Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1742
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: 42033
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Found at i:1658 original size:1 final size:1
Alignment explanation
Indices: 1652--1678 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1642 AATTCAGGGG
1652 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1679 GAAGCAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3356 original size:20 final size:20
Alignment explanation
Indices: 3331--3411 Score: 83
Period size: 20 Copynumber: 4.0 Consensus size: 20
3321 AATTCATGCA
*
3331 TATAAAAATTATTTATAAAT
1 TATAAAAATTATTAATAAAT
*
3351 TATAAAAATTATGAAT-AAT
1 TATAAAAATTATTAATAAAT
* * *
3370 AATTAAAATTATATCAAAAAAT
1 TATAAAAATTAT-T-AATAAAT
*
3392 TATAAAAATTATAAATAAAT
1 TATAAAAATTATTAATAAAT
3412 AATTAAGTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
19 13 0.27
20 20 0.42
21 2 0.04
22 13 0.27
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (20 bp):
TATAAAAATTATTAATAAAT
Found at i:3361 original size:9 final size:9
Alignment explanation
Indices: 3331--3406 Score: 53
Period size: 9 Copynumber: 7.7 Consensus size: 9
3321 AATTCATGCA
3331 TATAAAAAT
1 TATAAAAAT
*
3340 TATTTATAAAT
1 TA--TAAAAAT
3351 TATAAAAAT
1 TATAAAAAT
*
3360 TATGAATAAT
1 TAT-AAAAAT
* *
3370 AATTAAAATT
1 TA-TAAAAAT
3380 ATATCAAAAAAT
1 -TAT--AAAAAT
3392 TATAAAAAT
1 TATAAAAAT
3401 TATAAA
1 TATAAA
3407 TAAATAATTA
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
9 23 0.44
10 11 0.21
11 13 0.25
12 5 0.10
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (9 bp):
TATAAAAAT
Found at i:9792 original size:25 final size:23
Alignment explanation
Indices: 9764--9815 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
9754 TTGTCGTGCG
9764 ATGTTCAAGGAAAAAAACCATTCAA
1 ATGTTCAAGG--AAAAACCATTCAA
* *
9789 ATGTTCAAGGTAAAGCCATTCAA
1 ATGTTCAAGGAAAAACCATTCAA
9812 ATGT
1 ATGT
9816 CATGTCAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 15 0.60
25 10 0.40
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (23 bp):
ATGTTCAAGGAAAAACCATTCAA
Found at i:10107 original size:23 final size:23
Alignment explanation
Indices: 10081--10143 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
10071 ATTATAAATT
10081 AATTAATAATAATATAATTAAAA
1 AATTAATAATAATATAATTAAAA
* *
10104 AATT-ATAAAAATTAAAATTAAAA
1 AATTAATAATAA-TATAATTAAAA
**
10127 TTTTAA-AATAAATATAA
1 AATTAATAAT-AATATAA
10144 AATATAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
22 6 0.19
23 22 0.71
24 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
AATTAATAATAATATAATTAAAA
Found at i:10363 original size:3 final size:3
Alignment explanation
Indices: 10357--10386 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
10347 TATTATGAAA
10357 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
10387 TGAATGAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:11745 original size:16 final size:16
Alignment explanation
Indices: 11724--11770 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
11714 ATAATAAATT
11724 TTAAATTTTAAATTAA
1 TTAAATTTTAAATTAA
* *
11740 TTAAA-TATCAATTAAA
1 TTAAATTTTAAATT-AA
11756 TTAAATTTTAAATTA
1 TTAAATTTTAAATTA
11771 TAAACTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 6 0.24
16 13 0.52
17 6 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATTTTAAATTAA
Found at i:18223 original size:2 final size:2
Alignment explanation
Indices: 18216--18241 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18206 ATAAGATAAC
18216 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
18242 CTTTTTATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19568 original size:6 final size:6
Alignment explanation
Indices: 19557--19586 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
19547 CATACCAACT
*
19557 CATATA CATATA CATATA CATATA TATATA
1 CATATA CATATA CATATA CATATA CATATA
19587 TATTTGTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (6 bp):
CATATA
Found at i:20805 original size:20 final size:20
Alignment explanation
