Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1840
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: 48465
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:1511 original size:2 final size:2
Alignment explanation
Indices: 1504--1551 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1494 CTTCAATCCT
1504 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1546 TC TC TC
1 TC TC TC
1552 CCCCCTTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3578 original size:2 final size:2
Alignment explanation
Indices: 3567--3595 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3557 TCCACTGCAA
3567 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3596 CCTTAAGTCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3845 original size:2 final size:2
Alignment explanation
Indices: 3840--3876 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3830 TCTCTCTCTC
3840 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3877 TTCAAACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4267 original size:7 final size:7
Alignment explanation
Indices: 4255--4282 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
4245 GATGATGATG
4255 ATCAAGA
1 ATCAAGA
4262 ATCAAGA
1 ATCAAGA
4269 ATCAAGA
1 ATCAAGA
4276 ATCAAGA
1 ATCAAGA
4283 TGCAACCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (7 bp):
ATCAAGA
Found at i:5820 original size:10 final size:10
Alignment explanation
Indices: 5804--5849 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
5794 CATGCATGCA
5804 TGTGTGCGTG
1 TGTGTGCGTG
*
5814 CGTGTGCGTG
1 TGTGTGCGTG
*
5824 TGTGTGTGTG
1 TGTGTGCGTG
*
5834 TGTGTGTGTG
1 TGTGTGCGTG
*
5844 TCTGTG
1 TGTGTG
5850 TATAACCCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.00, C:0.09, G:0.48, T:0.43
Consensus pattern (10 bp):
TGTGTGCGTG
Found at i:5822 original size:6 final size:6
Alignment explanation
Indices: 5804--5850 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
5794 CATGCATGCA
* * * *
5804 TGTGTG CGTGCG TGTGCG TGTGTG TGTGTG TGTGTG TGTGTC TGTGT
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGT
5851 ATAACCCTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.00, C:0.09, G:0.47, T:0.45
Consensus pattern (6 bp):
TGTGTG
Found at i:5828 original size:4 final size:4
Alignment explanation
Indices: 5804--5850 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
5794 CATGCATGCA
* * * *
5804 TGTG TGCG TGCG TGTG CGTG TGTG TGTG TGTG TGTG TGTG TCTG TGT
1 TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGT
5851 ATAACCCTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.00, C:0.09, G:0.47, T:0.45
Consensus pattern (4 bp):
TGTG
Found at i:8390 original size:30 final size:30
Alignment explanation
Indices: 7999--8372 Score: 633
Period size: 30 Copynumber: 12.5 Consensus size: 30
7989 TTTGTCATGG
*
7999 TCACAATCTCGGTCCCTATCCTTGTCCCGA
1 TCACGATCTCGGTCCCTATCCTTGTCCCGA
8029 TCACGATCTCGGTCCCTATCCTTGTCCCGA
1 TCACGATCTCGGTCCCTATCCTTGTCCCGA
8059 TCACGATCTCGGTCCCTATCCTTGTCCCGA
1 TCACGATCTCGGTCCCTATCCTTGTCCCGA
8089 TCACGATCTCGGTCCCTATCCTTGTCCCGA
1 TCACGATCTCGGTCCCTATCCTTGTCCCGA
*
8119 TCACGATCTCGGTCTCTATCCTTGTCCCGA
1 TCACGATCTCGGTCCCTATCCTTGTCCCGA
8149 TCACGATCTCGGTCCCTATCCTTGTCCCGA
1 TCACGATCTCGGTCCCTATCCTTGTCCCGA
*
8179 TCACGTTCTCGGTCCCTATCCTTGTCCCGA
1 TCACGATCTCGGTCCCTATCCTTGTCCCGA
*
8209 TCACGATCTTGGTCCCTATCCTTGTCCCGA
