Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1543
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: 108755
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:8362 original size:32 final size:32
Alignment explanation
Indices: 8320--8390 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
8310 TTTTAATTAA
8320 TATATTTATATAAATTTTAATATATTAAAAATT
1 TATA-TTATATAAATTTTAATATATTAAAAATT
* * *
8353 TATATTATATAAATTTTACTATATTATATATT
1 TATATTATATAAATTTTAATATATTAAAAATT
8385 TATATT
1 TATATT
8391 TTTATAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
32 31 0.89
33 4 0.11
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (32 bp):
TATATTATATAAATTTTAATATATTAAAAATT
Found at i:8370 original size:16 final size:16
Alignment explanation
Indices: 8320--8370 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
8310 TTTTAATTAA
8320 TATATTTATATAAATTT
1 TATA-TTATATAAATTT
*
8337 TA-A-TATATTAAAAATT
1 TATATTATA-T-AAATTT
8353 TATATTATATAAATTT
1 TATATTATATAAATTT
8369 TA
1 TA
8371 CTATATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
14 4 0.14
15 1 0.04
16 15 0.54
17 4 0.14
18 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATTATATAAATTT
Found at i:8380 original size:17 final size:16
Alignment explanation
Indices: 8328--8389 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
8318 AATATATTTA
8328 TATAAATTTTAATATAT
1 TATAAATTTT-ATATAT
*
8345 TA-AAAATTTATAT-T
1 TATAAATTTTATATAT
8359 ATATAAATTTTACTATAT
1 -TATAAATTTTA-TATAT
*
8377 TATATA-TTTATAT
1 TATAAATTTTATAT
8390 TTTTATAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 1 0.03
15 9 0.24
16 17 0.45
17 10 0.26
18 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TATAAATTTTATATAT
Found at i:8393 original size:24 final size:26
Alignment explanation
Indices: 8373--8420 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
8363 AAATTTTACT
8373 ATATTATA-TATTTA-TATTTTTATA
1 ATATTATATTATTTATTATTTTTATA
*
8397 ATATTATATTTTTTATTATTTTTA
1 ATATTATATTATTTATTATTTTTA
8421 ATTTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 5 0.24
26 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
ATATTATATTATTTATTATTTTTATA
Found at i:8422 original size:24 final size:23
Alignment explanation
Indices: 8373--8431 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
8363 AAATTTTACT
8373 ATATTATATATTTATATTTTTATA
1 ATATTATAT-TTTATATTTTTATA
* *
8397 ATATTATATTTTTTATTATTTTTA
1 ATATTATATTTTATATT-TTTATA
* *
8421 ATTTTTTATTT
1 ATATTATATTT
8432 AAAATTAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 7 0.23
24 23 0.77
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
ATATTATATTTTATATTTTTATA
Found at i:8824 original size:16 final size:18
Alignment explanation
Indices: 8786--8829 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
8776 TCAATTTTCT
8786 ATAATTCTTAATTTTGTATA
1 ATAATT-TT-ATTTTGTATA
8806 AT-ATTTTATTTTG-ATA
1 ATAATTTTATTTTGTATA
8822 ATAATTTT
1 ATAATTTT
8830 GTATTATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.22
17 11 0.48
18 2 0.09
19 3 0.13
20 2 0.09
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (18 bp):
ATAATTTTATTTTGTATA
Found at i:9825 original size:2 final size:2
Alignment explanation
Indices: 9818--9849 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9808 ATAGATTAAG
9818 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9850 GTAGTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10754 original size:3 final size:3
Alignment explanation
Indices: 10746--10782 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
10736 AAATTCAAAG
*
10746 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATT ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10783 AGGTCTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:12476 original size:2 final size:2
Alignment explanation
Indices: 12469--12499 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12459 TCATATGTAA
12469 AT 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 AT
12500 GAAAATTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13002 original size:2 final size:2
Alignment explanation
Indices: 12995--13028 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12985 GATAATTCTT
12995 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
13029 AAATCATAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13769 original size:11 final size:11
Alignment explanation
Indices: 13753--13784 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
13743 TATTTTTTTC
*
13753 TTTTACTTCTT
1 TTTTACTACTT
13764 TTTTACTACTT
1 TTTTACTACTT
13775 TTTTACTACT
1 TTTTACTACT
13785 CCTTTAGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTACTACTT
Found at i:15707 original size:27 final size:30
Alignment explanation
Indices: 15672--15727 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 30
15662 TAAAAATTTA
15672 ATATGTATT-AAATA-TTTTATA-TTAATT
1 ATATGTATTAAAATATTTTTATACTTAATT
*
15699 ATATTTATTAAAATATTTTTATACTTAAT
1 ATATGTATTAAAATATTTTTATACTTAAT
15728 AAACATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 8 0.32
28 5 0.20
29 7 0.28
30 5 0.20
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (30 bp):
ATATGTATTAAAATATTTTTATACTTAATT
Found at i:15715 original size:21 final size:22
Alignment explanation
Indices: 15690--15737 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
15680 TAAATATTTT
* *
15690 ATATTAATTATATTTATTAAA-
1 ATATTAATTATACTTAATAAAC
*
15711 ATATT-TTTATACTTAATAAAC
1 ATATTAATTATACTTAATAAAC
15732 ATATTA
1 ATATTA
15738 TTTTTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATTAATTATACTTAATAAAC
Found at i:15720 original size:20 final size:20
Alignment explanation
Indices: 15697--15764 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
15687 TTTATATTAA
15697 TTATATTTATTAAAATATTT
1 TTATATTTATTAAAATATTT
* *
15717 TTATACTTAATAAACATATTAT
1 TTATATTTATTAAA-ATATT-T
*
15739 TT-T-TTTA-T--CATATTT
1 TTATATTTATTAAAATATTT
15754 TTATATTTATT
1 TTATATTTATT
15765 TAATATTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
15 3 0.08
16 6 0.15
17 4 0.10
18 1 0.03
19 1 0.03
20 15 0.38
21 6 0.15
22 3 0.08
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATATTTATTAAAATATTT
Found at i:18612 original size:21 final size:21
Alignment explanation
Indices: 18573--18612 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18563 AAATCGATTG
*
18573 AATTAAAATATAATTAAATAA
1 AATTAAAATATAATAAAATAA
* *
18594 AATTTAAATATCATAAAAT
1 AATTAAAATATAATAAAAT
18613 TTTTTAAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
AATTAAAATATAATAAAATAA
Found at i:20353 original size:14 final size:14
Alignment explanation
Indices: 20331--20371 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
20321 TATGATTGTT
*
20331 TATAAAATTATATA
1 TATATAATTATATA
20345 TATATAATTATA-A
1 TATATAATTATATA
*
20358 T-TATAATTAAATA
1 TATATAATTATATA
20371 T
1 T
20372 TTATTTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 9 0.38
13 4 0.17
14 11 0.46
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TATATAATTATATA
Found at i:20649 original size:22 final size:22
Alignment explanation
Indices: 20624--20688 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
20614 AAATTAAATT
20624 ATAATTAAAATTATTTTATT-TC
1 ATAA-TAAAATTATTTTATTATC
**
20646 ATAATAATTTTATTTTATTATC
1 ATAATAAAATTATTTTATTATC
*
20668 ATAA-AATAATTATTTCATTAT
1 ATAATAA-AATTATTTTATTAT
20689 AATTATATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 15 0.42
22 21 0.58
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.54
Consensus pattern (22 bp):
ATAATAAAATTATTTTATTATC
Found at i:21363 original size:21 final size:20
Alignment explanation
Indices: 21334--21375 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
21324 AATATTATTT
* *
21334 TTATTTAAAATTAATTATAAA
1 TTATATAAAAATAATT-TAAA
21355 TTATATAAAAATAATTTAAA
1 TTATATAAAAATAATTTAAA
21375 T
1 T
21376 AGAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTATATAAAAATAATTTAAA
Found at i:21486 original size:22 final size:23
Alignment explanation
Indices: 21460--21514 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
21450 AAAATTAAAT
**
21460 ATTTATTCTAATTT-ATGAATAA
1 ATTTATTCTAATTTAAAAAATAA
*
21482 ATTTATT-TATTTTAAAAAATAA
1 ATTTATTCTAATTTAAAAAATAA
21504 ATTT-TTCTAAT
1 ATTTATTCTAAT
21515 AAAAGAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTATTCTAATTTAAAAAATAA
Found at i:25943 original size:22 final size:22
Alignment explanation
Indices: 25880--25943 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
25870 TTATTATTTA
*
25880 ATTAATAAAAAGTTATTTTT--T
1 ATTAATAAAAA-TAATTTTTAAT
* * *
25901 ATT--TAAATATAATTATAAAT
1 ATTAATAAAAATAATTTTTAAT
25921 ATTAATAAAAATAATTTTTAAT
1 ATTAATAAAAATAATTTTTAAT
25943 A
1 A
25944 ATATTTTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
18 5 0.16
19 5 0.16
20 4 0.12
21 3 0.09
22 15 0.47
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTAATAAAAATAATTTTTAAT
Found at i:26570 original size:23 final size:26
Alignment explanation
Indices: 26524--26575 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
26514 TTTCATTAAC
* *
26524 AAAATTATTAATTTCATAACAAAAGT
1 AAAATTAATAATTTCATAACAAAACT
26550 AAAATTAATAATTT-A-AA-AAAACT
1 AAAATTAATAATTTCATAACAAAACT
26573 AAA
1 AAA
26576 TTCTCATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.33