Indices: 20767--20805 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20757 TATTTTTTAA
*
20767 AAAAAAGATCCATCCTTTTT
1 AAAAAAGATCAATCCTTTTT
*
20787 AAAAAAGATTAAT-CTTTTT
1 AAAAAAGATCAATCCTTTTT
20806 GTGTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAAAAGATCAATCCTTTTT
Found at i:22896 original size:8 final size:9
Alignment explanation
Indices: 22871--22895 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
22861 TAAGATCTGC
22871 AAAAAAAAT
1 AAAAAAAAT
22880 AAAAAAAAT
1 AAAAAAAAT
22889 AAAAAAA
1 AAAAAAA
22896 TCAAGAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:24148 original size:13 final size:13
Alignment explanation
Indices: 24148--24172 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24138 ATAAAAATAT
24148 AAATATAATATAA
1 AAATATAATATAA
24161 AAATATAATATA
1 AAATATAATATA
24173 TTTTTAATAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:24154 original size:19 final size:18
Alignment explanation
Indices: 24130--24172 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 18
24120 TAGAACTTTG
24130 AATATAATATAAAAATAT
1 AATATAATATAAAAATAT
24148 AAATATAATATAAAAATAT
1 -AATATAATATAAAAATAT
24167 AATATA
1 AATATA
24173 TTTTTAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATAATATAAAAATAT
Found at i:24321 original size:22 final size:22
Alignment explanation
Indices: 24293--24341 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
24283 TACAATACAA
24293 TAAATACATAAATTATAAAATC
1 TAAATACATAAATTATAAAATC
24315 TAAATACATAAATTATAAAATC
1 TAAATACATAAATTATAAAATC
24337 TAAAT
1 TAAAT
24342 GATGCACATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAATACATAAATTATAAAATC
Found at i:24376 original size:6 final size:6
Alignment explanation
Indices: 24367--24393 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
24357 GCATATACAT
24367 ATGCAA ATGCAA ATGCAA ATGCAA ATG
1 ATGCAA ATGCAA ATGCAA ATGCAA ATG
24394 AGCCAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
ATGCAA
Found at i:24527 original size:15 final size:15
Alignment explanation
Indices: 24509--24560 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
24499 TCGTGTATTT
24509 ATAATTTTATATATA
1 ATAATTTTATATATA
* * *
24524 ATAATTATATTTAAA
1 ATAATTTTATATATA
*
24539 AT-ATTTTATATTTA
1 ATAATTTTATATATA
24553 TATAATTT
1 -ATAATTT
24561 ATTTATTAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
14 8 0.29
15 16 0.57
16 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATAATTTTATATATA
Found at i:24583 original size:11 final size:11
Alignment explanation
Indices: 24527--24618 Score: 63
Period size: 11 Copynumber: 8.6 Consensus size: 11
24517 ATATATAATA
*
24527 ATTATATTTAA
1 ATTATATTTAT
*
24538 AATAT-TTTAT
1 ATTATATTTAT
*
24548 ATT-TATATA-
1 ATTATATTTAT
24557 ATT-TATTTATT
1 ATTATATTTA-T
24568 AATTATATTTAT
1 -ATTATATTTAT
24580 ATTATATTT-T
1 ATTATATTTAT
*
24590 A-AATATTTTAT
1 ATTATA-TTTAT
24601 AATT-TATTTAT
1 -ATTATATTTAT
24612 ATTATAT
1 ATTATAT
24619 AAATATAATT
Statistics
Matches: 64, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
9 12 0.19
10 17 0.27
11 22 0.34
12 7 0.11
13 6 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTATATTTAT
Found at i:24587 original size:20 final size:20
Alignment explanation
Indices: 24514--24587 Score: 55
Period size: 20 Copynumber: 3.6 Consensus size: 20
24504 TATTTATAAT
*
24514 TTTATA-TATAATAATTATA
1 TTTATATTATATTAATTATA
* * *
24533 TTTAAAATATTTTATATTTATA
1 TTTATATTATATTA-A-TTATA
24555 TAATT-TATT-TATTAATTATA
1 T--TTATATTATATTAATTATA
24575 TTTATATTATATT
1 TTTATATTATATT
24588 TTAAATATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
18 2 0.05
19 9 0.21
20 15 0.36
21 2 0.05
22 10 0.24
23 2 0.05
24 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATATTATATTAATTATA
Found at i:24601 original size:21 final size:22
Alignment explanation
Indices: 24553--24609 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 22
24543 TTTATATTTA
*
24553 TATAATTTATTTATTAATTATATT
1 TATAATTTA-TT-TTAAATATATT
24577 TAT-ATTATATTTTAAATAT-TT
1 TATAATT-TATTTTAAATATATT
24598 TATAATTTATTT