1 TCACGATCTCGGTCCCTATCCTTGTCCCGA
*
8239 TCACGTTCTCGGTCCCTATCCTTGTCCCGA
1 TCACGATCTCGGTCCCTATCCTTGTCCCGA
* *
8269 TCACGTTCTCGGCCCCTATCCTTGTCCCGA
1 TCACGATCTCGGTCCCTATCCTTGTCCCGA
* *
8299 TCACGTTCTCGGAT-CCTATACTTGTCCCGA
1 TCACGATCTCGG-TCCCTATCCTTGTCCCGA
*
8329 TCACGTTCTCGGTCCCTATCCTTGTCCCGA
1 TCACGATCTCGGTCCCTATCCTTGTCCCGA
*
8359 TCACGTTCTCGGTC
1 TCACGATCTCGGTC
8373 ATGATCTTGC
Statistics
Matches: 330, Mismatches: 12, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
29 1 0.00
30 329 1.00
ACGTcount: A:0.13, C:0.39, G:0.17, T:0.32
Consensus pattern (30 bp):
TCACGATCTCGGTCCCTATCCTTGTCCCGA
Found at i:12917 original size:1 final size:1
Alignment explanation
Indices: 12911--12941 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
12901 GGCTTTTGTT
*
12911 CCCCCCCCCCCCCCCCCCCCCCCCCTCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
12942 ATCTTTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:13143 original size:10 final size:10
Alignment explanation
Indices: 13128--13210 Score: 66
Period size: 10 Copynumber: 8.5 Consensus size: 10
13118 AAAATTAATA
13128 AATATAAAAT
1 AATATAAAAT
*
13138 AATATAATAT
1 AATATAAAAT
13148 AAT-TAAATAT
1 AATATAAA-AT
*
13158 AATATAATAT
1 AATATAAAAT
*
13168 AATATAATAT
1 AATATAAAAT
*
13178 AAT-TAAATT
1 AATATAAAAT
*
13187 TAT-TAAAAT
1 AATATAAAAT
*
13196 ATTA-AAATAT
1 AATATAAA-AT
13206 AATAT
1 AATAT
13211 TTTAAATATA
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
9 18 0.31
10 37 0.64
11 3 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AATATAAAAT
Found at i:13144 original size:5 final size:5
Alignment explanation
Indices: 13123--13180 Score: 84
Period size: 5 Copynumber: 11.8 Consensus size: 5
13113 TTATTAAAAT
*
13123 TAATA -AATA TAAAA TAATA TAATA TAAT- TAAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA T-AATA TAATA TAATA TAATA
13172 TAATA TAAT
1 TAATA TAAT
13181 TAAATTTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
4 5 0.10
5 42 0.88
6 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
TAATA
Found at i:13236 original size:20 final size:19
Alignment explanation
Indices: 13131--13249 Score: 82
Period size: 20 Copynumber: 5.9 Consensus size: 19
13121 ATTAATAAAT
13131 ATAAA-ATAATATAATATA
1 ATAAATATAATATAATATA
13149 ATTAAATATAATATAATATA
1 A-TAAATATAATATAATATA
*
13169 ATATAATATAAT-TAAATTTA
1 ATA-AATATAATAT-AATATA
* *
13189 TTAAAATATTAAAATATAATATT
1 AT-AAATA-T--AATATAATATA
* *
13212 TTAAATATAATTATAATATG
1 ATAAATATAA-TATAATATA
*
13232 ATAAAAAT-ATATTAATAT
1 ATAAATATAATA-TAATAT
13250 TTAAATTATT
Statistics
Matches: 83, Mismatches: 7, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
18 3 0.04
19 16 0.19
20 46 0.55
21 3 0.04
22 5 0.06
23 9 0.11
24 1 0.01
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (19 bp):
ATAAATATAATATAATATA
Found at i:18561 original size:2 final size:2
Alignment explanation
Indices: 18554--18584 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18544 TTTATGCCAA
*
18554 AT AT AT AT AA 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
18585 AAGGAACCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:22337 original size:2 final size:2
Alignment explanation
Indices: 22330--22359 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
22320 CGCAAAGGGG
22330 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