24 2 0.08
25 1 0.04
26 13 0.54
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (26 bp):
AAAATTAATAATTTCATAACAAAACT
Found at i:29241 original size:25 final size:22
Alignment explanation
Indices: 29212--29258 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
29202 AAACTTAAGG
29212 TCAATGTAAAATTCAATTTTTTTTA
1 TCAAT-TAAAA-T-AATTTTTTTTA
*
29237 TCAATTTAAATAATTTTTTTTA
1 TCAATTAAAATAATTTTTTTTA
29259 AAAGTGGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 11 0.52
23 1 0.05
24 4 0.19
25 5 0.24
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.55
Consensus pattern (22 bp):
TCAATTAAAATAATTTTTTTTA
Found at i:29928 original size:3 final size:3
Alignment explanation
Indices: 29920--29965 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
29910 GTTTATTCAA
29920 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
29966 CATGAAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:30222 original size:2 final size:2
Alignment explanation
Indices: 30215--30245 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30205 ATTTATTATC
30215 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
30246 AGTTCATGCT
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:34557 original size:17 final size:16
Alignment explanation
Indices: 34530--34561 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
34520 ACGAGTTTTT
34530 AAATTAATTCAAATTC
1 AAATTAATTCAAATTC
34546 AAATTCAATTCAAATT
1 AAATT-AATTCAAATT
34562 ATATTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTAATTCAAATTC
Found at i:34899 original size:24 final size:24
Alignment explanation
Indices: 34872--34920 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
34862 ATTAATGATC
34872 ATCCCAGTGGTAAGAAAAGTTTCA
1 ATCCCAGTGGTAAGAAAAGTTTCA
34896 ATCCCAGTGGTAAGAAAAGTTTCA
1 ATCCCAGTGGTAAGAAAAGTTTCA
34920 A
1 A
34921 GCATTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (24 bp):
ATCCCAGTGGTAAGAAAAGTTTCA
Found at i:35502 original size:23 final size:23
Alignment explanation
Indices: 35459--35503 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
35449 TTTATATAAT
*
35459 TATATTTAAGAAATAATATTTAA
1 TATATTTAAGAAATAAAATTTAA
*
35482 TATATTTAA-AATTTAAAATTTA
1 TATATTTAAGAA-ATAAAATTTA
35504 TTATTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TATATTTAAGAAATAAAATTTAA
Found at i:36642 original size:15 final size:15
Alignment explanation
Indices: 36622--36674 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
36612 ATTCAATAAA
36622 CATATTTATTAAAAT
1 CATATTTATTAAAAT
* *
36637 CATATTACTTTTAGAAT
1 CATATT--TATTAAAAT
*
36654 CACATTTATTAAAAT
1 CATATTTATTAAAAT
36669 CATATT
1 CATATT
36675 AGTTTTCATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 18 0.60
17 12 0.40
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (15 bp):
CATATTTATTAAAAT
Found at i:36819 original size:38 final size:37
Alignment explanation
Indices: 36769--36880 Score: 134
Period size: 38 Copynumber: 3.0 Consensus size: 37
36759 GGTAGCACGG
*
36769 GTCGAAACAAAAACTACTATTCTTACTAGTGGTATGA
1 GTCGAAACAAAAACTACTATTCTTACTAGTGGTACGA
* * * * *
36806 TTCGAAACAAAAAATCACTATTTTTACTGGTGGCACGA
1 GTCGAAACAAAAACT-ACTATTCTTACTAGTGGTACGA
* *
36844 GTCGAAATAAAAACTATTATTCTTAACTAGTGGTACG
1 GTCGAAACAAAAACTACTATTCTT-ACTAGTGGTACG
36881 GTTGGAACCG
Statistics
Matches: 60, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
37 20 0.33
38 40 0.67
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (37 bp):
GTCGAAACAAAAACTACTATTCTTACTAGTGGTACGA
Found at i:37752 original size:15 final size:15
Alignment explanation
Indices: 37723--37757 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
37713 AAATAGTACG
37723 ATTATAAAATAATTT
1 ATTATAAAATAATTT
37738 ATTA-AAAATATATTT
1 ATTATAAAATA-ATTT
37753 ATTAT
1 ATTAT
37758 GTCAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTATAAAATAATTT
Found at i:39470 original size:13 final size:13
Alignment explanation
Indices: 39452--39487 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
39442 CATATAAATG
39452 TTATAATAT-GATA
1 TTATAATATAG-TA
39465 TTATAATATAGTA
1 TTATAATATAGTA
39478 TTATAATATA
1 TTATAATATA
39488 AATATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 21 0.95
14 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (13 bp):
TTATAATATAGTA
Found at i:45443 original size:50 final size:49
Alignment explanation
Indices: 45388--45646 Score: 392
Period size: 50 Copynumber: 5.2 Consensus size: 49
45378 AATTGTTGCC
* * * * *
45388 ATTGTTGACTATCCTTTACCAACCTTTAACAATAGAGAGAAGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGAGGTGGCCATA
*
