus size: 18
598693 AGCAACTAGA
*
598703 AGAAGTGGAAGAGGAAGT
1 AGAAGTAGAAGAGGAAGT
*
598721 AGAAGTAGAAGAAGAAGT
1 AGAAGTAGAAGAGGAAGT
598739 AGAAGTAGAAGAGGAAGT
1 AGAAGTAGAAGAGGAAGT
* * *
598757 TGAAGAAGAAGATGAAG-
1 AGAAGTAGAAGAGGAAGT
598774 AGGAAG-AGGAAGAGGAAG
1 A-GAAGTA-GAAGAGGAAG
598792 AAGAGGAGGA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
17 1 0.02
18 60 0.98
ACGTcount: A:0.51, C:0.00, G:0.40, T:0.09
Consensus pattern (18 bp):
AGAAGTAGAAGAGGAAGT
Found at i:598792 original size:18 final size:17
Alignment explanation
Indices: 598703--598804 Score: 73
Period size: 18 Copynumber: 5.7 Consensus size: 17
598693 AGCAACTAGA
*
598703 AGAAGTGGAAGAGGAAG
1 AGAAGAGGAAGAGGAAG
*
598720 TAGAAGTA-GAAGAAGAAG
1 -AGAAG-AGGAAGAGGAAG
598738 TAGAAGTA-GAAGAGGAAG
1 -AGAAG-AGGAAGAGGAAG
* * *
598756 TTGAAGAAGAAGATGAAG
1 -AGAAGAGGAAGAGGAAG
598774 AGGAAGAGGAAGAGGAAG
1 A-GAAGAGGAAGAGGAAG
*
598792 AAGAGGAGGAAGA
1 -AGAAGAGGAAGA
598805 AGGATACGAT
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
17 1 0.01
18 69 0.97
19 1 0.01
ACGTcount: A:0.51, C:0.00, G:0.41, T:0.08
Consensus pattern (17 bp):
AGAAGAGGAAGAGGAAG
Found at i:598804 original size:12 final size:12
Alignment explanation
Indices: 598710--598806 Score: 90
Period size: 12 Copynumber: 8.1 Consensus size: 12
598700 AGAAGAAGTG
*
598710 GAAGAGGAAGTA
1 GAAGAGGAAGAA
598722 GAAGTA-GAAGAA
1 GAAG-AGGAAGAA
*
598734 GAAGTA-GAAGTA
1 GAAG-AGGAAGAA
**
598746 GAAGAGGAAGTT
1 GAAGAGGAAGAA
* *
598758 GAAGAAGAAGAT
1 GAAGAGGAAGAA
*
598770 GAAGAGGAAGAG
1 GAAGAGGAAGAA
598782 GAAGAGGAAGAA
1 GAAGAGGAAGAA
*
598794 GAGGAGGAAGAA
1 GAAGAGGAAGAA
598806 G
1 G
598807 GATACGATAA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
11 1 0.01
12 72 0.97
13 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.41, T:0.07
Consensus pattern (12 bp):
GAAGAGGAAGAA
Found at i:602419 original size:12 final size:12
Alignment explanation
Indices: 602402--602426 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
602392 TATAAACGTA
602402 ATATTAATATAT
1 ATATTAATATAT
602414 ATATTAATATAT
1 ATATTAATATAT
602426 A
1 A
602427 ATTTGATTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATTAATATAT
Found at i:602826 original size:2 final size:2
Alignment explanation
Indices: 602819--602853 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
602809 TATATTGTAT
602819 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
602854 CAATTGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:603312 original size:43 final size:44
Alignment explanation
Indices: 603263--603355 Score: 152
Period size: 43 Copynumber: 2.1 Consensus size: 44
603253 GTAATCCTAT
**
603263 TATAATTATATAAATATTATGTAAATAAAATAATTAAAATA-AA
1 TATAATTATATAAATATTACATAAATAAAATAATTAAAATATAA
*
603306 TATAATTATATAATTATTACATAAATAAAATAATTAAAATATAA
1 TATAATTATATAAATATTACATAAATAAAATAATTAAAATATAA
603350 TATAAT
1 TATAAT
603356 ATAATTATCA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
43 38 0.83
44 8 0.17
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (44 bp):
TATAATTATATAAATATTACATAAATAAAATAATTAAAATATAA
Found at i:603358 original size:49 final size:48
Alignment explanation
Indices: 603263--603396 Score: 131
Period size: 49 Copynumber: 2.9 Consensus size: 48
603253 GTAATCCTAT
* **
603263 TATAATTATATAAATATTATGTAAATAAAATAATT---A-A-AATAAA
1 TATAATTATATAATTATTAAATAAATAAAATAATTAAAATATAATAAA
*
603306 TATAATTATATAATTATTACATAAATAAAATAATTAAAATATAATATAA
1 TATAATTATATAATTATTAAATAAATAAAATAATTAAAATATAATA-AA
*
603355 TATAATTATCA-AATT-TATAAAT-AATATAAATTATTAAAATAT
1 TATAATTAT-ATAATTAT-TAAATAAATA-AAATAATTAAAATAT
603397 TTTTTTAACA
Statistics
Matches: 77, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
43 32 0.42
46 1 0.01
47 1 0.01
48 9 0.12
49 33 0.43
50 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (48 bp):
TATAATTATATAATTATTAAATAAATAAAATAATTAAAATATAATAAA
Found at i:614549 original size:46 final size:46
Alignment explanation
Indices: 614474--614567 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 46
614464 ATACGGGCTT
* * * *
614474 CTGTTGCGACCGTCATTAGTACTGCGGGATCAGAATGAACCGTATC
1 CTGTTGCGACCATCATGAGTAATGCGGGATCAAAATGAACCGTATC
*
614520 CTGTTGCGACCATCATGAGTAATGTGGGATCAAAATGAACCGTATC
1 CTGTTGCGACCATCATGAGTAATGCGGGATCAAAATGAACCGTATC
614566 CT
1 CT
614568 ATGTTACGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (46 bp):
CTGTTGCGACCATCATGAGTAATGCGGGATCAAAATGAACCGTATC
Found at i:614930 original size:3 final size:3
Alignment explanation
Indices: 614922--614959 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
614912 ACCCTTTAAA
*
614922 AAT AAT AAT TAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
614960 AAGGTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:619846 original size:28 final size:28
Alignment explanation
Indices: 619806--619860 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
619796 GATATAATAG
619806 ATGATTATATGAATAAATTAAATTGAAC
1 ATGATTATATGAATAAATTAAATTGAAC
* *
619834 ATGATTGTGTGAATAAATTAAATTGAA
1 ATGATTATATGAATAAATTAAATTGAA
619861 TATCGGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.47, C:0.02, G:0.15, T:0.36
Consensus pattern (28 bp):
