Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold20
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: 3599867
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 51021 characters in sequence are not A, C, G, or T
File 25 of 25
Found at i:3548624 original size:31 final size:31
Alignment explanation
Indices: 3548586--3548646 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
3548576 AATAATTAAG
*
3548586 TAATTTAAACATAAATAAAAATAAATAAAAT
1 TAATTTAAAAATAAATAAAAATAAATAAAAT
*
3548617 TAATTTAAAAATAAATAAAACTAAATAAAA
1 TAATTTAAAAATAAATAAAAATAAATAAAA
3548647 ATATAGAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (31 bp):
TAATTTAAAAATAAATAAAAATAAATAAAAT
Found at i:3548627 original size:21 final size:20
Alignment explanation
Indices: 3548592--3548649 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 20
3548582 TAAGTAATTT
3548592 AAACATAAATAAAAATAAATA
1 AAAC-TAAATAAAAATAAATA
* *
3548613 AAATTAATTTAAAAATAAATA
1 AAACTAA-ATAAAAATAAATA
3548634 AAACTAAATAAAAATA
1 AAACTAAATAAAAATA
3548650 TAGAAAGCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.24
Consensus pattern (20 bp):
AAACTAAATAAAAATAAATA
Found at i:3549907 original size:13 final size:14
Alignment explanation
Indices: 3549889--3549921 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3549879 GTTTTTGATG
3549889 ATTAAATAAAT-AT
1 ATTAAATAAATAAT
3549902 ATTAAA-AAATAAT
1 ATTAAATAAATAAT
3549915 ATTAAAT
1 ATTAAAT
3549922 CCGAAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATTAAATAAATAAT
Found at i:3550628 original size:14 final size:14
Alignment explanation
Indices: 3550579--3550637 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
3550569 ATACATGTGA
* *
3550579 TTAATTTTTTTAAT
1 TTAATATTTTAAAT
*
3550593 ATAATATTTAATAAAT
1 TTAATATTT--TAAAT
3550609 TTAATA-TTTAAAT
1 TTAATATTTTAAAT
3550622 CTTAATATTTTAAAT
1 -TTAATATTTTAAAT
3550637 T
1 T
3550638 ATATTTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 5 0.14
14 14 0.38
15 9 0.24
16 9 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAATATTTTAAAT
Found at i:3551675 original size:10 final size:10
Alignment explanation
Indices: 3551657--3551711 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
3551647 CTAAATAAGT
*
3551657 TAAACATAAA
1 TAAAAATAAA
3551667 TAAAAATAAA
1 TAAAAATAAA
* *
3551677 TAAAATTAAT
1 TAAAAATAAA
*
3551687 TCAAAAA-AAT
1 T-AAAAATAAA
3551697 TAAAAATAAA
1 TAAAAATAAA
3551707 TAAAA
1 TAAAA
3551712 TCTAAATGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
9 5 0.13
10 29 0.76
11 4 0.11
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.24
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:3551703 original size:30 final size:31
Alignment explanation
Indices: 3551667--3551730 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
3551657 TAAACATAAA
*
3551667 TAAAAATAAATAAAAT-TAATTCAAAAAAAT
1 TAAAAATAAATAAAATCTAAATCAAAAAAAT
* *
3551697 TAAAAATAAATAAAATCTAAATGAAAAACAT
1 TAAAAATAAATAAAATCTAAATCAAAAAAAT
3551728 TAA
1 TAA
3551731 GATTTAGCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.25
Consensus pattern (31 bp):
TAAAAATAAATAAAATCTAAATCAAAAAAAT
Found at i:3554586 original size:11 final size:11
Alignment explanation
Indices: 3554570--3554608 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
3554560 ACTAAATTAG
3554570 TTTTATATATT
1 TTTTATATATT
*
3554581 TTTTATAAATT
1 TTTTATATATT
3554592 TTTTATA-A-T
1 TTTTATATATT
3554601 TTTTATAT
1 TTTTATAT
3554609 TTGTTTAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 8 0.31
10 1 0.04
11 17 0.65
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTATATATT
Found at i:3554598 original size:20 final size:20