45438 ATTGTTTACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAA-GAGGTGGCCATA
45488 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAA-GAGGTGGCCATA
45538 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAG-AAGAGGTGGCCATA
* * *
45588 ATTGTTGACGATTCTTCACCAACTTTTGACAATGGAGGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGAGGTGGCCATA
45638 ATTGTTGAC
1 ATTGTTGAC
45647 TCTAAGTATA
Statistics
Matches: 196, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
49 2 0.01
50 192 0.98
51 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (49 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGAGGTGGCCATA
Found at i:45948 original size:2 final size:2
Alignment explanation
Indices: 45941--45977 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
45931 TAAGGCTTAA
45941 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45978 AACTTGATTC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52246 original size:27 final size:29
Alignment explanation
Indices: 52212--52279 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
52202 TATCTTTAAA
52212 AAGTAAA-TTATTAAATTATTA-ATTTTT
1 AAGTAAATTTATTAAATTATTATATTTTT
*
52239 AAGTAAATTTTTATTATATTATTATATTTTT
1 AAGTAAA--TTTATTAAATTATTATATTTTT
*
52270 AA-TATATTTA
1 AAGTAAATTTA
52280 ATTATTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 7 0.20
28 4 0.11
30 16 0.46
31 8 0.23
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (29 bp):
AAGTAAATTTATTAAATTATTATATTTTT
Found at i:52285 original size:19 final size:19
Alignment explanation
Indices: 52245--52286 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
52235 TTTTAAGTAA
* *
52245 ATTTTTATTATATTATTAT
1 ATTTTTAATATATTAATAT
52264 ATTTTTAATATATTTAAT-T
1 ATTTTTAATATA-TTAATAT
52283 ATTT
1 ATTT
52287 ATTTATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTTAATATATTAATAT
Found at i:52350 original size:18 final size:18
Alignment explanation
Indices: 52311--52350 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
52301 ATATTTATAT
*
52311 ATAAAATTAATTTGTTAT
1 ATAAAATTAATTTGTTAA
52329 ATAAAATTAATTT-TTCAA
1 ATAAAATTAATTTGTT-AA
52347 ATAA
1 ATAA
52351 TTTGTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
ATAAAATTAATTTGTTAA
Found at i:53574 original size:16 final size:16
Alignment explanation
Indices: 53542--53582 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
53532 TTAGACTGTC
*
53542 TCGAGTTTGGACTATT
1 TCGAGTTCGGACTATT
53558 TCGAGTTCGGA-TAATT
1 TCGAGTTCGGACT-ATT
53574 TCGAGTTCG
1 TCGAGTTCG
53583 AATTTTTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.04
16 22 0.96
ACGTcount: A:0.20, C:0.15, G:0.27, T:0.39
Consensus pattern (16 bp):
TCGAGTTCGGACTATT
Found at i:53988 original size:15 final size:15
Alignment explanation
Indices: 53968--54016 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
53958 ATTTACATAA
53968 TATATTCAACTTATC
1 TATATTCAACTTATC
*
53983 TATATTC-A--TA-A
1 TATATTCAACTTATC
53994 TATATTCAACTTATC
1 TATATTCAACTTATC
54009 TATATTCA
1 TATATTCA
54017 TAAATAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
11 7 0.25
12 3 0.11
14 3 0.11
15 15 0.54
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATTCAACTTATC
Found at i:53993 original size:26 final size:26
Alignment explanation
Indices: 53963--54019 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
53953 CGAATATTTA
53963 CATAATATATTCAACTTATCTATATT
1 CATAATATATTCAACTTATCTATATT
53989 CATAATATATTCAACTTATCTATATT
1 CATAATATATTCAACTTATCTATATT
54015 CATAA
1 CATAA
54020 ATAAATTCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (26 bp):
CATAATATATTCAACTTATCTATATT
Found at i:54882 original size:30 final size:29
Alignment explanation
Indices: 54846--54903 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
54836 TTGTTTTAAA
*
54846 TTTTTTTAATTGAATTTATTTTAAATTTAG
1 TTTTTTTAATTG-AGTTATTTTAAATTTAG
* *
54876 TTTTTTTATTTGAGTTATTTTAGATTTA
1 TTTTTTTAATTGAGTTATTTTAAATTTA
54904 AATATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (29 bp):
TTTTTTTAATTGAGTTATTTTAAATTTAG
Found at i:54912 original size:30 final size:31
Alignment explanation
Indices: 54840--54913 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
54830 ATTACGTTGT
*
54840 TTTAAATTTTTTTAATTGAATTTATTTTAAA
1 TTTAAATTTTTTTAATTGAAGTTATTTTAAA
* * *
54871 TTT-AGTTTTTTTATTTG-AGTTATTTTAGA
1 TTTAAATTTTTTTAATTGAAGTTATTTTAAA
54900 TTTAAATATTTTTT
1 TTTAAAT-TTTTTT
54914 TATATCATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 13 0.36
30 14 0.39
31 9 0.25
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (31 bp):
TTTAAATTTTTTTAATTGAAGTTATTTTAAA
Found at i:55776 original size:27 final size:29
Alignment explanation
