Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1544
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: 38694
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.37
Found at i:1161 original size:18 final size:20
Alignment explanation
Indices: 1138--1183 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
1128 TCACATCTTT
*
1138 AAATAATTTATTTA-AT-TC
1 AAATAATTCATTTATATCTC
*
1156 AAATAATTCATTTATTTCTC
1 AAATAATTCATTTATATCTC
1176 AAATAATT
1 AAATAATT
1184 ATAATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 13 0.54
19 1 0.04
20 10 0.42
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATAATTCATTTATATCTC
Found at i:1200 original size:21 final size:20
Alignment explanation
Indices: 1143--1201 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
1133 TCTTTAAATA
1143 ATTTATTTAATTCAAATAATTC
1 ATTTATTT--TTCAAATAATTC
*
1165 ATTTATTTCTCAAATAATT-
1 ATTTATTTTTCAAATAATTC
*
1184 ATAATTTTTTTTCAAATA
1 AT--TTATTTTTCAAATA
1202 CACACCAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 2 0.06
20 10 0.31
21 12 0.38
22 8 0.25
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTATTTTTCAAATAATTC
Found at i:2325 original size:22 final size:22
Alignment explanation
Indices: 2295--2340 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2285 ATATTAGACG
2295 TATTGAAGAA-TTTAAATTAGTT
1 TATTGAAGAAGTTTAAATT-GTT
* *
2317 TATTTAAGAAGTTTAAGTTGTT
1 TATTGAAGAAGTTTAAATTGTT
2339 TA
1 TA
2341 AATTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (22 bp):
TATTGAAGAAGTTTAAATTGTT
Found at i:2407 original size:20 final size:20
Alignment explanation
Indices: 2371--2408 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2361 GAAATTAATT
*
2371 TAATTAAAATTAATATTTAA
1 TAATTAAAATAAATATTTAA
2391 TAATTAAAA-AAAGTATTT
1 TAATTAAAATAAA-TATTT
2409 TATTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
TAATTAAAATAAATATTTAA
Found at i:2479 original size:13 final size:14
Alignment explanation
Indices: 2461--2492 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2451 TTTATTAATT
2461 ATAAATAATA-AAC
1 ATAAATAATATAAC
2474 ATAAATAATATAAC
1 ATAAATAATATAAC
2488 -TAAAT
1 ATAAAT
2493 TAAATTGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAATAATATAAC
Found at i:2740 original size:17 final size:17
Alignment explanation
Indices: 2713--2765 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
2703 TGATTAGATG
* *
2713 TTAATATTTATTGAATAT
1 TTAA-ATTTATTAAATAA
2731 TTAAATTTATTAAATAA
1 TTAAATTTATTAAATAA
*
2748 TTAAATTTTTTATAATAA
1 TTAAATTTATTA-AATAA
2766 AATGTCATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 22 0.71
18 9 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTAAATAA
Found at i:5624 original size:32 final size:33
Alignment explanation
Indices: 5550--5624 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 33
5540 ATAATCATAT
* *
5550 TTAAAATTTTATATTTATATAAATTTTTATAAA
1 TTAAAATTTTATATTTATATAAAATTTAATAAA
*
5583 TTAATATTTTATA-TTATATAAAATTTAATACAA
1 TTAAAATTTTATATTTATATAAAATTTAATA-AA
5616 -TAAAATTTT
1 TTAAAATTTT
5625 TGTATTGTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 23 0.62
33 14 0.38
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (33 bp):
TTAAAATTTTATATTTATATAAAATTTAATAAA
Found at i:8698 original size:16 final size:16
Alignment explanation
Indices: 8679--8735 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 16
8669 TTATTATAAT
8679 TATAT-TTAAAATATTA
1 TATATATTAAAAT-TTA
8695 TATATATTAAAATTT-
1 TATATATTAAAATTTA
8710 TAATATATTAATAATTTA
1 T-ATATATTAA-AATTTA
8728 TATTATAT
1 TA-TATAT
8736 AAATTTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.03
16 16 0.44
17 13 0.36
18 6 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATATTAAAATTTA
Found at i:8710 original size:40 final size:39