ATGATTATATGAATAAATTAAATTGAAC
Found at i:621214 original size:2 final size:2
Alignment explanation
Indices: 621207--621240 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
621197 AATATGCATG
*
621207 TA TA TA TA TC 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
621241 GGAATTGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:621500 original size:2 final size:2
Alignment explanation
Indices: 621493--621521 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
621483 CAAAATACTT
621493 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
621522 GAAATCCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:624524 original size:2 final size:2
Alignment explanation
Indices: 624519--624549 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
624509 AAAAAAAAAC
624519 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 A
624550 ATGAAAGATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:624923 original size:19 final size:20
Alignment explanation
Indices: 624895--624949 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
624885 AAATTTAAAA
624895 TTTATCA-TTTTATTTAAATT
1 TTTATCATTTTTA-TTAAATT
624915 TTTAT-ATTTTTATTAAATT
1 TTTATCATTTTTATTAAATT
**
624934 TAAATCAATTTTTATT
1 TTTATC-ATTTTTATT
624950 TCTAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 11 0.37
20 10 0.33
21 9 0.30
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTATCATTTTTATTAAATT
Found at i:624943 original size:29 final size:29
Alignment explanation
Indices: 624909--625013 Score: 124
Period size: 29 Copynumber: 3.6 Consensus size: 29
624899 TCATTTTATT
624909 TAAATTTTTATATTTTTA-TTAAATTTAAA
1 TAAATTTTTA-ATTTTTATTTAAATTTAAA
* *
624938 TCAATTTTT-ATTTCTAATTTAAATTTAAA
1 TAAATTTTTAATTT-TTATTTAAATTTAAA
* **
624967 TAAATTATTAATTTTTTATTTTTATTTAAA
1 TAAATTTTTAA-TTTTTATTTAAATTTAAA
624997 TAAATTTTTAATTTTTA
1 TAAATTTTTAATTTTTA
625014 AATTATTAGT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
27 4 0.06
28 2 0.03
29 32 0.50
30 23 0.36
31 3 0.05
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (29 bp):
TAAATTTTTAATTTTTATTTAAATTTAAA
Found at i:625027 original size:30 final size:30
Alignment explanation
Indices: 624963--625029 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
624953 AATTTAAATT
* * *
624963 TAAATAAATTATTAATTTTTTATTTTTATT
1 TAAATAAATTATTAATTTTTAATTATTATG
*
624993 TAAATAAATTTTTAATTTTTAAATTATTA-G
1 TAAATAAATTATTAATTTTT-AATTATTATG
625023 TAAATAA
1 TAAATAA
625030 GTCAAAACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (30 bp):
TAAATAAATTATTAATTTTTAATTATTATG
Found at i:625311 original size:20 final size:21
Alignment explanation
Indices: 625265--625311 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
625255 AATTTTTAAG
* *
625265 ATATAATTATATTAAAGTATT
1 ATATATTTATATAAAAGTATT
*
625286 AAATATTTATATAAAAGT-TT
1 ATATATTTATATAAAAGTATT
625306 ATATAT
1 ATATAT
625312 AAATATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (21 bp):
ATATATTTATATAAAAGTATT
Found at i:625329 original size:13 final size:13
Alignment explanation
Indices: 625282--625338 Score: 73
Period size: 13 Copynumber: 4.4 Consensus size: 13
625272 TATATTAAAG
625282 TATTAAATATTTA
1 TATTAAATATTTA
625295 TA-TAAA-AGTTTA
1 TATTAAATA-TTTA
625307 TATATAAATATTTA
1 TAT-TAAATATTTA
*
625321 TATTAAATATCTA
1 TATTAAATATTTA
625334 TATTA
1 TATTA
625339 TGTAATATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 1 0.03
12 10 0.26
13 16 0.41
14 11 0.28
15 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (13 bp):
TATTAAATATTTA
Found at i:625879 original size:27 final size:27
Alignment explanation
Indices: 625825--625887 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
625815 GTGTTTTTGA
* *
625825 ATTTTAAA-AT-TTAAATTTATTTATT
1 ATTTTAAATATATTAAATTTATGTAAT
*
625850 ATTTTAAATATATTTAATTTATGTAAT
1 ATTTTAAATATATTAAATTTATGTAAT
625877 A-TTTAAATATA
1 ATTTTAAATATA
625888 AATATAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.24
26 12 0.36
27 13 0.39
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
ATTTTAAATATATTAAATTTATGTAAT
Found at i:626267 original size:33 final size:37
Alignment explanation
Indices: 626207--626328 Score: 109
Period size: 37 Copynumber: 3.4 Consensus size: 37
626197 TAATTTAATT
*
626207 AAATATA-TAAATAT-TTTAAAA-TT-TATAAAAAT-
1 AAATATATTAAATATAATTAAAATTTATATAAAAATA
626239 AAAT-TATTAAA-AT-ATTAAAATTTATATAAAAATA
1 AAATATATTAAATATAATTAAAATTTATATAAAAATA
* *
626273 AAATATTTTAAATATAATTAAAATATA-ATAAAATATA
1 AAATATATTAAATATAATTAAAATTTATATAAAA-ATA
*
626310 TTAATATAATATAAATATA
1 -AAATAT-AT-TAAATATA
626329 TAAATAGTTA
Statistics
Matches: 74, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
31 10 0.14
32 10 0.14
33 9 0.12
34 4 0.05
35 6 0.08
36 8 0.11
37 13 0.18
38 5 0.07
39 1 0.01
40 8 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (37 bp):
AAATATATTAAATATAATTAAAATTTATATAAAAATA
Found at i:626282 original size:20 final size:20
Alignment explanation
Indices: 626259--626298 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
626249 AATATTAAAA
*
626259 TTTATATAAAAATAAAATAT
1 TTTAAATAAAAATAAAATAT
* *
626279 TTTAAATATAATTAAAATAT
1 TTTAAATAAAAATAAAATAT