22360 AAGAACTCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:27811 original size:24 final size:25
Alignment explanation
Indices: 27779--27831 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
27769 AATTATAATC
* *
27779 ATAATTATTATAATTATAAATA-TA
1 ATAAATATTATAATGATAAATATTA
*
27803 ATAAATATTATTATGATAAATATTA
1 ATAAATATTATAATGATAAATATTA
27828 ATAA
1 ATAA
27832 TAAATTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
ATAAATATTATAATGATAAATATTA
Found at i:28353 original size:19 final size:17
Alignment explanation
Indices: 28320--28359 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
28310 TTTTCATAAT
*
28320 TATATTTTAAAATTTTA
1 TATATTTTAAAATTTAA
28337 TATATTTATATAAATTTAA
1 TATATTT-TA-AAATTTAA
28356 TATA
1 TATA
28360 CTAATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 2 0.10
19 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATTTTAAAATTTAA
Found at i:28425 original size:19 final size:20
Alignment explanation
Indices: 28403--28440 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
28393 AAATATATTA
*
28403 ATATCATAT-TTATATTTTT
1 ATATCATATGTAATATTTTT
*
28422 ATATTATATGTAATATTTT
1 ATATCATATGTAATATTTT
28441 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (20 bp):
ATATCATATGTAATATTTTT
Found at i:32609 original size:18 final size:18
Alignment explanation
Indices: 32586--32694 Score: 59
Period size: 18 Copynumber: 5.7 Consensus size: 18
32576 TTTTACTTTA
32586 ATAATTTTAAATATAAAT
1 ATAATTTTAAATATAAAT
*
32604 ATAATTATACAA-ATATAAT
1 ATAATTTTA-AATATA-AAT
32623 ATATATTTTAAATTTATATAAT
1 ATA-ATTTTAAA--TATA-AAT
32645 ATAAATTATTAATATATTAAA-
1 AT-AATT-TTAA-ATA-TAAAT
32666 AT--TTATATAAATATAAA-
1 ATAATT-T-TAAATATAAAT
32683 AT-ATTTTAAATA
1 ATAATTTTAAATA
32695 AGATTATAAT
Statistics
Matches: 77, Mismatches: 2, Indels: 26
0.73 0.02 0.25
Matches are distributed among these distances:
16 6 0.08
17 7 0.09
18 20 0.26
19 13 0.17
20 5 0.06
21 2 0.03
22 16 0.21
23 7 0.09
24 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTTTAAATATAAAT
Found at i:32636 original size:27 final size:27
Alignment explanation
Indices: 32608--32693 Score: 77
Period size: 32 Copynumber: 3.0 Consensus size: 27
32598 ATAAATATAA
32608 TTATACAAATATAATATATATTTTAAAT
1 TTATA-AAATATAATATATATTTTAAAT
* *
32636 TTATATAATATAAATTATTAATATATTAAAAT
1 TTATAAAATAT-AA-TA-T-ATAT-TTTAAAT
32668 TTATATAAATATAA-A-ATATTTTAAAT
1 TTATA-AAATATAATATATATTTTAAAT
32694 AAGATTATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
26 6 0.12
27 9 0.19
28 7 0.15
29 2 0.04
30 2 0.04
31 4 0.08
32 13 0.27
33 5 0.10
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (27 bp):
TTATAAAATATAATATATATTTTAAAT
Found at i:32657 original size:13 final size:15
Alignment explanation
Indices: 32631--32682 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
32621 ATATATATTT
32631 TAAATTTATATAATA
1 TAAATTTATATAATA
*
32646 TAAATTATTAATATATTA
1 TAAA-T-TT-ATATAATA
32664 -AAATTTATATAAATA
1 TAAATTTATAT-AATA
32679 TAAA
1 TAAA
32683 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.13
15 9 0.30
16 5 0.17
17 5 0.17
18 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAATTTATATAATA
Found at i:32660 original size:20 final size:20
Alignment explanation
Indices: 32595--32661 Score: 52
Period size: 22 Copynumber: 3.4 Consensus size: 20
32585 AATAATTTTA
32595 AATATA-AATAT-AATTA-T
1 AATATATAATATAAATTATT