Alignment explanation
Indices: 3554570--3554607 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3554560 ACTAAATTAG
*
3554570 TTTTATATATTTTTTATAAA
1 TTTTATATAATTTTTATAAA
*
3554590 TTTTTTATAATTTTTATA
1 TTTTATATAATTTTTATA
3554608 TTTGTTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATATAATTTTTATAAA
Found at i:3554944 original size:15 final size:15
Alignment explanation
Indices: 3554924--3554978 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
3554914 TATTATAATT
3554924 ATATTATATCAA-ATA
1 ATATTATAT-AATATA
3554939 ATATTATATAATATA
1 ATATTATATAATATA
3554954 ATA-TATATAATTATAA
1 ATATTATATAA-TAT-A
3554970 ATATT-TATA
1 ATATTATATA
3554979 CAAATATTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 9 0.25
15 18 0.50
16 8 0.22
17 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATTATATAATATA
Found at i:3555243 original size:25 final size:25
Alignment explanation
Indices: 3555193--3555244 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
3555183 TAATACACAA
* * *
3555193 ATTATATTATATGTAATATGTTTAT
1 ATTATATTATATGTAAAATATATAT
3555218 ATTATATTATA-GTATAAATATATAT
1 ATTATATTATATGTA-AAATATATAT
3555243 AT
1 AT
3555245 ACATGCACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (25 bp):
ATTATATTATATGTAAAATATATAT
Found at i:3555279 original size:22 final size:22
Alignment explanation
Indices: 3555254--3555299 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3555244 TACATGCACA
*
3555254 ATAAAATATATCATA-TTATGTT
1 ATAAAATAAAT-ATATTTATGTT
3555276 ATAAAATAAATATATTTATGTT
1 ATAAAATAAATATATTTATGTT
3555298 AT
1 AT
3555300 TAAAGTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
ATAAAATAAATATATTTATGTT
Found at i:3558214 original size:2 final size:2
Alignment explanation
Indices: 3558207--3558233 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3558197 TGTATCACTA
3558207 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 A
3558234 CAAAAGGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3561783 original size:15 final size:14
Alignment explanation
Indices: 3561736--3561783 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
3561726 AAATATTAAA
3561736 TTAAAAATA-AAAT
1 TTAAAAATACAAAT
*
3561749 TTATAAAATATCAAAA
1 TTA-AAAATA-CAAAT
3561765 TTAAAAATACATAAT
1 TTAAAAATACA-AAT
3561780 TTAA
1 TTAA
3561784 TATTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 3 0.10
14 8 0.28
15 12 0.41
16 6 0.21
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (14 bp):
TTAAAAATACAAAT
Found at i:3562149 original size:18 final size:18
Alignment explanation
Indices: 3562094--3562152 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 18
3562084 TATAAATAAA
3562094 ATTTTA-TAATTT-ATTT
1 ATTTTATTAATTTAATTT
3562110 ATTTTTTAATTAAATATTAATTT
1 A--TTTT-ATT-AAT-TTAATTT
3562133 ATTTTATTAATTTAATTT
1 ATTTTATTAATTTAATTT
3562151 AT
1 AT
3562153 AAAATAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
16 1 0.03
18 13 0.36
19 4 0.11
20 4 0.11
21 7 0.19
22 2 0.06
23 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTATTAATTTAATTT
Found at i:3562728 original size:2 final size:2
Alignment explanation
Indices: 3562721--3562747 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3562711 CTTCTCAAAT
3562721 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
3562748 GAGAATGAAG
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:3564593 original size:2 final size:2
Alignment explanation
Indices: 3564586--3564612 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3564576 CAATTTTATA
3564586 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
3564613 ATATCTTTTC
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:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3567634 original size:2 final size:2