626299 AATAAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTAAATAAAAATAAAATAT
Found at i:626293 original size:10 final size:10
Alignment explanation
Indices: 626280--626328 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 10
626270 ATAAAATATT
626280 TTAAATATAA
1 TTAAATATAA
626290 TTAAAATATAA
1 TT-AAATATAA
*
626301 TAAAATAT-A
1 TTAAATATAA
626310 TT-AATATAA
1 TTAAATATAA
626319 TATAAATATA
1 T-TAAATATA
626329 TAAATAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
8 5 0.15
9 4 0.12
10 9 0.27
11 15 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TTAAATATAA
Found at i:626298 original size:11 final size:11
Alignment explanation
Indices: 626282--626331 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 11
626272 AAAATATTTT
626282 AAATATAATTA
1 AAATATAATTA
626293 AAATATAA-TA
1 AAATATAATTA
626303 AAATAT-ATT-
1 AAATATAATTA
626312 -AATATAATATA
1 AAATATAAT-TA
626323 AATATATAA
1 AA-ATATAA
626332 ATAGTTAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
8 5 0.15
9 3 0.09
10 10 0.30
11 8 0.24
12 1 0.03
13 6 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AAATATAATTA
Found at i:626304 original size:20 final size:21
Alignment explanation
Indices: 626271--626330 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
626261 TATATAAAAA
**
626271 TAAAATATTTTAAATATA-AT
1 TAAAATATAATAAATATATAT
626291 TAAAATATAATAAA-ATATAT
1 TAAAATATAATAAATATATAT
*
626311 TAATATA-ATATAAATATATA
1 TAAAATATA-ATAAATATATA
626331 AATAGTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 4 0.12
20 25 0.74
21 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAATATAATAAATATATAT
Found at i:628254 original size:13 final size:13
Alignment explanation
Indices: 628236--628260 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
628226 ATCTCAGATG
628236 TTTATTTATTTTA
1 TTTATTTATTTTA
628249 TTTATTTATTTT
1 TTTATTTATTTT
628261 GGTGTTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:629645 original size:22 final size:21
Alignment explanation
Indices: 629608--629655 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 21
629598 TAATTTAATT
*
629608 AAAATATTATTTAATAATATA
1 AAAATAATATTTAATAATATA
629629 AAAATAATATTTTAATAATATA
1 AAAATAATA-TTTAATAATATA
629651 AAAAT
1 AAAAT
629656 TTTTCAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATAATATTTAATAATATA
Found at i:632092 original size:23 final size:24
Alignment explanation
Indices: 632066--632120 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
632056 GAAATTTCAC
* *
632066 TTAATTTAT-TTATATAATTATTT
1 TTAATTTATATAATATAATAATTT
* *
632089 TTAAGTGATATAATATAATAATTT
1 TTAATTTATATAATATAATAATTT
*
632113 TAAATTTA
1 TTAATTTA
632121 AATTTTAATA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
TTAATTTATATAATATAATAATTT
Found at i:632135 original size:14 final size:13
Alignment explanation
Indices: 632108--632140 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
632098 ATAATATAAT
632108 AATTTTAAATTTA
1 AATTTTAAATTTA
632121 AATTTTAATATTTA
1 AATTTTAA-ATTTA
632135 AATTTT
1 AATTTT
632141 TTTATATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
AATTTTAAATTTA
Found at i:632965 original size:18 final size:18
Alignment explanation
Indices: 632855--632965 Score: 62
Period size: 18 Copynumber: 5.7 Consensus size: 18
632845 TAAATTTGAT
* *
632855 ATTATTAATATATAAAAA
1 ATTATTAAAATATAATAA
* *
632873 ATAATTAAAATACAATATA
1 ATTATTAAAATATAATA-A
* *
632892 ATTTTTAAAAAATAATTAAA
1 ATTATTAAAATATAA-T-AA
*
632912 TATTATTTAAATAT-ATAA
1 -ATTATTAAAATATAATAA
*
632930 TTATATTTAAATTTATATAATAA
1 AT-TA-TTAAA---ATATAATAA
632953 ATTATTAAAATAT
1 ATTATTAAAATAT
632966 TTAAATTTTT
Statistics
Matches: 69, Mismatches: 14, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
17 1 0.01
18 21 0.30
19 17 0.25
20 3 0.04
21 16 0.23
22 6 0.09
23 5 0.07
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTATTAAAATATAATAA
Found at i:633158 original size:19 final size:20
Alignment explanation
Indices: 633111--633159 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
633101 GCAATAATAT
633111 TTTTTATATTAAATTTGATGA
1 TTTTTA-ATTAAATTTGATGA
** *
633132 TTAATAATT-AATTTGATTA
1 TTTTTAATTAAATTTGATGA
633151 TTTTTAATT
1 TTTTTAATT
633160 TATTAAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 16 0.70
20 3 0.13
21 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (20 bp):
TTTTTAATTAAATTTGATGA
Found at i:634158 original size:2 final size:2
Alignment explanation
Indices: 634151--634179 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
634141 AATATTCATT
634151 TC 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 TC T
634180 TTTCCTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:637370 original size:12 final size:12
Alignment explanation
Indices: 637353--637377 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
637343 CCCTAAGTAG
637353 GCCTGGCGACAT
1 GCCTGGCGACAT
637365 GCCTGGCGACAT
1 GCCTGGCGACAT
637377 G
1 G
637378 TGCAGTAGCT
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:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (12 bp):
GCCTGGCGACAT
Found at i:637818 original size:6 final size:6