* *
32612 ACAAATATAATATATATT-TT
1 A-ATATATAATATAAATTATT
32632 AAATTTATATAATATAAATTATT
1 -AA--TATATAATATAAATTATT
32655 AATATAT
1 AATATAT
32662 TAAAATTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
17 1 0.03
18 4 0.11
19 5 0.13
20 10 0.26
21 1 0.03
22 15 0.39
23 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (20 bp):
AATATATAATATAAATTATT
Found at i:32679 original size:33 final size:33
Alignment explanation
Indices: 32602--32687 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 33
32592 TTAAATATAA
* *
32602 ATATAATTATACAAATATAATATATATTTTAAATTT
1 ATATAA-TATA-AAATATTA-ATATATTTAAAATTT
*
32638 ATATAATATAAATTATTAATATA-TTAAAATTT
1 ATATAATATAAAATATTAATATATTTAAAATTT
32670 ATATAAATATAAAATATT
1 ATAT-AATATAAAATATT
32688 TTAAATAAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
32 12 0.27
33 17 0.38
34 6 0.13
35 4 0.09
36 6 0.13
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (33 bp):
ATATAATATAAAATATTAATATATTTAAAATTT
Found at i:32682 original size:17 final size:17
Alignment explanation
Indices: 32632--32684 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
32622 TATATATTTT
32632 AAATTTATAT-AATAT-
1 AAATTTATATAAATATA
32647 AAA-TTAT-TAATATATTA
1 AAATTTATATAA-ATA-TA
32664 AAATTTATATAAATATA
1 AAATTTATATAAATATA
32681 AAAT
1 AAAT
32685 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 6 0.19
16 1 0.03
17 9 0.28
18 7 0.22
19 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTTATATAAATATA
Found at i:32690 original size:20 final size:20
Alignment explanation
Indices: 32593--32695 Score: 52
Period size: 20 Copynumber: 5.2 Consensus size: 20
32583 TTAATAATTT
*
32593 TAAATAT-AAATATAATTATA
1 TAAATATAAAATAT-TTTATA
* *
32613 CAAATATAATATATATTTTAAA
1 TAAATATAA-A-ATATTTTATA
** * **
32635 TTTATATAATATAAATTAT-
1 TAAATATAAAATATTTTATA
*
32654 TAATATATTAAA-A-TTTATA
1 TAA-ATATAAAATATTTTATA
*
32673 TAAATATAAAATATTTTAAA
1 TAAATATAAAATATTTTATA
32693 TAA
1 TAA
32696 GATTATAATG
Statistics
Matches: 59, Mismatches: 17, Indels: 14
0.66 0.19 0.16
Matches are distributed among these distances:
18 11 0.19
19 6 0.10
20 26 0.44
21 1 0.02
22 11 0.19
23 4 0.07
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAATATAAAATATTTTATA
Found at i:32749 original size:27 final size:27
Alignment explanation
Indices: 32643--32750 Score: 82
Period size: 27 Copynumber: 4.0 Consensus size: 27
32633 AATTTATATA
* *
32643 ATATAAAT-TATTAATATATTAAAATTT
1 ATATAAATATATAAATATATT-AAATTG
* *
32670 ATATAAATATA-AAATATTTTAAATAAG
1 ATATAAATATATAAATATATTAAAT-TG
*
32697 AT-TATAATGTAATAAA-ATATATAAATCTG
1 ATATA-AATAT-ATAAATATAT-TAAAT-TG
32726 ATATAAATATATAAAT-TATTAAATT
1 ATATAAATATATAAATATATTAAATT
32751 TAATTTAATA
Statistics
Matches: 64, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
26 7 0.11
27 26 0.41
28 14 0.22
29 15 0.23
30 2 0.03
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.42
Consensus pattern (27 bp):
ATATAAATATATAAATATATTAAATTG
Found at i:33185 original size:18 final size:18
Alignment explanation
Indices: 33163--33201 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
33153 AAATTTAATT
33163 TTTTTTTATAATTAAATAA
1 TTTTTTTA-AATTAAATAA
*
33182 TTTTTTTAAATTAATTAA
1 TTTTTTTAAATTAAATAA
33200 TT
1 TT
33202 AACTAAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTTTTAAATTAAATAA
Found at i:33196 original size:22 final size:21