Alignment explanation
Indices: 8666--8781 Score: 110
Period size: 40 Copynumber: 2.9 Consensus size: 39
8656 TATATATTTT
8666 ATTTTATTATAATTATATTTAAAATATTATATATATTAAA
1 ATTTTATTAT-ATTATATTTAAAATATTATATATATTAAA
* * * * *
8706 ATTTTAATATATTAATAATTTATATTA-TATAAATTTTAAA
1 ATTTTATTATATT-AT-ATTTAAAATATTATATATATTAAA
* * *
8746 AATAT-TTATATTATATTTAAAATTTTATATTATATT
1 ATTTTATTATATTATATTTAAAATATTATA-TATATT
8782 TTAATTATTT
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
37 7 0.12
38 6 0.10
39 13 0.22
40 25 0.42
41 8 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (39 bp):
ATTTTATTATATTATATTTAAAATATTATATATATTAAA
Found at i:8756 original size:21 final size:20
Alignment explanation
Indices: 8693--8785 Score: 63
Period size: 20 Copynumber: 4.6 Consensus size: 20
8683 TTTAAAATAT
*
8693 TATATATATT-AAAATTTTA
1 TATATATTTTAAAAATTTTA
*
8712 -ATATA--TTAATAATTTATA
1 TATATATTTTAAAAATTT-TA
8730 TTATATAAATTTTAAAAATATTTA
1 -TATAT--ATTTTAAAAAT-TTTA
8754 TAT-TATATTT-AAAATTTTA
1 TATATAT-TTTAAAAATTTTA
8773 TATTATATTTTAA
1 TA-TATATTTTAA
8786 TTATTTTTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 24
0.69 0.02 0.28
Matches are distributed among these distances:
16 2 0.03
17 6 0.10
18 7 0.12
19 6 0.10
20 15 0.25
21 7 0.12
22 2 0.03
23 3 0.05
24 9 0.15
25 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATATTTTAAAAATTTTA
Found at i:8799 original size:61 final size:58
Alignment explanation
Indices: 8642--8781 Score: 147
Period size: 61 Copynumber: 2.2 Consensus size: 58
8632 AATTTTTTAT
* *
8642 ATTTGTAATATATTTATATATTTTATTTTATTATAATTATATTT-AAAATATTATATATATTAAA
1 ATTT-TAATATA-TTA-ATAATTTATATTA-TATAA--AT-TTTAAAAATATTATATATATTAAA
8706 ATTTTAATATATTAATAATTTATATTATATAAATTTTAAAAATATTTATATTATATTTAAA
1 ATTTTAATATATTAATAATTTATATTATATAAATTTTAAAAATA-TTATA-TATA-TTAAA
8767 ATTTTATATTATATT
1 ATTTTA-A-TATATT
8782 TTAATTATTT
Statistics
Matches: 68, Mismatches: 2, Indels: 13
0.82 0.02 0.16
Matches are distributed among these distances:
57 3 0.04
58 8 0.12
59 5 0.07
60 9 0.13
61 22 0.32
62 4 0.06
63 13 0.19
64 4 0.06
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.56
Consensus pattern (58 bp):
ATTTTAATATATTAATAATTTATATTATATAAATTTTAAAAATATTATATATATTAAA
Found at i:9091 original size:30 final size:32
Alignment explanation
Indices: 9051--9111 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
9041 TATTTAAAAT
* *
9051 ATTATATA-TTTATAT-ATTTTTAATATATTA
1 ATTATATATTTTATATAAATTATAATATATTA
*
9081 ATTATTTATTTTATATAAATTATAATATATT
1 ATTATATATTTTATATAAATTATAATATATT
9112 TATATAGTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 7 0.27
31 7 0.27
32 12 0.46
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (32 bp):
ATTATATATTTTATATAAATTATAATATATTA
Found at i:9610 original size:15 final size:16
Alignment explanation
Indices: 9584--9613 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9574 TAAATTTACT
9584 TTATATTATATTTTAA
1 TTATATTATATTTTAA
9600 TTATA-TATATTTTA
1 TTATATTATATTTTA
9614 TTTAAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATATTATATTTTAA
Found at i:11092 original size:22 final size:24
Alignment explanation
Indices: 11056--11112 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
11046 TTAATTTATA
11056 TAATTATATTTAAAAAATAAAATT
1 TAATTATATTTAAAAAATAAAATT
* *
11080 TAATTA-A-TTAAAAATTTAAATTT
1 TAATTATATTTAAAAA-ATAAAATT
11103 TAATATATAT
1 TAAT-TATAT
11113 AATTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 7 0.26
23 11 0.41
24 8 0.30
25 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAATTATATTTAAAAAATAAAATT
Found at i:16064 original size:17 final size:17
Alignment explanation
Indices: 16044--16081 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