Alignment explanation
Indices: 637807--637841 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
637797 TGAACTGCTC
*
637807 TGTGCG TGTGCG TGTGCG TGTGCG TGTGTG TGTGC
1 TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG TGTGC
637842 CCGTGTGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.14, G:0.49, T:0.37
Consensus pattern (6 bp):
TGTGCG
Found at i:638175 original size:17 final size:19
Alignment explanation
Indices: 638153--638197 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
638143 CATGTTTTAA
638153 ATATTTATAAT-T-TATAT
1 ATATTTATAATATATATAT
* *
638170 ATATTTTTAATATATTTAT
1 ATATTTATAATATATATAT
638189 ATATTTATA
1 ATATTTATA
638198 TTAAATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 10 0.43
18 1 0.04
19 12 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATATTTATAATATATATAT
Found at i:638218 original size:19 final size:19
Alignment explanation
Indices: 638161--638219 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
638151 AAATATTTAT
*
638161 AATTTATATATATTTTTAATA
1 AATTTATAT-TA-TTTTATTA
*
638182 TATTTATA-TATTTATATTA
1 AATTTATATTATTT-TATTA
638201 AATTTATATTATTTTATTA
1 AATTTATATTATTTTATTA
638220 TGATGTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.09
19 18 0.55
20 5 0.15
21 7 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
AATTTATATTATTTTATTA
Found at i:639546 original size:35 final size:38
Alignment explanation
Indices: 639501--639590 Score: 95
Period size: 35 Copynumber: 2.6 Consensus size: 38
639491 AATATTTTAT
639501 ATAATT-TATTATAAAATTTAAGTTTAT-TGAAT-TAA
1 ATAATTATATTATAAAATTTAAGTTTATATGAATATAA
* * * *
639536 A-AATTATATTATTATATTT-ATTTTATATTAATATAA
1 ATAATTATATTATAAAATTTAAGTTTATATGAATATAA
639572 ATAA-TATATT-TAAAATTTA
1 ATAATTATATTATAAAATTTA
639591 TACAAATAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
34 10 0.23
35 22 0.50
36 10 0.23
37 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (38 bp):
ATAATTATATTATAAAATTTAAGTTTATATGAATATAA
Found at i:640671 original size:17 final size:16
Alignment explanation
Indices: 640642--640677 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
640632 TTTATTTTTT
*
640642 TATAATTATATTTAAA
1 TATAATTAAATTTAAA
640658 TATATATTAAATTTAAA
1 TATA-ATTAAATTTAAA
640675 TAT
1 TAT
640678 TTAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATAATTAAATTTAAA
Found at i:648833 original size:29 final size:29
Alignment explanation
Indices: 648804--648881 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 29
648794 TTTGAATTAT
648804 TATTTAAAAATAAAAATA-ATTTTATATA
1 TATTTAAAAATAAAAATATATTTTATATA
*
648832 T-TTTAAATAAT-AAAATATATTTTATTTA
1 TATTTAAA-AATAAAAATATATTTTATATA
*
648860 AATTTAAAAAAATAAAAATATA
1 TATTT--AAAAATAAAAATATA
648882 ATAATACTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
27 12 0.29
28 13 0.31
29 3 0.07
30 3 0.07
31 11 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
TATTTAAAAATAAAAATATATTTTATATA
Found at i:649803 original size:20 final size:19
Alignment explanation
Indices: 649778--649817 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
649768 TTAAAGAATC
649778 ATAATTA-AAATATATAAAAA
1 ATAATTATAAA-AT-TAAAAA
649798 ATAATTATAAAATTAAAAA
1 ATAATTATAAAATTAAAAA
649817 A
1 A
649818 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 9 0.47
21 3 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAATTATAAAATTAAAAA
Found at i:650184 original size:3 final size:3
Alignment explanation
Indices: 650176--650206 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
650166 AGATCTCTTC
650176 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
650207 TGCTTAATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:650781 original size:3 final size:3
Alignment explanation
Indices: 650773--650818 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
650763 ATTTATTTCT
*
650773 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
650819 GTTGATCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:651062 original size:25 final size:25
Alignment explanation
Indices: 651034--651081 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
651024 CTATAGTACT
*
651034 TAGTGTATTAAATAAAAATATTACA
1 TAGTATATTAAATAAAAATATTACA
651059 TAGTATATTAAATAAAAATATTA
1 TAGTATATTAAATAAAAATATTA
651082 ATGTACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (25 bp):
TAGTATATTAAATAAAAATATTACA
Found at i:651081 original size:13 final size:13
Alignment explanation
Indices: 651039--651082 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
651029 GTACTTAGTG
651039 TATTAAATAAAAA
1 TATTAAATAAAAA
* **
651052 TATTACAT-AGTA
1 TATTAAATAAAAA
651064 TATTAAATAAAAA
1 TATTAAATAAAAA
651077 TATTAA
1 TATTAA
651083 TGTACATAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (13 bp):
TATTAAATAAAAA
Found at i:651351 original size:10 final size:10
Alignment explanation
Indices: 651336--651386 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
651326 TTGTACTCTA
651336 AATTATATTT
1 AATTATATTT
651346 AA-T-TATTT
1 AATTATATTT
651354 -ATATATATTT
1 AAT-TATATTT
*
651364 TATTATATTAT
1 AATTATATT-T
651375 AATTATATTT
1 AATTATATTT
651385 AA
1 AA
651387 AATTTTTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