Alignment explanation
Indices: 3567629--3567731 Score: 57
Period size: 2 Copynumber: 50.5 Consensus size: 2
3567619 ACACACACAC
* * * * * *
3567629 AT AT AT AT AT AT AT AT A- AT CAC CT GAT AT TT AC AT AC AT AC AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT -AT AT AT AT AT AT AT AT AT
* * * * *
3567672 AT AT AT AT AT AT AT AT AT AT AT A- AT CAC CT GAT AT TT AC AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT -AT AT AT AT AT AT
3567715 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
3567732 AACAGCTAAT
Statistics
Matches: 73, Mismatches: 22, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
1 2 0.03
2 67 0.92
3 4 0.05
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:3567655 original size:43 final size:43
Alignment explanation
Indices: 3567600--3567688 Score: 133
Period size: 43 Copynumber: 2.1 Consensus size: 43
3567590 CACACTGATA
*
3567600 ATAATTACCTGATATATACACACACACACATATATATATATAT
1 ATAATCACCTGATATATACACACACACACATATATATATATAT
* * * *
3567643 ATAATCACCTGATATTTACATACATACATATATATATATATAT
1 ATAATCACCTGATATATACACACACACACATATATATATATAT
3567686 ATA
1 ATA
3567689 TATATAATCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.36
Consensus pattern (43 bp):
ATAATCACCTGATATATACACACACACACATATATATATATAT
Found at i:3567699 original size:49 final size:49
Alignment explanation
Indices: 3567629--3567731 Score: 197
Period size: 49 Copynumber: 2.1 Consensus size: 49
3567619 ACACACACAC
3567629 ATATATATATATATATAATCACCTGATATTTACATACATACATATATAT
1 ATATATATATATATATAATCACCTGATATTTACATACATACATATATAT
*
3567678 ATATATATATATATATAATCACCTGATATTTACATACATATATATATAT
1 ATATATATATATATATAATCACCTGATATTTACATACATACATATATAT
3567727 ATATA
1 ATATA
3567732 AACAGCTAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.42
Consensus pattern (49 bp):
ATATATATATATATATAATCACCTGATATTTACATACATACATATATAT
Found at i:3567940 original size:3 final size:3
Alignment explanation
Indices: 3567932--3567958 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3567922 TTTAGGCTAA
3567932 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
3567959 TTTACCTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3575345 original size:6 final size:6
Alignment explanation
Indices: 3575324--3575376 Score: 63
Period size: 6 Copynumber: 8.7 Consensus size: 6
3575314 AATTTTAAAA
* *
3575324 TTTTAT TATT-T TTTTAT TTTTAT TTTTAT TCTTAT TTTTAAT TTTTAAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT-AT TTTT-AT
3575373 TTTT
1 TTTT
3575377 TAATTTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
5 4 0.10
6 24 0.59
7 13 0.32
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:3575360 original size:18 final size:17
Alignment explanation
Indices: 3575324--3575375 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
3575314 AATTTTAAAA
3575324 TTTTATTATTT-TTTTAT
1 TTTTATT-TTTATTTTAT
3575341 TTTTATTTTTATTCTTAT
1 TTTTATTTTTATT-TTAT
3575359 TTTTAATTTTTAATTTT
1 TTTT-ATTTTT-ATTTT
3575376 TTAATTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.10
17 9 0.29
18 8 0.26
19 8 0.26
20 3 0.10
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTATTTTTATTTTAT
Found at i:3576784 original size:19 final size:20
Alignment explanation
Indices: 3576747--3576784 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3576737 TTAATTAACT
*
3576747 TTTTTAATTTTTTTAAATTA
1 TTTTTAATTTTATTAAATTA
*
3576767 TTTTT-ATTTTATTCAATT
1 TTTTTAATTTTATTAAATT
3576785 TACATCTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTAATTTTATTAAATTA
Found at i:3576849 original size:6 final size:6
Alignment explanation