16034 TAAAAGTTAG
16044 TTTTT-AATTTTTAAAAA
1 TTTTTAAATTTTT-AAAA
16061 TTTTTAAATTTTTAAAA
1 TTTTTAAATTTTTAAAA
16078 TTTT
1 TTTT
16082 AACGGTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTTAAATTTTTAAAA
Found at i:16449 original size:29 final size:30
Alignment explanation
Indices: 16408--16482 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
16398 CATTAAATAT
* *
16408 AATAATTTA-CATATT-TATATTTTATTT-A
1 AATATTTTATCATATTATA-ATTATATTTAA
*
16436 TATATTTTATCATATTATAATTATATTTAA
1 AATATTTTATCATATTATAATTATATTTAA
16466 AATATTTTAT-AT-TTATA
1 AATATTTTATCATATTATA
16483 TAAAATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 12 0.30
29 16 0.40
30 12 0.30
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
AATATTTTATCATATTATAATTATATTTAA
Found at i:16490 original size:27 final size:30
Alignment explanation
Indices: 16437--16529 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 30
16427 TTTTATTTAT
* *
16437 ATATTTTATCATATTATAATTATATTTAAA
1 ATATTTTATCATATTATAATAAAATTTAAA
*
16467 ATATTTTAT-AT-TTAT-ATAAAATTTAAT
1 ATATTTTATCATATTATAATAAAATTTAAA
* * *
16494 ATATTAATAATTATATTAT-ATAAATTTTAATA
1 ATATT--TTATCATATTATAATAAAATTTAA-A
16526 ATAT
1 ATAT
16530 CATATCTTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
27 14 0.27
28 4 0.08
29 5 0.10
30 11 0.21
31 14 0.27
32 4 0.08
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (30 bp):
ATATTTTATCATATTATAATAAAATTTAAA
Found at i:16498 original size:76 final size:78
Alignment explanation
Indices: 16404--16554 Score: 177
Period size: 78 Copynumber: 2.0 Consensus size: 78
16394 TCGGCATTAA
* * * * *
16404 ATATAATAATTTACATATTTAT-ATTTTATT-TATATATTTT-ATCATATTATA-ATTATATTTA
1 ATATAATAATTTACATATTAATAATTATATTATATAAATTTTAATAATATCATATATTATA-TT-
16465 AAATATTTTATATTT
64 AAATATTTTATATTT
* *
16480 ATATAA-AATTTAATATATTAATAATTATATTATATAAATTTTAATAATATCATATCTTATATTA
1 ATATAATAATTT-ACATATTAATAATTATATTATATAAATTTTAATAATATCATATATTATATTA
16544 AATATTTTATA
65 AATATTTTATA
16555 CATATTATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
75 5 0.08
76 14 0.22
77 7 0.11
78 21 0.33
79 11 0.17
80 5 0.08
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (78 bp):
ATATAATAATTTACATATTAATAATTATATTATATAAATTTTAATAATATCATATATTATATTAA
ATATTTTATATTT
Found at i:16508 original size:12 final size:13
Alignment explanation
Indices: 16493--16588 Score: 54
Period size: 14 Copynumber: 7.2 Consensus size: 13
16483 TAAAATTTAA
16493 TATATTA-ATAAT
1 TATATTATATAAT
16505 TATATTATATAAAT
1 TATATTATAT-AAT
* * *
16519 TTTAATAATATCA-
1 TAT-ATTATATAAT
* *
16532 TATCTTATATTAAA
1 TATATTATA-TAAT
* *
16546 TATTTTATACATAT
1 TATATTATATA-AT
16560 TATATTTATATAAT
1 TATA-TTATATAAT
*
16574 TATATT-TAAAAT
1 TATATTATATAAT
16586 TAT
1 TAT
16589 TAGATTTACC
Statistics
Matches: 64, Mismatches: 13, Indels: 14
0.70 0.14 0.15
Matches are distributed among these distances:
12 19 0.30
13 9 0.14
14 24 0.38
15 12 0.19
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATTATATAAT
Found at i:16540 original size:32 final size:31
Alignment explanation
Indices: 16467--16543 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 31
16457 TATATTTAAA
* *
16467 ATATTTTATATTTATATAAAATTTAATATATT
1 ATATATTATA-TTATATAAAATTTAATATATC
*
16499 A-ATAATTATATTATATAAATTTTAATAATATC
1 ATAT-ATTATATTATATAAAATTTAAT-ATATC
*
16531 ATATCTTATATTA
1 ATATATTATATTA
16544 AATATTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
31 17 0.45
32 19 0.50
33 2 0.05
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (31 bp):
ATATATTATATTATATAAAATTTAATATATC
Found at i:16970 original size:3 final size:3
Alignment explanation
Indices: 16964--17004 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
16954 CAACAACAAC
*