1 TATAATTTATTT
24610 ATATTATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 10 0.33
22 10 0.33
23 5 0.17
24 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATAATTTATTTTAAATATATT
Found at i:24609 original size:45 final size:40
Alignment explanation
Indices: 24506--24618 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 40
24496 AATTCGTGTA
24506 TTTATAATTTTATATATAATAATTATATTTAAAATATTTTATAT
1 TTTATAA-TTTAT-T-T-ATAATTATATTTAAAATATTTTATAT
*
24550 TTATATAATTTATTTATTAATTATATTTATATTATATTTTAAATAT
1 TT-TATAATTTATTTA-TAATTATATTTA-A-AATATTTT--ATAT
24596 TTTATAATTTATTTAT-ATTATAT
1 TTTATAATTTATTTATAATTATAT
24619 AAATATAATT
Statistics
Matches: 62, Mismatches: 1, Indels: 13
0.82 0.01 0.17
Matches are distributed among these distances:
41 1 0.02
42 13 0.21
43 9 0.15
44 15 0.24
45 18 0.29
46 6 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (40 bp):
TTTATAATTTATTTATAATTATATTTAAAATATTTTATAT
Found at i:26551 original size:2 final size:2
Alignment explanation
Indices: 26544--26583 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
26534 CAATTTATCC
*
26544 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26584 GTTATGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26942 original size:32 final size:32
Alignment explanation
Indices: 26906--27050 Score: 148
Period size: 31 Copynumber: 4.3 Consensus size: 32
26896 TTTGATTGGA
*
26906 TTAAAATAATTAATAATTTAAATTTAAATAAT
1 TTAAAATAATAAATAATTTAAATTTAAATAAT
*
26938 TTAAATTAA-AAATAATTTAAATTTAAATAAT
1 TTAAAATAATAAATAATTTAAATTTAAATAAT
* * *
26969 TTAAATTAAAAAATAATTAAAATTTAAATGATTTGGAT
1 TTAAAATAATAAATAATTTAAATTTAAAT-A-----AT
* *
27007 TTAAAATAATAAATGATTTAAATTTAAAATGAT
1 TTAAAATAATAAATAATTTAAATTT-AAATAAT
27040 TATAAAATAAT
1 T-TAAAATAAT
27051 TTTAAAAATT
Statistics
Matches: 96, Mismatches: 8, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
31 30 0.31
32 26 0.27
33 4 0.04
34 9 0.09
38 23 0.24
39 4 0.04
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (32 bp):
TTAAAATAATAAATAATTTAAATTTAAATAAT
Found at i:27026 original size:17 final size:17
Alignment explanation
Indices: 27004--27050 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
26994 AAATGATTTG
27004 GATTTAAAATAATAAAT
1 GATTTAAAATAATAAAT
* *
27021 GATTTAAATTTA-AAAT
1 GATTTAAAATAATAAAT
27037 GATTATAAAATAAT
1 GATT-TAAAATAAT
27051 TTTAAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
GATTTAAAATAATAAAT
Found at i:27036 original size:16 final size:16
Alignment explanation
Indices: 26917--27016 Score: 116
Period size: 15 Copynumber: 6.4 Consensus size: 16
26907 TAAAATAATT
26917 AATAATTTAAATTT-A
1 AATAATTTAAATTTAA
*
26932 AATAATTTAAATTAAA
1 AATAATTTAAATTTAA
26948 AATAATTTAAATTT-A
1 AATAATTTAAATTTAA
*
26963 AATAATTTAAATTAAAA
1 AATAATTTAAATT-TAA
*
26980 AATAATTAAAATTT-A
1 AATAATTTAAATTTAA
* **
26995 AATGATTTGGATTTAA
1 AATAATTTAAATTTAA
27011 AATAAT
1 AATAAT
27017 AAATGATTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
15 38 0.54
16 20 0.28
17 13 0.18
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATAATTTAAATTTAA
Found at i:27358 original size:16 final size:17
Alignment explanation
Indices: 27337--27370 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
27327 GATAAATAAT
27337 TTTCA-TATTAATTTTA
1 TTTCATTATTAATTTTA
*
27353 TTTCATTTTTAATTTTA
1 TTTCATTATTAATTTTA
27370 T
1 T
27371 AAAATTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTCATTATTAATTTTA
Found at i:30619 original size:2 final size:2
Alignment explanation
Indices: 30567--30600 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
30557 GAAGCTGTCT
* *
30567 TA TA GA TA TA TG 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
30601 CAAAAATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:31971 original size:31 final size:31
Alignment explanation
Indices: 31930--32007 Score: 77
Period size: 32 Copynumber: 2.5 Consensus size: 31
31920 AAATATCTTT
* *
31930 TTTTAAATAATTATATTAATTAAATTTTAAA
1 TTTTATATAATTATATGAATTAAATTTTAAA
* * * *
31961 TTTTATATAATATTTATGACTTAATTTTTATA
1 TTTTATATAAT-TATATGAATTAAATTTTAAA