Alignment explanation
Indices: 33158--33199 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33148 ATAAAAAATT
**
33158 TAATTTTTTTTTATAATTAAA
1 TAATTTTTTTAAATAATTAAA
33179 TAATTTTTTTAAATTAATTAA
1 TAATTTTTTTAAA-TAATTAA
33200 TTAACTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TAATTTTTTTAAATAATTAAA
Found at i:35841 original size:15 final size:15
Alignment explanation
Indices: 35764--35850 Score: 52
Period size: 15 Copynumber: 5.9 Consensus size: 15
35754 ATTTTATTTT
*
35764 TAAAACTTTT-AAAA
1 TAAAATTTTTAAAAA
*
35778 TACAAAGTTTTAAAAA
1 TA-AAATTTTTAAAAA
* * *
35794 -ATAATTCTTAAAGA
1 TAAAATTTTTAAAAA
** ***
35808 TAATTTTTTTAATTT
1 TAAAATTTTTAAAAA
35823 TAAAATTTTTAAAAA
1 TAAAATTTTTAAAAA
*
35838 TAAATTTTTTAAA
1 TAAAATTTTTAAA
35851 TAATTATTAA
Statistics
Matches: 52, Mismatches: 18, Indels: 5
0.69 0.24 0.07
Matches are distributed among these distances:
14 11 0.21
15 37 0.71
16 4 0.08
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (15 bp):
TAAAATTTTTAAAAA
Found at i:35903 original size:52 final size:49
Alignment explanation
Indices: 35808--35905 Score: 117
Period size: 52 Copynumber: 1.9 Consensus size: 49
35798 TTCTTAAAGA
*
35808 TAATTTTTTTAATTTTAAAATTTTTAAAAATAAATTTTTTAAATAATTAT
1 TAATTTTTTTAATTTTAAAATTTTTAAAAATAAA-TTTCTAAATAATTAT
**
35858 TAATTATTTTTAATTTTTAAAATTTTATATAATTTAAA-TTCTAAATAA
1 TAATT-TTTTTAA-TTTTAAAATTTT-TA-AAAATAAATTTCTAAATAA
35906 ACATATTTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
50 5 0.12
51 7 0.17
52 21 0.51
53 2 0.05
54 6 0.15
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (49 bp):
TAATTTTTTTAATTTTAAAATTTTTAAAAATAAATTTCTAAATAATTAT
Found at i:37299 original size:18 final size:18
Alignment explanation
Indices: 37255--37301 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
37245 AAAGTTGTTG
* *
37255 ATAATATTTTCATCAAAA
1 ATAATTTTTTTATCAAAA
*
37273 AT-ATCTTTTTTATCAAGA
1 ATAAT-TTTTTTATCAAAA
37291 ATAATTTTTTT
1 ATAATTTTTTT
37302 CGATGAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (18 bp):
ATAATTTTTTTATCAAAA
Found at i:38108 original size:19 final size:19
Alignment explanation
Indices: 38080--38116 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
38070 TATAACGATA
38080 ATAATAATATATTTAAAAT
1 ATAATAATATATTTAAAAT
*
38099 ATAATTATATATTTAAAA
1 ATAATAATATATTTAAAA
38117 AATTATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAATAATATATTTAAAAT
Found at i:38134 original size:24 final size:24
Alignment explanation
Indices: 38101--38177 Score: 93
Period size: 23 Copynumber: 3.1 Consensus size: 24
38091 TTTAAAATAT
38101 AATTATATATTTAAAAAATTATTTA
1 AATT-TATATTTAAAAAATTATTTA
*
38126 AATTTATATTT-AAAAATTAATTA
1 AATTTATATTTAAAAAATTATTTA
*
38149 AATTTATAATGTAAATAAAATTATTTA
1 AATTTAT-AT-TTAA-AAAATTATTTA
38176 AA
1 AA
38178 AATTAATTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
23 18 0.40
24 9 0.20
25 5 0.11
26 1 0.02
27 12 0.27
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (24 bp):
AATTTATATTTAAAAAATTATTTA
Found at i:38907 original size:50 final size:50
Alignment explanation
Indices: 38832--38958 Score: 182
Period size: 50 Copynumber: 2.5 Consensus size: 50
38822 ACCTTTCTCC
* * * *
38832 ATTGTCAAAGGTTGGTGAAGAATCGTTAACAATTATGGCTACCTCTCTTT
1 ATTGTCAAAGGTTGGTGAAGAATCGTTAACAATTATGACCACCTCCCTCT
* *
38882 ATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATTACCACCTCCCTCT
1 ATTGTCAAAGGTTGGTGAAGAATCGTTAACAATTATGACCACCTCCCTCT
* *
38932 ATTATCAAAGGTTGGTGAAAAATCGTT
1 ATTGTCAAAGGTTGGTGAAGAATCGTT
38959 GGTGAAGAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 68 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (50 bp):
ATTGTCAAAGGTTGGTGAAGAATCGTTAACAATTATGACCACCTCCCTCT
Found at i:38961 original size:14 final size:14
Alignment explanation
Indices: 38942--38971 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
38932 ATTATCAAAG
38942 GTTGGTGAAAAATC
1 GTTGGTGAAAAATC
*
38956 GTTGGTGAAGAATC
1 GTTGGTGAAAAATC
38970 GT
1 GT
38972 CAACAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (14 bp):
GTTGGTGAAAAATC
Found at i:38971 original size:64 final size:64
Alignment explanation
Indices: 38892--39021 Score: 215
Period size: 64 Copynumber: 2.0 Consensus size: 64
38882 ATTGTCAAAG
*
38892 GTTGGTGAAGAATCGTCAACAATTATTACCACCTCCCTCTATTATCAAAGGTTGGTGAAAAATC
1 GTTGGTGAAGAATCGTCAACAATTATGACCACCTCCCTCTATTATCAAAGGTTGGTGAAAAATC
* * * *
38956 GTTGGTGAAGAATCGTCAACAATTATGGCCACCTCCCTCTATTGTTAAAGGTTGGTGAAGAATC
1 GTTGGTGAAGAATCGTCAACAATTATGACCACCTCCCTCTATTATCAAAGGTTGGTGAAAAATC
39020 GT
1 GT
39022 CAACAATTAC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (64 bp):
GTTGGTGAAGAATCGTCAACAATTATGACCACCTCCCTCTATTATCAAAGGTTGGTGAAAAATC
Found at i:39015 original size:50 final size:50
Alignment explanation
Indices: 38956--39157 Score: 323
Period size: 50 Copynumber: 4.0 Consensus size: 50
38946 GTGAAAAATC
* * *
38956 GTTGGTGAAGAATCGTCAACAATTATGGCCACCTCCCTCTATTGTTAAAG
1 GTTGGTGAAGAATCATCAACAATTATGGCCACCTCTCTCTATTGTCAAAG
* ** *
39006 GTTGGTGAAGAATCGTCAACAATTACAGCCACCTCTCTCTATTATCAAAG
1 GTTGGTGAAGAATCATCAACAATTATGGCCACCTCTCTCTATTGTCAAAG
*
39056 GTTGGTGAAGAATCATCAATAATTATGGCCACCTCTCTCTATTGTCAAAG
1 GTTGGTGAAGAATCATCAACAATTATGGCCACCTCTCTCTATTGTCAAAG
*
39106 GTTGGTGAAGAATCATCAATAATTATGGCCACCTCTCTCTATTGTCAAAG
1 GTTGGTGAAGAATCATCAACAATTATGGCCACCTCTCTCTATTGTCAAAG
39156 GT
1 GT
39158 ACTTTCTACC
Statistics
Matches: 142, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 142 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (50 bp):
GTTGGTGAAGAATCATCAACAATTATGGCCACCTCTCTCTATTGTCAAAG
Found at i:43836 original size:19 final size:18
Alignment explanation
Indices: 43788--43837 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
43778 AAATTTCCTT
*
43788 AAAAATAA-TTTTGATGA
1 AAAAATAATTTTTGATCA
43805 AAAAATTAATTTTTGATCA
1 AAAAA-TAATTTTTGATCA
43824 AAAAATAACTTTTT
1 AAAAATAA-TTTTT
43838 TCGATGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 5 0.17
18 6 0.21
19 18 0.62
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (18 bp):
AAAAATAATTTTTGATCA
Found at i:45289 original size:7 final size:7
Alignment explanation
Indices: 45268--45339 Score: 54
Period size: 7 Copynumber: 9.4 Consensus size: 7
45258 TTTATTATAA
45268 TTATATT
1 TTATATT
* *
45275 TAAAATT
1 TTATATT
45282 TTATATT
1 TTATATT
45289 TTAATATT
1 TT-ATATT
45297 TATAATATT
1 T-T-ATATT
45306 TTATATTAT
1 TTATA-T-T
45315 TTATATT
1 TTATATT
*
45322 ATTATTTT
1 -TTATATT
*
45330 TTATTTT
1 TTATATT
45337 TTA
1 TTA
45340 ATAATGTCAT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
7 26 0.47
8 15 0.27
9 14 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TTATATT
Found at i:45317 original size:19 final size:17
Alignment explanation
Indices: 45262--45324 Score: 58