16964 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17005 ATACTTCTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:22282 original size:18 final size:18
Alignment explanation
Indices: 22259--22321 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
22249 AAAATTAAAT
22259 TAATTTTATATAATTTTA
1 TAATTTTATATAATTTTA
22277 TAATTTTTATATAA-TTTA
1 TAA-TTTTATATAATTTTA
* *
22295 T-A-TTTATTTAATTTAA
1 TAATTTTATATAATTTTA
*
22311 TATTTTTATAT
1 TAATTTTATAT
22322 TTTATTATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 8 0.22
16 4 0.11
17 1 0.03
18 14 0.38
19 10 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TAATTTTATATAATTTTA
Found at i:22306 original size:15 final size:16
Alignment explanation
Indices: 22258--22325 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
22248 TAAAATTAAA
22258 TTAAT-TTTATATAATTT
1 TTAATATTTATATAA--T
*
22275 TATAATTTTTATATAAT
1 T-TAATATTTATATAAT
*
22292 TT-ATATTTATTTAAT
1 TTAATATTTATATAAT
* *
22307 TTAATATTTTTATATT
1 TTAATATTTATATAAT
22323 TTA
1 TTA
22326 TTATCTATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
15 13 0.30
16 14 0.33
17 3 0.07
18 4 0.09
19 9 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTAATATTTATATAAT
Found at i:22340 original size:31 final size:32
Alignment explanation
Indices: 22269--22341 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 32
22259 TAATTTTATA
* *
22269 TAATTTTATAATTTTTATATAATTTATATTTATT
1 TAATTTAAT-ATTTTTATAT-ATTTATATCTATT
22303 TAATTTAATATTTTTATAT-TTTATTATCTATT
1 TAATTTAATATTTTTATATATTTA-TATCTATT
22335 T-ATTTAA
1 TAATTTAA
22342 ATTATATACG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
31 10 0.28
32 8 0.22
33 10 0.28
34 8 0.22
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (32 bp):
TAATTTAATATTTTTATATATTTATATCTATT
Found at i:22420 original size:28 final size:27
Alignment explanation
Indices: 22366--22459 Score: 75
Period size: 28 Copynumber: 3.3 Consensus size: 27
22356 ATTTTAAGTA
* *
22366 AAAAATATTTAAATATTT-ATTAAATATG
1 AAAAATATTTATAT-TTTAAAT-AATATG
* *
22394 AAAAA-ATTTTTATTATTAAATATATATT
1 AAAAATATTTATATT-TTAAATA-ATATG
*
22422 AAAAATATTTATATTTTAGATAATATG
1 AAAAATATTTATATTTTAAATAATATG
22449 ATTAAAATATT
1 A--AAAATATT
22460 AAATTAAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
26 1 0.02
27 14 0.26
28 22 0.42
29 16 0.30
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (27 bp):
AAAAATATTTATATTTTAAATAATATG
Found at i:22425 original size:27 final size:30
Alignment explanation
Indices: 22366--22459 Score: 78
Period size: 29 Copynumber: 3.3 Consensus size: 30
22356 ATTTTAAGTA
* *
22366 AAAAATATTTAAATATTT-ATTAAATATGA--
1 AAAAATATTTATAT-TTTAAAT-AATATGATT
22395 AAAAAT-TTT-TATTATTAAAT-ATAT-ATT
1 AAAAATATTTATATT-TTAAATAATATGATT
*
22422 AAAAATATTTATATTTTAGATAATATGATT
1 AAAAATATTTATATTTTAAATAATATGATT
22452 -AAAATATT
1 AAAAATATT
22460 AAATTAAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
25 1 0.02
26 5 0.09
27 10 0.19
28 13 0.24
29 22 0.41
30 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (30 bp):
AAAAATATTTATATTTTAAATAATATGATT
Found at i:22616 original size:26 final size:25
Alignment explanation
Indices: 22560--22617 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
22550 TCATGACAAT
*
22560 TTATA-AAATTAATTTAATTTTATA
1 TTATATAAATAAATTTAATTTTATA
* *
22584 TTAATATAAATAAATTTTATTTTCTA
1 TT-ATATAAATAAATTTAATTTTATA
22610 TATATATA
1 T-TATATA
22618 TATTTTGTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 2 0.07
25 3 0.11
26 22 0.79
27 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
TTATATAAATAAATTTAATTTTATA
Found at i:24190 original size:2 final size:2
Alignment explanation
Indices: 24183--24227 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
24173 AAGCTATTAT
* * *