7 1 0.03
8 5 0.14
9 2 0.06
10 16 0.46
11 11 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
AATTATATTT
Found at i:651357 original size:14 final size:15
Alignment explanation
Indices: 651337--651383 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
651327 TGTACTCTAA
651337 ATTATATTTAATTAT
1 ATTATATTTAATTAT
* *
651352 -TTATATAT-ATTTT
1 ATTATATTTAATTAT
651365 ATTATATTATAATTAT
1 ATTATATT-TAATTAT
651381 ATT
1 ATT
651384 TAAAATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
13 4 0.16
14 13 0.52
15 1 0.04
16 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTATATTTAATTAT
Found at i:651698 original size:17 final size:17
Alignment explanation
Indices: 651649--651702 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
651639 GTCCAACAAT
* *
651649 TTATTTTAATATTTAAA
1 TTATATTAATATTTATA
** *
651666 AAATATTAAAATTTTATA
1 TTATATTAATA-TTTATA
651684 TTATATTAATATTTATA
1 TTATATTAATATTTATA
651701 TT
1 TT
651703 TTTTTATAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTAATATTTATA
Found at i:651703 original size:24 final size:23
Alignment explanation
Indices: 651667--651723 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
651657 ATATTTAAAA
*
651667 AATATTAAAATTTTATATTAT-ATT
1 AATATTTAAATTTT-T-TTATAATT
*
651691 AATATTTATATTTTTTTATAATT
1 AATATTTAAATTTTTTTATAATT
651714 AA-ATTTAAAT
1 AATATTTAAAT
651724 ATAAATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 11 0.38
23 6 0.21
24 12 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AATATTTAAATTTTTTTATAATT
Found at i:652394 original size:52 final size:52
Alignment explanation
Indices: 652338--652441 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
652328 ACGTTCACAT
652338 CTAAGATCGAGATCAAATTATATAAAATATAATAGCTTGTTTGATGCACCAG
1 CTAAGATCGAGATCAAATTATATAAAATATAATAGCTTGTTTGATGCACCAG
** **
652390 CTAAGATCGAGATTGAATTATATAGGATATAATAGCTTGTTTGATGCACCAG
1 CTAAGATCGAGATCAAATTATATAAAATATAATAGCTTGTTTGATGCACCAG
652442 GGGCACCAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (52 bp):
CTAAGATCGAGATCAAATTATATAAAATATAATAGCTTGTTTGATGCACCAG
Found at i:655959 original size:2 final size:2
Alignment explanation
Indices: 655952--655982 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
655942 GGAAAATCAA
655952 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 A
655983 AAACACGCAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:656780 original size:29 final size:30
Alignment explanation
Indices: 656725--656781 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
656715 GTATTATTTT
*
656725 TTTTATTATATATTTATATAAAATTTAATA
1 TTTTAATATATATTTATATAAAATTTAATA
*
656755 TTTTAATATATA-TTATATAATATTTAA
1 TTTTAATATATATTTATATAAAATTTAA
656782 AATATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TTTTAATATATATTTATATAAAATTTAATA
Found at i:656822 original size:28 final size:30
Alignment explanation
Indices: 656733--656827 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 30
656723 TTTTTTATTA
* * * * *
656733 TATATTTATATAAAATTTAATATTTTAATA
1 TATATTTATATAATATTTAAAATATTAGTT
*
656763 TATA-TTATATAATATTTAAAATATTATTT
1 TATATTTATATAATATTTAAAATATTAGTT
* * *
656792 TATTTTTATATTATATTTTAAA-ATT-GTT
1 TATATTTATATAATATTTAAAATATTAGTT
656820 TATATTTA
1 TATATTTA
656828 ACATTATTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
28 9 0.17
29 26 0.48
30 19 0.35
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (30 bp):
TATATTTATATAATATTTAAAATATTAGTT
Found at i:657558 original size:16 final size:16
Alignment explanation
Indices: 657537--657571 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
657527 CTTATTTCAT
* *
657537 AAATTTTATAAATTTA
1 AAATTTTAAAAATATA
657553 AAATTTTAAAAATATA
1 AAATTTTAAAAATATA
657569 AAA
1 AAA
657572 ATATATCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTTTAAAAATATA
Found at i:657663 original size:2 final size:2
Alignment explanation
Indices: 657656--657684 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
657646 ATTACTGGTA
657656 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
657685 TATTTAAATA
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:660845 original size:21 final size:21
Alignment explanation
Indices: 660821--660862 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
660811 TTATTTTACA
660821 TGCATAT-TCAACTTGGCTCCC
1 TGCATATATCAACTT-GCTCCC
*
660842 TGCATATATCAAGTTGCTCCC
1 TGCATATATCAACTTGCTCCC
660863 AATAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.33
Consensus pattern (21 bp):
TGCATATATCAACTTGCTCCC
Found at i:663721 original size:113 final size:109
Alignment explanation
Indices: 663485--663692 Score: 319
Period size: 109 Copynumber: 1.9 Consensus size: 109
663475 TTTTTATTTG
*
663485 CTGTAAAATAGACTTTTTTGGGTGGATAGGTTTCAAATAGCTTGCTTTTTTTTTTTTTTTTTTAT
1 CTGTAAAATGGACTTTTTTGGGTGGATAGGTTTCAAATAGCTTGC---TTTTTTTTTTTTTTTAT
* * *
663550 TTGAGATGATTTGATCTTCCAAGGTGTTACAAAGGGAATTTTTATTTG
63 TTGAGATGATTTGATCTTCCAAGGTGTTAAAAAGGGAATTTTCA-TTA
*
663598 CTGTAAAATGGACTTTTTTTGGTGGATAGGTTTCAAATAGCTTGC-TTTTTTTTTTTTTTATTTG
1 CTGTAAAATGGACTTTTTTGGGTGGATAGGTTTCAAATAGCTTGCTTTTTTTTTTTTTTTATTTG
*
663662 AGATGGTTTGATCTTCCAAGGTGTTAAAAAG