Period size: 19 Copynumber: 3.6 Consensus size: 17
45252 ATTTAATTTA
*
45262 TTATAATTATATTTAAAAT
1 TTATAA-TAT-TTTAATAT
45281 TT-T-ATATTTTAATAT
1 TTATAATATTTTAATAT
45296 TTATAATATTTTATATTAT
1 TTATAATATTTTA-A-TAT
*
45315 TTATATTATT
1 TTATAATATT
45325 ATTTTTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 9 0.24
16 4 0.11
17 9 0.24
18 2 0.05
19 14 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATAATATTTTAATAT
Found at i:45335 original size:19 final size:19
Alignment explanation
Indices: 45284--45324 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
45274 TTAAAATTTT
45284 ATATTTTA-A-TATTTATA
1 ATATTTTATATTATTTATA
45301 ATATTTTATATTATTTATA
1 ATATTTTATATTATTTATA
*
45320 TTATT
1 ATATT
45325 ATTTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 1 0.05
19 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATATTTTATATTATTTATA
Found at i:45836 original size:66 final size:66
Alignment explanation
Indices: 45729--45852 Score: 171
Period size: 66 Copynumber: 1.9 Consensus size: 66
45719 TTTTGTTGGC
* * *
45729 TTCAATATTTTATTATAAAATATTAATCAATTAAGAAAAAAAAGTAAATTAAAAAATATTAATCA
1 TTCAATATTTTATGATAAAATATTAATCAATGAAGAAAAAAAAGGAAATTAAAAAATATTAATCA
45794 T
66 T
* *
45795 TTCAATATTTTATGATAAAATATTGAAGTTAA-GAA-AAAAAAAAGGAAATTGAAAAATA
1 TTCAATATTTTATGATAAAATATT-AA-TCAATGAAGAAAAAAAAGGAAATTAAAAAATA
45853 ATAACAAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
66 44 0.86
67 4 0.08
68 3 0.06
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.33
Consensus pattern (66 bp):
TTCAATATTTTATGATAAAATATTAATCAATGAAGAAAAAAAAGGAAATTAAAAAATATTAATCA
T
Found at i:46083 original size:2 final size:2
Alignment explanation
Indices: 46076--46116 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
46066 TTACAAGTGT
46076 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46117 TAATTTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46302 original size:16 final size:15
Alignment explanation
Indices: 46286--46318 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
46276 AATAAAGATA
*
46286 AAATTTTTTAAAAAT
1 AAATTATTTAAAAAT
46301 AAATTATTTAAAAA-
1 AAATTATTTAAAAAT
46315 AAAT
1 AAAT
46319 CATTACGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATTATTTAAAAAT
Found at i:47074 original size:25 final size:23
Alignment explanation
Indices: 47051--47106 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
47041 ACGTGTAATG
* *
47051 TTATATATATATATATATACTAA
1 TTATATAAATATAAATATACTAA
47074 TTATATAAATATAAATATA--AA
1 TTATATAAATATAAATATACTAA
47095 TTAT-TAAATATA
1 TTATATAAATATA
47107 TCAAAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 8 0.26
21 6 0.19
23 17 0.55
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TTATATAAATATAAATATACTAA
Found at i:48035 original size:18 final size:18
Alignment explanation
Indices: 48005--48076 Score: 50
Period size: 16 Copynumber: 4.3 Consensus size: 18
47995 ATTTAGAGAT
*
48005 TAATTTAATTAATTTTTA
1 TAATTTAATTAATATTTA
48023 TAATTATAA-TAATA-TT-
1 TAATT-TAATTAATATTTA
* *
48039 TAATATATTTAA-ATTT-
1 TAATTTAATTAATATTTA
*
48055 TAAATT--TTAATATTTA
1 TAATTTAATTAATATTTA
48071 TAATTT
1 TAATTT
48077 TTTATTATCA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
14 4 0.09
15 7 0.16
16 18 0.42
17 2 0.05
18 9 0.21
19 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATTTAATTAATATTTA
Done.