24183 TA TA TA TA TG TA CA CA 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
24225 TA T
1 TA T
24228 GCTGCCGTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:25211 original size:50 final size:50
Alignment explanation
Indices: 25151--25338 Score: 286
Period size: 50 Copynumber: 3.8 Consensus size: 50
25141 TATACTTAGA
* * *
25151 GTCAACAATTATGGCCACCTTTCTCTATTGTCAAAGGTTTGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * * *
25201 GTCAATAATTACGGCCACCTCTCTTTATTATCAAAGGTTGGTAAAAAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
25251 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAATGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
25301 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGT
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGT
25339 ACTTTCCACC
Statistics
Matches: 122, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 122 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.32
Consensus pattern (50 bp):
GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:29750 original size:30 final size:30
Alignment explanation
Indices: 29711--29768 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
29701 CACTTTTCTC
* *
29711 TATTGTCAAAGGTTGGTGAAGAATCGTCCT
1 TATTATCAAAAGTTGGTGAAGAATCGTCCT
29741 TATTATCAAAAGTTGGTGAAGAATCGTC
1 TATTATCAAAAGTTGGTGAAGAATCGTC
29769 AACAATTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (30 bp):
TATTATCAAAAGTTGGTGAAGAATCGTCCT
Found at i:30781 original size:2 final size:2
Alignment explanation
Indices: 30776--30805 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30766 ATATATATAT
30776 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30806 TAACAGCTAT
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):
AG
Found at i:31593 original size:21 final size:21
Alignment explanation
Indices: 31569--31610 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
31559 TTTTAAAATT
*
31569 TTTAATA-TCTTAATTAATTAA
1 TTTAATATTATTAATT-ATTAA
*
31590 TTTATTATTATTAATTATTAA
1 TTTAATATTATTAATTATTAA
31611 ACAAGAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAATATTATTAATTATTAA
Found at i:32469 original size:27 final size:27
Alignment explanation
Indices: 32422--32478 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
32412 ATATATATAT
* *
32422 TTATATATTATAATTATTTTTAAAATA
1 TTATATATTATAATAAATTTTAAAATA
*
32449 TTATATATT-TATATAAATTTTAACATA
1 TTATATATTATA-ATAAATTTTAAAATA
32476 TTA
1 TTA
32479 ATAATTCGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
TTATATATTATAATAAATTTTAAAATA
Found at i:32792 original size:2 final size:2
Alignment explanation
Indices: 32785--32817 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
32775 TTATGCCAAC
32785 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 T
32818 TCCCTATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33239 original size:18 final size:18
Alignment explanation
Indices: 33218--33276 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
33208 TTAACCTTTA
33218 ATTTATATTTAAATAAAT
1 ATTTATATTTAAATAAAT
* *
33236 ATTTA-A-TAAAACTTAAT
1 ATTTATATTTAAA-TAAAT
*
33253 ATTT-TATTTGAAATAAAA
1 ATTTATATTT-AAATAAAT
33271 ATTTAT
1 ATTTAT
33277 TTGAGTACAA
Statistics
Matches: 31, Mismatches: 5, Indels: 9
0.69 0.11 0.20
Matches are distributed among these distances:
16 4 0.13
17 10 0.32
18 13 0.42
19 4 0.13
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTATATTTAAATAAAT
Found at i:36116 original size:2 final size:2
Alignment explanation
Indices: 36111--36139 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36101 ATTATATATA
36111 TG 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 TG T
36140 CCAGCGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Done.