Indices: 55741--55794 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
55731 TATTATTATA
*
55741 AAAAAATAT-TTTAAAA-AATTAAAATAT
1 AAAAAATATATTTAAAACAATAAAAATAT
55768 AAAAAATATATTTAAAACAATAAAAAT
1 AAAAAATATATTTAAAACAATAAAAAT
55795 TTAAGATAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 9 0.38
28 7 0.29
29 8 0.33
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (29 bp):
AAAAAATATATTTAAAACAATAAAAATAT
Found at i:56602 original size:14 final size:15
Alignment explanation
Indices: 56572--56605 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
56562 TCTTTTTTGT
56572 TTAATTTAATAATAA
1 TTAATTTAATAATAA
*
56587 TTAATTTTAT-ATAA
1 TTAATTTAATAATAA
56601 TTAAT
1 TTAAT
56606 GATATATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATTTAATAATAA
Found at i:57210 original size:16 final size:15
Alignment explanation
Indices: 57177--57217 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
57167 TTAAATTATC
* *
57177 TTTTTATATTTATAT
1 TTTTTAGATTTAAAT
57192 TTTTTAGATTTAAAT
1 TTTTTAGATTTAAAT
57207 TTTTTAGATTT
1 TTTTTAGATTT
57218 GATAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (15 bp):
TTTTTAGATTTAAAT
Found at i:57412 original size:16 final size:16
Alignment explanation
Indices: 57365--57412 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 16
57355 AATCAGCATC
*
57365 AATCATAAATTTTAAG
1 AATCATAAATTTTAAA
57381 AATCATAAATTTTTTTAAA
1 AATCATAAA---TTTTAAA
*
57400 AATTATAAATTTT
1 AATCATAAATTTT
57413 TGACTCCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 13 0.48
19 14 0.52
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (16 bp):
AATCATAAATTTTAAA
Found at i:57412 original size:18 final size:19
Alignment explanation
Indices: 57374--57413 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
57364 CAATCATAAA
*
57374 TTTTAAGAATCATAAATTT
1 TTTTAAAAATCATAAATTT
*
57393 TTTTAAAAATTATAAATTT
1 TTTTAAAAATCATAAATTT
57412 TT
1 TT
57414 GACTCCAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTTAAAAATCATAAATTT
Found at i:58949 original size:20 final size:22
Alignment explanation
Indices: 58924--58972 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
58914 CACTTTTAAC
* *
58924 TTTAATTAT-TAAATTATAA-T
1 TTTAATTATAAAAATTAAAATT
58944 TTTAATTATAAAAATTAAAATT
1 TTTAATTATAAAAATTAAAATT
58966 TTTAATT
1 TTTAATT
58973 TATTTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.36
21 8 0.32
22 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAATTATAAAAATTAAAATT
Found at i:60143 original size:14 final size:14
Alignment explanation
Indices: 60124--60156 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
60114 TATCATTTTA
*
60124 ATAATTTTTTAAAG
1 ATAATTTTTAAAAG
60138 ATAA-TTTTAAAAG
1 ATAATTTTTAAAAG
60151 ATAATT
1 ATAATT
60157 ATCATAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (14 bp):
ATAATTTTTAAAAG
Found at i:60729 original size:13 final size:14
Alignment explanation
Indices: 60702--60737 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
60692 AAATAAAAAT
60702 AAATTATAAATATTA
1 AAATT-TAAATATTA
60717 AAATTTAAA-ATTA
1 AAATTTAAATATTA
60730 AAATTTAA
1 AAATTTAA
60738 TAAATATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.57
14 4 0.19
15 5 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATTTAAATATTA
Found at i:61680 original size:31 final size:31
Alignment explanation
Indices: 61645--61705 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
61635 AAATTAATTA
* *
61645 ATAATAATTTATTAT-ATTTTTAAATATTTTT
1 ATAATAATTTATT-TGATATTTAAAAATTTTT
*
61676 ATAATTATTTATTTGATATTTAAAAATTTT
1 ATAATAATTTATTTGATATTTAAAAATTTT
61706 AAATATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (31 bp):
ATAATAATTTATTTGATATTTAAAAATTTTT
Found at i:61730 original size:16 final size:16
Alignment explanation
Indices: 61694--61738 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
61684 TTATTTGATA
61694 TTTAAAAATTT-TAAAT
1 TTTAAAAATTTAT-AAT
*
61710 ATTAAAAATTTATAAT
1 TTTAAAAATTTATAAT
61726 TTT-AAAATTTATA
1 TTTAAAAATTTATA
61739 TTTACATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 10 0.38
16 15 0.58
17 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTAAAAATTTATAAT
Found at i:63471 original size:2 final size:2
Alignment explanation
Indices: 63464--63513 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
63454 GGCTTAGCAA
* *
63464 AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT 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
63506 AT AT AT AT
1 AT AT AT AT
63514 CATCTAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:63487 original size:18 final size:18
Alignment explanation