*
31993 TTTAAT-TAATTATAT
1 TTTTATATAATTATAT
32008 AATATTTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
30 4 0.11
31 14 0.37
32 20 0.53
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (31 bp):
TTTTATATAATTATATGAATTAAATTTTAAA
Found at i:32936 original size:8 final size:8
Alignment explanation
Indices: 32923--32956 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
32913 TGAACACTAT
32923 AAAAATTA
1 AAAAATTA
32931 AAAAATTA
1 AAAAATTA
32939 AAAAATTA
1 AAAAATTA
32947 AAAAATTA
1 AAAAATTA
32955 AA
1 AA
32957 GTTAATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAAATTA
Found at i:33001 original size:13 final size:13
Alignment explanation
Indices: 32983--33057 Score: 50
Period size: 15 Copynumber: 5.8 Consensus size: 13
32973 TTTTAAAAAA
32983 TAAAAATTATTTT
1 TAAAAATTATTTT
32996 T-AAAA--A-TTT
1 TAAAAATTATTTT
*
33005 TAAAAATAAATTTTT
1 TAAAAAT-TA-TTTT
*
33020 TAATAATTATTTT
1 TAAAAATTATTTT
*
33033 TTAAAATTATGTTT
1 TAAAAATTAT-TTT
*
33047 GTAAAACTTAT
1 -TAAAAATTAT
33058 AAAATTTAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
9 4 0.08
10 5 0.10
12 4 0.08
13 14 0.29
14 4 0.08
15 17 0.35
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (13 bp):
TAAAAATTATTTT
Found at i:34852 original size:16 final size:16
Alignment explanation
Indices: 34831--34863 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
34821 AAATTTCACT
34831 TAAAATATATTATAAA
1 TAAAATATATTATAAA
*
34847 TAAAATATTTTATAAA
1 TAAAATATATTATAAA
34863 T
1 T
34864 TTATAACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAATATATTATAAA
Found at i:34862 original size:28 final size:24
Alignment explanation
Indices: 34801--34862 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 24
34791 TCGTAACCTA
34801 TTTATAAAATATAAAAATAAAAAT
1 TTTATAAAATATAAAAATAAAAAT
*
34825 TTCACTTAAAATATATTATAAATAAAATAT
1 TTTA--TAAAATATA--A-AAATAAAA-AT
34855 TTTATAAA
1 TTTATAAA
34863 TTTATAACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
24 3 0.10
26 9 0.30
28 5 0.17
29 8 0.27
30 5 0.17
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (24 bp):
TTTATAAAATATAAAAATAAAAAT
Found at i:35685 original size:18 final size:17
Alignment explanation
Indices: 35636--35690 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
35626 AATTTACTTT
*
35636 TAAAATTTTTAT-AATA
1 TAAAATTTATATAAATA
35652 T-AAA-TTAT-TAACATA
1 TAAAATTTATATAA-ATA
35667 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
35685 TAAAAT
1 TAAAAT
35691 ACATTAAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
13 1 0.03
14 4 0.12
15 6 0.19
16 2 0.06
17 9 0.28
18 7 0.22
19 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:36337 original size:25 final size:26
Alignment explanation
Indices: 36309--36378 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 26
36299 TGATGAATTT
36309 ATATTATATATTTATATATT-TTAAA
1 ATATTATATATTTATATATTATTAAA
* *
36334 ATATTA-ATAATTA-ATTTTAATTAAA
1 ATATTATATATTTATATATT-ATTAAA
*
36359 AT-TTAATATATTTATTTATT
1 ATATT-ATATATTTATATATT
36379 CATATTTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
23 4 0.11
24 8 0.23
25 14 0.40
26 6 0.17
27 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATATTATATATTTATATATTATTAAA
Found at i:40466 original size:2 final size:2
Alignment explanation
Indices: 40459--40489 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40449 CTTTAATTTC
40459 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
40490 ATCCAACAAC
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:41050 original size:26 final size:27
Alignment explanation
Indices: 41001--41066 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
40991 CCCCATTTAG
* *
41001 TTGTAAAAAATGATGGTTATTTTG-GT
1 TTGTCAAAAATGGTGGTTATTTTGAGT
*
41027 TTGTCAAAAATGGTGGTT-TCTTTGATT
1 TTGTCAAAAATGGTGGTTAT-TTTGAGT
*
41054 TTGTCAAATATGG
1 TTGTCAAAAATGG
41067 GAGCTTGGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.03
26 20 0.59
27 13 0.38
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.45
Consensus pattern (27 bp):
TTGTCAAAAATGGTGGTTATTTTGAGT
Done.