66 AGATGATTTGATCTTCCAAGGTGTTAAAAAG
663693 AGCTGAGCAT
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
109 48 0.53
113 43 0.47
ACGTcount: A:0.23, C:0.08, G:0.20, T:0.49
Consensus pattern (109 bp):
CTGTAAAATGGACTTTTTTGGGTGGATAGGTTTCAAATAGCTTGCTTTTTTTTTTTTTTTATTTG
AGATGATTTGATCTTCCAAGGTGTTAAAAAGGGAATTTTCATTA
Found at i:665403 original size:8 final size:8
Alignment explanation
Indices: 665390--665415 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
665380 TATATATTAG
665390 AAGCAACA
1 AAGCAACA
665398 AAGCAACA
1 AAGCAACA
665406 AAGCAACA
1 AAGCAACA
665414 AA
1 AA
665416 TCTTTGAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.23, G:0.12, T:0.00
Consensus pattern (8 bp):
AAGCAACA
Found at i:665823 original size:149 final size:149
Alignment explanation
Indices: 665553--665850 Score: 578
Period size: 149 Copynumber: 2.0 Consensus size: 149
665543 CAGATTTGTA
*
665553 CCCAATACATAACACATGAAAATGAATTATTGAATAACAATTGGTCAGCGTCTATATTGAAGCAT
1 CCCAATACATAAAACATGAAAATGAATTATTGAATAACAATTGGTCAGCGTCTATATTGAAGCAT
665618 TTTATCCCAGAGTTTTTGAATACTTCCCGAAAAAAACCATAGATACATTTGCTCAAATATGGCTT
66 TTTATCCCAGAGTTTTTGAATACTTCCCGAAAAAAACCATAGATACATTTGCTCAAATATGGCTT
665683 GATTGTGGATTAATATACC
131 GATTGTGGATTAATATACC
665702 CCCAATACATAAAACATGAAAATGAATTATTGAATAACAATTGGTCAGCGTCTATATTGAAGCAT
1 CCCAATACATAAAACATGAAAATGAATTATTGAATAACAATTGGTCAGCGTCTATATTGAAGCAT
665767 TTTATCCCAGAGTTTTTGAATACTTCCCGAAAAAAACCATAGATACATTTGCTCAAATATGGCTT
66 TTTATCCCAGAGTTTTTGAATACTTCCCGAAAAAAACCATAGATACATTTGCTCAAATATGGCTT
*
665832 GATTGTGGATTCATATACC
131 GATTGTGGATTAATATACC
665851 TTCAAATTGA
Statistics
Matches: 147, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 147 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (149 bp):
CCCAATACATAAAACATGAAAATGAATTATTGAATAACAATTGGTCAGCGTCTATATTGAAGCAT
TTTATCCCAGAGTTTTTGAATACTTCCCGAAAAAAACCATAGATACATTTGCTCAAATATGGCTT
GATTGTGGATTAATATACC
Found at i:674353 original size:11 final size:12
Alignment explanation
Indices: 674328--674372 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
674318 TGAGATTTAA
674328 ATATTAAATTTT
1 ATATTAAATTTT
674340 ATATTAAATTTAT
1 ATATTAAATTT-T
674353 ATAATTAAATATTT
1 AT-ATTAAAT-TTT
674367 -TATTAA
1 ATATTAA
674373 TTATTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 16 0.53
13 4 0.13
14 8 0.27
15 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATTAAATTTT
Found at i:674385 original size:28 final size:26
Alignment explanation
Indices: 674322--674372 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
674312 TATCATTGAG
*
674322 ATTTAAAT-ATTAAATTTTATATTAA
1 ATTTATATAATTAAATTTTATATTAA
674347 ATTTATATAATTAAATATTT-TATTAA
1 ATTTATATAATTAAAT-TTTATATTAA
674373 TTATTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 13 0.57
27 3 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTTATATAATTAAATTTTATATTAA
Found at i:675472 original size:17 final size:18
Alignment explanation
Indices: 675439--675473 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
675429 GAAAAATAAA
675439 AATTTATGATAATTTTTG
1 AATTTATGATAATTTTTG
675457 AATTT-TGATATATTTTT
1 AATTTATGATA-ATTTTT
675474 ATGAGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (18 bp):
AATTTATGATAATTTTTG
Found at i:675555 original size:22 final size:23
Alignment explanation
Indices: 675516--675568 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
675506 ATATAAAAGC
*
675516 TTAAATATGAATTTTTTTAATGAA
1 TTAAA-ATGAATTATTTTAATGAA
* *
675540 TTAAAAT-AATTATTTTTATTAA
1 TTAAAATGAATTATTTTAATGAA
675562 TTAAAAT
1 TTAAAAT
675569 TTTAAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 19 0.73
23 2 0.08
24 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
TTAAAATGAATTATTTTAATGAA
Found at i:675630 original size:18 final size:18
Alignment explanation
Indices: 675603--675659 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
675593 TTAATATAAT
675603 ATTAATAAATCTTATCAA
1 ATTAATAAATCTTATCAA
* * *
675621 ATTGATAAATATT-TTAA
1 ATTAATAAATCTTATCAA
*
675638 TATTAATAAATCTGATCAA
1 -ATTAATAAATCTTATCAA
675657 ATT
1 ATT
675660 TTTAAGTGAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
17 3 0.10
18 24 0.80
19 3 0.10
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (18 bp):
ATTAATAAATCTTATCAA
Found at i:675706 original size:34 final size:35
Alignment explanation
Indices: 675668--675738 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 35
675658 TTTTTAAGTG
675668 AAAATTTTAATTTTATTAAAAAAAG-T-TTAAAATA
1 AAAATTTTAATTTTATT-AAAAAAGTTATTAAAATA
*
675702 AAAATTTTAATTTTATTTAAAAAGTTATTAAAATA
1 AAAATTTTAATTTTATTAAAAAAGTTATTAAAATA
675737 AA
1 AA
675739 TTTATTTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 6 0.18
34 18 0.53
35 10 0.29
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (35 bp):
AAAATTTTAATTTTATTAAAAAAGTTATTAAAATA
Found at i:675911 original size:90 final size:95
Alignment explanation
Indices: 675730--675913 Score: 211
Period size: 90 Copynumber: 2.0 Consensus size: 95
675720 AAAAAGTTAT
* * * *
675730 TAAAATAAATTTATTTGATAATAGATAAAAGAGAGTTAATATTTATTTTAAATTGTTTTATTTCA
1 TAAAATAAATTTATTTGATAATAGATAAAAGAGAATTAAAACTTATTATAAATTGTTTTATTTCA