Indices: 3576828--3576906 Score: 51
Period size: 6 Copynumber: 13.7 Consensus size: 6
3576818 TTTATTTTAA
* * *
3576828 TTAAACT TTTAAT TTAAAT TTAAA- -TAAAT TTAAAT TTAAAT ATATAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * *
3576875 TT-TA- TTAAAT AT-ATT TTAAAT ATTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT -TTAAAT TTAA
3576907 TTATTTTAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
4 6 0.11
5 6 0.11
6 34 0.61
7 10 0.18
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:3576859 original size:16 final size:16
Alignment explanation
Indices: 3576838--3576869 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3576828 TTAAACTTTT
3576838 AATTTAAATTTAAATA
1 AATTTAAATTTAAATA
3576854 AATTTAAATTTAAATA
1 AATTTAAATTTAAATA
3576870 TATATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Found at i:3576912 original size:22 final size:22
Alignment explanation
Indices: 3576885--3576939 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
3576875 TTTATTAAAT
3576885 ATATTTTAA-ATATTAAATTTA
1 ATATTTTAATATATTAAATTTA
* * *
3576906 ATTATTTTAATTTATTTAATTTT
1 A-TATTTTAATATATTAAATTTA
3576929 ATATTTTAATA
1 ATATTTTAATA
3576940 ATAAAAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.04
22 17 0.61
23 10 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTAATATATTAAATTTA
Found at i:3576926 original size:23 final size:23
Alignment explanation
Indices: 3576869--3576939 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
3576859 AAATTTAAAT
* *
3576869 ATATATTTTATTAAATATATTTTA
1 ATATATTTAATTTAAT-TATTTTA
*
3576893 A-ATATTAAATTTAATTATTTTA
1 ATATATTTAATTTAATTATTTTA
* *
3576915 ATTTATTTAATTTTA-TATTTTA
1 ATATATTTAATTTAATTATTTTA
3576937 ATA
1 ATA
3576940 ATAAAAAATC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
22 17 0.44
23 21 0.54
24 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
ATATATTTAATTTAATTATTTTA
Found at i:3577014 original size:14 final size:13
Alignment explanation
Indices: 3576993--3577036 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
3576983 TCGATAAAAA
3576993 AATAAATTAAATT
1 AATAAATTAAATT
*
3577006 AACTAAATTAATTT
1 AA-TAAATTAAATT
*
3577020 AATCAAATTTAATT
1 AAT-AAATTAAATT
3577034 AAT
1 AAT
3577037 TTTTTTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 3 0.12
14 23 0.88
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (13 bp):
AATAAATTAAATT
Found at i:3582679 original size:20 final size:20
Alignment explanation
Indices: 3582654--3582702 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
3582644 TTTATTAAAA
3582654 ATCTTAAATTAATTTTTTTT
1 ATCTTAAATTAATTTTTTTT
* *
3582674 ATCTTATTATTTTATTTTTTTT
1 ATCTTA--AATTAATTTTTTTT
3582696 AT-TTAAA
1 ATCTTAAA
3582703 ATTTTTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 1 0.04
20 6 0.25
21 3 0.12
22 14 0.58
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
ATCTTAAATTAATTTTTTTT
Found at i:3582708 original size:16 final size:17
Alignment explanation
Indices: 3582687--3582719 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3582677 TTATTATTTT
*
3582687 ATTTTT-TTTATTTAAA
1 ATTTTTATTAATTTAAA
3582703 ATTTTTATTAATTTAAA
1 ATTTTTATTAATTTAAA
3582720 TATTAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTTATTAATTTAAA
Found at i:3582711 original size:22 final size:22
Alignment explanation
Indices: 3582665--3582707 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3582655 TCTTAAATTA
**
3582665 ATTTTTTTTATCTTATTATTTT
1 ATTTTTTTTATCTTAAAATTTT
3582687 ATTTTTTTTAT-TTAAAATTTT
1 ATTTTTTTTATCTTAAAATTTT
3582708 TATTAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
ATTTTTTTTATCTTAAAATTTT
Found at i:3586346 original size:24 final size:23