Indices: 63464--63513 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
63454 GGCTTAGCAA
63464 ATATATATATATATATTT
1 ATATATATATATATATTT
63482 ATATATATATATATATTT
1 ATATATATATATATATTT
63500 ATATATATATATAT
1 ATATATATATATAT
63514 CATCTAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATATATATATATATTT
Found at i:71514 original size:19 final size:20
Alignment explanation
Indices: 71490--71527 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
71480 TTTTCCACGT
71490 CTTCTTTGCT-TTGT-TTTTG
1 CTTC-TTGCTGTTGTGTTTTG
71509 CTTCTTGCTGTTGTGTTTT
1 CTTCTTGCTGTTGTGTTTT
71528 CACTTCATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.00, C:0.16, G:0.18, T:0.66
Consensus pattern (20 bp):
CTTCTTGCTGTTGTGTTTTG
Found at i:71745 original size:25 final size:25
Alignment explanation
Indices: 71699--71748 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
71689 TTATTATTTA
*
71699 TTAATAAAAATATTTTTATTTAAAT
1 TTAATAAAAATATATTTATTTAAAT
*
71724 TTAATAATAATATAATTT-TTTAAAT
1 TTAATAAAAATAT-ATTTATTTAAAT
71749 AGTGATACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAATAAAAATATATTTATTTAAAT
Found at i:73297 original size:3 final size:3
Alignment explanation
Indices: 73289--73320 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
73279 CTTGTCCACT
73289 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
73321 TGGAAGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:77298 original size:20 final size:20
Alignment explanation
Indices: 77273--77313 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
77263 AAGTTAATTT
77273 TTGATAATCAAATATGATCA
1 TTGATAATCAAATATGATCA
77293 TTGATAATCAAATATGATCA
1 TTGATAATCAAATATGATCA
77313 T
1 T
77314 ACCTTGTGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (20 bp):
TTGATAATCAAATATGATCA
Found at i:78254 original size:2 final size:2
Alignment explanation
Indices: 78247--78278 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
78237 ACCGTATTAC
*
78247 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78279 TACTCTAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81411 original size:27 final size:27
Alignment explanation
Indices: 81381--81437 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
81371 TCAAAAATTA
*
81381 TGGTTACTTTGTGTTTATAAAAAATGG
1 TGGTTACTTTGTATTTATAAAAAATGG
* * * *
81408 TGGTTTCTTTTTATTTGTCAAAAATGG
1 TGGTTACTTTGTATTTATAAAAAATGG
81435 TGG
1 TGG
81438 CATGTTGTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.47
Consensus pattern (27 bp):
TGGTTACTTTGTATTTATAAAAAATGG
Found at i:85732 original size:27 final size:27
Alignment explanation
Indices: 85697--85765 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
85687 AAACACCCAT
*
85697 TGTTTGTCAAAAATTATGGTTACTTTG
1 TGTTTGTCAAAAATGATGGTTACTTTG
* *
85724 TGTTTGTCAAAAATGATGGTTTCTTTT
1 TGTTTGTCAAAAATGATGGTTACTTTG
* *
85751 TATTTATCAAAAATG
1 TGTTTGTCAAAAATG
85766 GTGACATGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (27 bp):
TGTTTGTCAAAAATGATGGTTACTTTG
Found at i:86430 original size:13 final size:13
Alignment explanation
Indices: 86412--86453 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
86402 AGATTTAAAT
86412 TATTTTAATTTTA
1 TATTTTAATTTTA
*
86425 TATTTTAAAATTTA
1 TATTTT-AATTTTA
86439 T-TTTT-ATTTTA
1 TATTTTAATTTTA
86450 TATT
1 TATT
86454 AGATATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 6 0.24
12 2 0.08
13 10 0.40
14 7 0.28
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTTTAATTTTA
Found at i:86693 original size:21 final size:21
Alignment explanation
Indices: 86669--86709 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
86659 AAAAAGTATT
*
86669 ATTCAATGAGAAAA-AAAAATC
1 ATTCAAT-ACAAAATAAAAATC
86690 ATTCAATACAAAATAAAAAT
1 ATTCAATACAAAATAAAAAT
86710 TTTTAGGGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.63, C:0.10, G:0.05, T:0.22
Consensus pattern (21 bp):
ATTCAATACAAAATAAAAATC
Found at i:87305 original size:20 final size:21
Alignment explanation
Indices: 87269--87308 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
87259 TTATAAAGAA
87269 TTAAAATATAAAAAAATATAT
1 TTAAAATATAAAAAAATATAT
*
87290 TTAAAATA-ATAAAAATATA
1 TTAAAATATAAAAAAATATA
87309 AGATACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TTAAAATATAAAAAAATATAT
Found at i:87398 original size:20 final size:20
Alignment explanation
Indices: 87383--87430 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
87373 TTTTAATTTT
87383 TAATTTTAATTATTAAATTA
1 TAATTTTAATTATTAAATTA
*
87403 TAATTTTAATTATAAAAATTA
1 TAATTTTAATTAT-TAAATTA
*
87424 AAATTTT
1 TAATTTT
87431 GTATACATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATTTTAATTATTAAATTA
Found at i:88456 original size:51 final size:51
Alignment explanation
Indices: 88375--88473 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
88365 GAAAAACGTG
* **
88375 AGAAAAACGTGGCAAAGGAAATTGTAACAAGCAACTTGCCCATTCCAACTC
1 AGAAAAACGTGACAAAGGAAATCATAACAAGCAACTTGCCCATTCCAACTC
*
88426 AGAAAAACGTGACAAAGGAAATCATGACAAGCAACTTGCCCATTCCAA
1 AGAAAAACGTGACAAAGGAAATCATAACAAGCAACTTGCCCATTCCAA
88474 GCAAAGCTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.16
Consensus pattern (51 bp):
AGAAAAACGTGACAAAGGAAATCATAACAAGCAACTTGCCCATTCCAACTC
Found at i:88767 original size:153 final size:151
Alignment explanation
Indices: 88421--88871 Score: 690
Period size: 153 Copynumber: 3.0 Consensus size: 151
88411 TGCCCATTCC
* ** *
88421 AACTCAGAAAAACGTGACAAAGGAAATCATGACAAGCAACTTGCCCATTCCAAGCAAAGCTAATA
1 AACTGAGAAAAACGTGACAAAGGAAATTGTAACAAGCAACTTGCCCATTCCAAGCAAAGCTAATA
* * * * *
88486 GTAAAAAGAAGGGAGAAAACCATTCTCGTGAAAAACC-AAAGGTAAA-TTTTATTGAGTAAACAA
66 GTAAAAAGAAGGGGGAAAACCATTCTTGTGAAAGACCGAAAGGTAAATTTTTTTTGAGTAAACGA
* * *
88549 ATTTGAAAAAAATTTCGTTTA
131 ATCTGAAAAAATTTTCGTTAA
* *
88570 AACTGAGAGAAACGTGACACAGGAAATTGTAACAAGCAACTTGCCCATTCCAAGCAAAGCTAATA
1 AACTGAGAAAAACGTGACAAAGGAAATTGTAACAAGCAACTTGCCCATTCCAAGCAAAGCTAATA
* *
88635 GTAAAAAGAAGGGGGAAAATCATTCTTGTGAAAGACCGAAAGGTAAATTTTTTTTTTGAGTAAGC
66 GTAAAAAGAAGGGGGAAAACCATTCTTGTGAAAGACCGAAAGGTAAA--TTTTTTTTGAGTAAAC
*
88700 GAATCTGAAAGAATTTTCGTTAA
129 GAATCTGAAAAAATTTTCGTTAA
88723 AACTGAGAAAAACGTGACAAAGGAAATTGTAACAAGCAACTTGCCCATTCCAAGCAAAGCTAATA
1 AACTGAGAAAAACGTGACAAAGGAAATTGTAACAAGCAACTTGCCCATTCCAAGCAAAGCTAATA
* * *
88788 GTAAAAAGAAGGGGGAAGACCGTTCTTGTGAAAGACCGAAAGGTAAATTTTTTTTGAGTAAATGA
66 GTAAAAAGAAGGGGGAAAACCATTCTTGTGAAAGACCGAAAGGTAAATTTTTTTTGAGTAAACGA
88853 ATCTGAAAAAATTTTCGTT
131 ATCTGAAAAAATTTTCGTT
88872 GAAATTTTAG
Statistics
Matches: 273, Mismatches: 25, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
149 92 0.34
150 9 0.03
151 34 0.12
153 138 0.51
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (151 bp):
AACTGAGAAAAACGTGACAAAGGAAATTGTAACAAGCAACTTGCCCATTCCAAGCAAAGCTAATA
GTAAAAAGAAGGGGGAAAACCATTCTTGTGAAAGACCGAAAGGTAAATTTTTTTTGAGTAAACGA
ATCTGAAAAAATTTTCGTTAA
Found at i:89652 original size:25 final size:24
Alignment explanation
Indices: 89624--89748 Score: 106
Period size: 27 Copynumber: 4.9 Consensus size: 24
89614 AAGCCACCCA
89624 TTTGTTTGTCAAAAATGGTGGTTATT
1 TTTGTTTGTCAAAAATGGTGG-T-TT
89650 TTGTGTTTGTCAAAAATGGTGGTTT
1 TT-TGTTTGTCAAAAATGGTGGTTT
* * *
89675 CCTTTGTATTTGTCAAATATGGAGGCTTG
1 --TTTG--TTTGTCAAAAATGGTGG-TTT
* * *
89704 TTTATTTGTCAAAATTGGTGGCTT
1 TTTGTTTGTCAAAAATGGTGGTTT
* *
89728 GTTGTTTGTCAAAATTGGTGG
1 TTTGTTTGTCAAAAATGGTGG
89749 CTAATTTTTA
Statistics
Matches: 82, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
24 20 0.24
25 16 0.20
26 5 0.06
27 24 0.29
28 15 0.18
29 2 0.02
ACGTcount: A:0.21, C:0.07, G:0.26, T:0.46
Consensus pattern (24 bp):
TTTGTTTGTCAAAAATGGTGGTTT
Found at i:89735 original size:24 final size:25
Alignment explanation
Indices: 89681--89750 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
89671 GTTTCCTTTG
*
89681 TATTTGTC-AAATATGGAGGCTTGTT
1 TATTTGTCAAAAT-TGGTGGCTTGTT
89706 TATTTGTCAAAATTGGTGGCTTG-T
1 TATTTGTCAAAATTGGTGGCTTGTT
*
89730 TGTTTGTCAAAATTGGTGGCT
1 TATTTGTCAAAATTGGTGGCT
89751 AATTTTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 17 0.40
26 4 0.10
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.44
Consensus pattern (25 bp):
TATTTGTCAAAATTGGTGGCTTGTT
Found at i:94246 original size:25 final size:24
Alignment explanation
Indices: 94218--94342 Score: 88
Period size: 27 Copynumber: 4.9 Consensus size: 24
94208 AAGCCACCCA
94218 TTTGTTTGTCAAAAATGGTGGTTATT
1 TTTGTTTGTCAAAAATGGTGG-T-TT
*
94244 TTGTGTTTATCAAAAATGGTGGTTT
1 TT-TGTTTGTCAAAAATGGTGGTTT
* * *
94269 CCTTTGTATTTGTCAAATATGGAGGCTTG
1 --TTTG--TTTGTCAAAAATGGTGG-TTT
* * * *
94298 TTTATTTGTCAAAATTTGTGGCTT
1 TTTGTTTGTCAAAAATGGTGGTTT
* *
94322 GTTGTTTGTCAAAATTGGTGG
1 TTTGTTTGTCAAAAATGGTGG
94343 CTAATTTTTA
Statistics
Matches: 78, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
24 19 0.24
25 15 0.19
26 5 0.06
27 23 0.29
28 14 0.18
29 2 0.03
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.47
Consensus pattern (24 bp):
TTTGTTTGTCAAAAATGGTGGTTT
Found at i:94275 original size:28 final size:27
Alignment explanation
Indices: 94220--94290 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
94210 GCCACCCATT
94220 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
*
94247 TGTTTATCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
94275 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