**
675795 AAATTTTAATTTTTTATTAATCTTAAAAAC
66 AAATTTTAATTTTAGATTAATCTTAAAAAC
* *
675825 TAAAATAAATTTATTTGAT-A-A-ATAAAA-A-AATTAAAACTTA-TATGAATTTTTTTATTTTC
1 TAAAATAAATTTATTTGATAATAGATAAAAGAGAATTAAAACTTATTATAAATTGTTTTA-TTTC
* *
675884 ATATTTTTAATTTTAGATTAA-CATTAAAAA
65 AAAATTTTAATTTTAGATTAATC-TTAAAAA
675914 TAATGGTATT
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
89 12 0.16
90 37 0.48
91 1 0.01
92 6 0.08
93 1 0.01
94 1 0.01
95 19 0.25
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (95 bp):
TAAAATAAATTTATTTGATAATAGATAAAAGAGAATTAAAACTTATTATAAATTGTTTTATTTCA
AAATTTTAATTTTAGATTAATCTTAAAAAC
Found at i:676347 original size:22 final size:20
Alignment explanation
Indices: 676316--676356 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
676306 ATTCAGGTTT
*
676316 AAATTGAATTTAGTTGATTTAA
1 AAATTAAATTTA-TT-ATTTAA
676338 AAATTAAATTTATTATTTA
1 AAATTAAATTTATTATTTA
676357 TAATAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
AAATTAAATTTATTATTTAA
Found at i:676376 original size:22 final size:23
Alignment explanation
Indices: 676348--676416 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
676338 AAATTAAATT
676348 TATTA-TTTATAATAATATTAAA
1 TATTATTTTATAATAATATTAAA
* *
676370 TATTATTTTATATTAATATT-TA
1 TATTATTTTATAATAATATTAAA
*
676392 TA-TATTTTATAATTAATTTTAAA
1 TATTATTTTATAA-TAATATTAAA
676415 TA
1 TA
676417 AAAAATTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 9 0.23
22 14 0.36
23 16 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTATTTTATAATAATATTAAA
Found at i:676793 original size:16 final size:17
Alignment explanation
Indices: 676772--676812 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
676762 TTTAAAATTA
*
676772 TATATTTAT-ATTTTAT
1 TATATTTATAATGTTAT
*
676788 TATATTT-TAATGTTCT
1 TATATTTATAATGTTAT
676804 TATATTTAT
1 TATATTTAT
676813 TATATTCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 19 0.90
17 1 0.05
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (17 bp):
TATATTTATAATGTTAT
Found at i:676840 original size:15 final size:15
Alignment explanation
Indices: 676832--676863 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
676822 ATTATCATAT
676832 TTAAAATTATAATTA
1 TTAAAATTATAATTA
676847 TTAAAATT-TAATT-
1 TTAAAATTATAATTA
676860 TTAA
1 TTAA
676864 TAACTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.24
14 5 0.29
15 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAAAATTATAATTA
Found at i:680917 original size:14 final size:14
Alignment explanation
Indices: 680894--680932 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
680884 AACCCTTCGT
*
680894 TCTCTCTCTCTCTC
1 TCTCTTTCTCTCTC
680908 TCTCTTTCTCTCTC
1 TCTCTTTCTCTCTC
* *
680922 TATATTTCTCT
1 TCTCTTTCTCT
680933 TGTGAATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.56
Consensus pattern (14 bp):
TCTCTTTCTCTCTC
Found at i:688079 original size:2 final size:2
Alignment explanation
Indices: 688066--688106 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
688056 ACATAATTTG
*
688066 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
688107 GCACGTATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:688400 original size:13 final size:14
Alignment explanation
Indices: 688341--688416 Score: 68
Period size: 13 Copynumber: 5.4 Consensus size: 14
688331 TTATAAAATT
688341 TTTAATTAAATAAAA
1 TTTAA-TAAATAAAA
*
688356 TTATAATTAATAAAA
1 TT-TAATAAATAAAA
* *
688371 TTTATTTAAA-AATA
1 TTTA-ATAAATAAAA
688385 TTTAATAAAT-AAA
1 TTTAATAAATAAAA
*
688398 TTTAA-AATTAAAA
1 TTTAATAAATAAAA
688411 TTTAAT
1 TTTAAT
688417 TATATAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
12 3 0.06
13 19 0.39
14 9 0.18
15 15 0.31
16 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTAATAAATAAAA
Found at i:688505 original size:16 final size:16
Alignment explanation
Indices: 688475--688510 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
688465 ATATAAGAAA
688475 ATGATTAAAATATAAT
1 ATGATTAAAATATAAT
688491 ATGATATAAAA-ATAAT
1 ATGAT-TAAAATATAAT
688507 ATGA
1 ATGA
688511 GAGAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (16 bp):
ATGATTAAAATATAAT
Found at i:688598 original size:32 final size:32
Alignment explanation
Indices: 688530--688598 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
688520 ATGAATATGT
* *
688530 AAATATTTATATAAAATGAATTATTAATGTAT
1 AAATATTTATATAAAATGAAATATTAATGTAC
* * *
688562 AAATATTTATATAAATTTATAATATT-TTGTAC
1 AAATATTTATATAAAATGA-AATATTAATGTAC
688594 AAATA
1 AAATA
688599 AAAATAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 26 0.84
33 5 0.16
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (32 bp):
AAATATTTATATAAAATGAAATATTAATGTAC
Found at i:689456 original size:27 final size:28
Alignment explanation
Indices: 689420--689477 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
689410 AAATAAAACG
689420 AATTATTAATATGTAAAAAT-TTATAAAA
1 AATTATTAATATGTAAAAATCTTA-AAAA
* *
689448 AATTA-TAATATTTAAAACTCTTAAAAA
1 AATTATTAATATGTAAAAATCTTAAAAA
689475 AAT
1 AAT
689478 AATATGAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (28 bp):
AATTATTAATATGTAAAAATCTTAAAAA
Found at i:689550 original size:15 final size:15