Alignment explanation
Indices: 3586323--3586364 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3586313 AATTTGAATT
3586323 ATTATA-TTTA-AATAATAAAAA
1 ATTATATTTTATAATAATAAAAA
*
3586344 ATTATATTTTATAATTATAAA
1 ATTATATTTTATAATAATAAA
3586365 TATATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 4 0.22
23 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTATATTTTATAATAATAAAAA
Found at i:3586365 original size:30 final size:29
Alignment explanation
Indices: 3586324--3586407 Score: 80
Period size: 33 Copynumber: 2.7 Consensus size: 29
3586314 ATTTGAATTA
*
3586324 TTAT-ATTTAAATAATAAAAAATTATATT
1 TTATAATTTAAATAATAAAAAATAATATT
*
3586352 TTATAATTATAAATATATAAATAAAATAATTTT
1 TTATAATT-TAAATA-AT-AA-AAAATAATATT
3586385 TAATATAATTTTAAATAATAAAA
1 T--TATAA-TTTAAATAATAAAA
3586408 TAAATTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
28 4 0.09
29 3 0.07
30 6 0.13
31 2 0.04
32 4 0.09
33 12 0.26
34 2 0.04
35 11 0.24
36 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TTATAATTTAAATAATAAAAAATAATATT
Found at i:3586384 original size:31 final size:31
Alignment explanation
Indices: 3586319--3586415 Score: 80
Period size: 30 Copynumber: 3.2 Consensus size: 31
3586309 ACGTAATTTG
*
3586319 AATTATTAT-ATT-TAAATA-ATAAA-AAATT
1 AATT-TTATAATTATAAATATATAAATAAAAT
3586347 ATATTTTATAATTATAAATATATAAATAAAAT
1 A-ATTTTATAATTATAAATATATAAATAAAAT
* * *
3586379 AATTTT-TAA-TATAATTTTAAATAATAAAAT
1 AATTTTATAATTATAAATATATA-AATAAAAT
3586409 AAATTTT
1 -AATTTT
3586416 TTATTCGATC
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
28 5 0.09
29 15 0.26
30 17 0.29
31 16 0.28
32 5 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
AATTTTATAATTATAAATATATAAATAAAAT
Found at i:3588252 original size:2 final size:2
Alignment explanation
Indices: 3588247--3588297 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
3588237 TGTGTGTGTG
3588247 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3588289 TA TA TA TA T
1 TA TA TA TA T
3588298 TGAGGAGATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3590442 original size:20 final size:18
Alignment explanation
Indices: 3590400--3590457 Score: 71
Period size: 20 Copynumber: 3.1 Consensus size: 18
3590390 TAACACTTTT
3590400 TTCTCTTGTAAAAAATTAC
1 TTCTCTT-TAAAAAATTAC
*
3590419 TTCTCTTTTAAAAATTATC
1 TTCTCTTTAAAAAATTA-C
*
3590438 ATTCTCTTAAAAAAATTAC
1 -TTCTCTTTAAAAAATTAC
3590457 T
1 T
3590458 ATTACTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 10 0.29
19 9 0.26
20 15 0.44
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.45
Consensus pattern (18 bp):
TTCTCTTTAAAAAATTAC
Found at i:3590742 original size:12 final size:12
Alignment explanation
Indices: 3590727--3590751 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3590717 ATTTATAATT
3590727 AAATTTAAATAA
1 AAATTTAAATAA
3590739 AAATTTAAATAA
1 AAATTTAAATAA
3590751 A
1 A
3590752 TTACTTTAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATTTAAATAA
Found at i:3594128 original size:20 final size:21
Alignment explanation
Indices: 3594114--3594156 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3594104 TAATACTATT
3594114 TTAAAAATAAAAATAAATATA
1 TTAAAAATAAAAATAAATATA
* *
3594135 TTAAAAGTAAAAAAAAAT-TA
1 TTAAAAATAAAAATAAATATA
3594155 TT
1 TT
3594157 GAAGTTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
TTAAAAATAAAAATAAATATA
Found at i:3598533 original size:2 final size:2
Alignment explanation
Indices: 3598528--3598553 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3598518 TCTCTCTCTC
3598528 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3598554 AATAATGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.