94291 AGGCTTGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:94329 original size:24 final size:25
Alignment explanation
Indices: 94275--94344 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 25
94265 GTTTCCTTTG
*
94275 TATTTGTC-AAATATGGAGGCTTGTT
1 TATTTGTCAAAAT-TGGTGGCTTGTT
*
94300 TATTTGTCAAAATTTGTGGCTTG-T
1 TATTTGTCAAAATTGGTGGCTTGTT
*
94324 TGTTTGTCAAAATTGGTGGCT
1 TATTTGTCAAAATTGGTGGCT
94345 AATTTTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
24 20 0.50
25 16 0.40
26 4 0.10
ACGTcount: A:0.21, C:0.09, G:0.24, T:0.46
Consensus pattern (25 bp):
TATTTGTCAAAATTGGTGGCTTGTT
Found at i:97610 original size:20 final size:20
Alignment explanation
Indices: 97572--97624 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
97562 ACGATACAAA
*
97572 TATATAAATATATTAAAATT
1 TATATAAATATAATAAAATT
97592 TATATAAA-ATAATATAAATAT
1 TATATAAATATAATA-AAAT-T
* *
97613 CATACAAATATA
1 TATATAAATATA
97625 TAGATATATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 5 0.19
20 12 0.44
21 7 0.26
22 3 0.11
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
TATATAAATATAATAAAATT
Found at i:99652 original size:21 final size:19
Alignment explanation
Indices: 99627--99691 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
99617 GATCGTTAAA
99627 AAATTTTAAAATATTGTATTT
1 AAATTTTAAAATA-T-TATTT
99648 AAA-TTT-AAATATT-TTT
1 AAATTTTAAAATATTATTT
* *
99664 AATTTTTAAATTATTATTT
1 AAATTTTAAAATATTATTT
*
99683 AAATATTAA
1 AAATTTTAA
99692 TAAAAATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 5 0.14
17 4 0.11
18 7 0.19
19 15 0.41
20 3 0.08
21 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
AAATTTTAAAATATTATTT
Found at i:100157 original size:13 final size:13
Alignment explanation
Indices: 100139--100163 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
100129 AATTTATCTT
100139 TTTTAAATTCAAA
1 TTTTAAATTCAAA
100152 TTTTAAATTCAA
1 TTTTAAATTCAA
100164 TGGTGAAATA
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTAAATTCAAA
Found at i:100554 original size:29 final size:29
Alignment explanation
Indices: 100496--100554 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
100486 GACTTCTCAC
* * * *
100496 TACAAAATATACATTTTAACTATTATTTT
1 TACAAAATATAAATATTAAATAATATTTT
100525 TACAAAATATCAAATATTAAATAATATTTT
1 TACAAAATAT-AAATATTAAATAATATTTT
100555 GTTAACAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (29 bp):
TACAAAATATAAATATTAAATAATATTTT
Found at i:101294 original size:28 final size:30
Alignment explanation
Indices: 101248--101304 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
101238 TTATATTTTA
*
101248 TATATTATGTAATTTTTAT-GATATAAAAAT
1 TATATTATGTAATTATTATAG-TATAAAAAT
101278 TATA-TATGTAA-TATTATAGTATAAAAA
1 TATATTATGTAATTATTATAGTATAAAAA
101305 ATAAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 13 0.52
29 8 0.32
30 4 0.16
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (30 bp):
TATATTATGTAATTATTATAGTATAAAAAT
Found at i:101390 original size:13 final size:13
Alignment explanation
Indices: 101359--101415 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
101349 AAAATTATTA
*
101359 ATTTAATAAAATTAA
1 ATTTAA-AAAA-TAT
*
101374 ATTTTAAAAATAT
1 ATTTAAAAAATAT
*
101387 ATTTAAAAAATAA
1 ATTTAAAAAATAT
*
101400 ATTACAAAAAATAT
1 ATT-TAAAAAATAT
101414 AT
1 AT
101416 AATTTGAGCA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
13 16 0.46
14 14 0.40
15 5 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTTAAAAAATAT
Found at i:101575 original size:41 final size:41
Alignment explanation
Indices: 101528--101610 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
101518 GGTTCATATG
101528 AATTTAGGTTTGATTGTTTTAGATTGCTTTACATATATGTA
1 AATTTAGGTTTGATTGTTTTAGATTGCTTTACATATATGTA
101569 AATTTAGGTTTGATTGTTTTAGATTGCTTTACATATATGTA
1 AATTTAGGTTTGATTGTTTTAGATTGCTTTACATATATGTA
101610 A
1 A
101611 GGTTCCATGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.28, C:0.05, G:0.17, T:0.51
Consensus pattern (41 bp):
AATTTAGGTTTGATTGTTTTAGATTGCTTTACATATATGTA
Found at i:102291 original size:38 final size:39
Alignment explanation
Indices: 102228--102310 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 39
102218 AGACATTTCC
*
102228 ATTCTA-TAAGTTATACAATGTCCTAATTAAACACTTTT
1 ATTCTATTAAGTTATACAATGACCTAATTAAACACTTTT
*
102266 ATTCTATTAATTTATACAAT-ACCTAATTAAACACTTTT
1 ATTCTATTAAGTTATACAATGACCTAATTAAACACTTTT
102304 ATTCTAT
1 ATTCTAT
102311 ATTGTGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
38 30 0.71
39 12 0.29
ACGTcount: A:0.37, C:0.16, G:0.02, T:0.45
Consensus pattern (39 bp):
ATTCTATTAAGTTATACAATGACCTAATTAAACACTTTT
Done.