Alignment explanation
Indices: 689526--689556 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
689516 TCTTTCTTTT
*
689526 CTTTCTTTCTCTCTC
1 CTTTCCTTCTCTCTC
689541 CTTTCCTTCTCTCTC
1 CTTTCCTTCTCTCTC
689556 C
1 C
689557 CTTCACGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (15 bp):
CTTTCCTTCTCTCTC
Found at i:690200 original size:16 final size:17
Alignment explanation
Indices: 690158--690202 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
690148 ACACATAAAT
690158 TTTTTTCTTTTTTCTTTC
1 TTTTTT-TTTTTTCTTTC
**
690176 TTTCCTTTTTTT-TTTC
1 TTTTTTTTTTTTCTTTC
690192 TTTTTTTTTTT
1 TTTTTTTTTTT
690203 CACCTCAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.57
17 6 0.26
18 4 0.17
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (17 bp):
TTTTTTTTTTTTCTTTC
Found at i:693427 original size:3 final size:3
Alignment explanation
Indices: 693419--693443 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
693409 GTCTGTGACG
693419 GTT GTT GTT GTT GTT GTT GTT GTT G
1 GTT GTT GTT GTT GTT GTT GTT GTT G
693444 CATCACCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (3 bp):
GTT
Found at i:695339 original size:29 final size:27
Alignment explanation
Indices: 695306--695378 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
695296 TAATAATAAA
*
695306 AATATTAAAATAATTATTTTTAAATTTTT
1 AATATTAAAATAATTA-ATTTAAA-TTTT
695335 AATATTTTATAAATAA-TAATTTAAATTTT
1 AATA--TTA-AAATAATTAATTTAAATTTT
*
695364 AA-ATTAAAAAAATTA
1 AATATTAAAATAATTA
695379 GATCATAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
25 5 0.13
26 5 0.13
28 1 0.03
29 10 0.26
30 6 0.16
31 5 0.13
32 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
AATATTAAAATAATTAATTTAAATTTT
Found at i:698043 original size:17 final size:18
Alignment explanation
Indices: 698003--698046 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
697993 AATAATAATT
* *
698003 TTATTTATTATTTTCATA
1 TTATATATTATTATCATA
*
698021 TAATATATTATTAT-ATA
1 TTATATATTATTATCATA
698038 TTATATATT
1 TTATATATT
698047 TAAAATATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATATTATTATCATA
Found at i:699799 original size:3 final size:3
Alignment explanation
Indices: 699793--699830 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
699783 CAAAGCAGCA
*
699793 AAT AAT AAT -AT AAT AAT AAT AGT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
699831 TAAGTAGGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:703872 original size:21 final size:20
Alignment explanation
Indices: 703846--703889 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
703836 TCAAATTTAA
703846 TTAATTATAATTAAAAAATTT
1 TTAATT-TAATTAAAAAATTT
*
703867 TTAATTTCATTAAAAAATTT
1 TTAATTTAATTAAAAAATTT
703887 TTA
1 TTA
703890 TTAAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAATTTAATTAAAAAATTT
Found at i:705357 original size:17 final size:17
Alignment explanation
Indices: 705318--705350 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
705308 TTAAATATAA
*
705318 GTATTTAATATGAATAC
1 GTATTTAATATAAATAC
705335 GTATTTAATATAAATA
1 GTATTTAATATAAATA
705351 TTTATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (17 bp):
GTATTTAATATAAATAC
Found at i:705428 original size:17 final size:18
Alignment explanation
Indices: 705408--705450 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
705398 CATATTTTTT
*
705408 AATTAAATTTAAATAT-A
1 AATTAAATATAAATATCA
*
705425 AATTTAATATAAATATCA
1 AATTAAATATAAATATCA
705443 AA-TAAATA
1 AATTAAATA
705451 CATATAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AATTAAATATAAATATCA
Found at i:705435 original size:11 final size:11
Alignment explanation
Indices: 705405--705438 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
705395 TATCATATTT
705405 TTTAAT-TAAA
1 TTTAATATAAA
705415 TTTAAATATAAA
1 TTT-AATATAAA
705427 TTTAATATAAA
1 TTTAATATAAA
705438 T
1 T
705439 ATCAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 12 0.55
12 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTTAATATAAA
Found at i:707668 original size:3 final size:3
Alignment explanation
Indices: 707660--707689 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
707650 GAAACTCATA
707660 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
707690 AGTTTAGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:708213 original size:18 final size:18
Alignment explanation
Indices: 708170--708224 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
708160 ACATTACTAG
*
708170 TTTATTAATATATTATTAA
1 TTTATTAA-ATTTTATTAA
**
708189 TAAATTAAATTTTATTAA
1 TTTATTAAATTTTATTAA
708207 TTTATTAGAATTTT-TTAA
1 TTTATTA-AATTTTATTAA
708225 AGATAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 18 0.60
19 12 0.40
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTATTAAATTTTATTAA
Found at i:712731 original size:13 final size:14
Alignment explanation
Indices: 712706--712734 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
712696 TATATATATT
712706 TTATTTAAATTATA
1 TTATTTAAATTATA
712720 TTATTT-AATTATA
1 TTATTTAAATTATA
712733 TT
1 TT
712735 TTTTTTAAAA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTTAAATTATA
Done.