Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold230
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: 2055625
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 1 of 14
Found at i:1072 original size:24 final size:20
Alignment explanation
Indices: 1006--1054 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
996 ATTAAAATTA
**
1006 AAATTTATTTATTATTTATATT
1 AAATTTATAAATTA-TTAT-TT
1028 AAATTTATAAATTATTATTT
1 AAATTTATAAATTATTATTT
1048 AAATTTA
1 AAATTTA
1055 ATTAAATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.36
21 4 0.16
22 12 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AAATTTATAAATTATTATTT
Found at i:1089 original size:16 final size:16
Alignment explanation
Indices: 1068--1104 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1058 AAATGATATT
* *
1068 ATTTATTAGATTTTAA
1 ATTTATTAAAATTTAA
1084 ATTTATTAAAATTTAA
1 ATTTATTAAAATTTAA
1100 ATTTA
1 ATTTA
1105 ATAAGTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
ATTTATTAAAATTTAA
Found at i:1234 original size:15 final size:15
Alignment explanation
Indices: 1214--1257 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1204 TTTATTCATA
1214 TAAATAATGTAAATT
1 TAAATAATGTAAATT
1229 TAAATAATGT--ATT
1 TAAATAATGTAAATT
*
1242 TAAAT-ATTTAAATT
1 TAAATAATGTAAATT
1256 TA
1 TA
1258 TTATTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 3 0.12
13 8 0.31
14 5 0.19
15 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (15 bp):
TAAATAATGTAAATT
Found at i:1286 original size:15 final size:15
Alignment explanation
Indices: 1268--1300 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1258 TTATTTATAA
1268 AAATAATATAA-ATTT
1 AAATAATA-AATATTT
1283 AAATAATAAATATTT
1 AAATAATAAATATTT
1298 AAA
1 AAA
1301 AATTTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATAATAAATATTT
Found at i:3285 original size:17 final size:17
Alignment explanation
Indices: 3265--3298 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3255 TATTTATATA
3265 AATTT-TAATATGATAAT
1 AATTTATAATAT-ATAAT
3282 AATTTATAATATATAAT
1 AATTTATAATATATAAT
3299 TTTAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AATTTATAATATATAAT
Found at i:3306 original size:13 final size:14
Alignment explanation
Indices: 3280--3308 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3270 TAATATGATA
3280 ATAATTTATAATAT
1 ATAATTTATAATAT
3294 ATAATTT-TAATAT
1 ATAATTTATAATAT
3307 AT
1 AT
3309 TCATGTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAATTTATAATAT
Found at i:3308 original size:15 final size:15
Alignment explanation
Indices: 3259--3308 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
3249 AATATATATT
3259 TATATA-AATTTTAA
1 TATATATAATTTTAA
3273 TATGATAATAA-TTT-A
1 TAT-AT-ATAATTTTAA
3288 TAATATATAATTTTAA
1 T-ATATATAATTTTAA
3304 TATAT
1 TATAT
3309 TCATGTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
14 7 0.23
15 13 0.43
16 8 0.27
17 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TATATATAATTTTAA
Found at i:3728 original size:34 final size:35
Alignment explanation
Indices: 3690--3756 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3680 AAATTAGTAG
* *
3690 ATATAATATATTAATTTTATA-TAGATAAAAATAA
1 ATATAATATATTAATCTTATATTAAATAAAAATAA
3724 ATATAATATATTAATCTTATATTAAATAAAAAT
1 ATATAATATATTAATCTTATATTAAATAAAAAT
3757 TAAAATCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 20 0.67
35 10 0.33
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (35 bp):
ATATAATATATTAATCTTATATTAAATAAAAATAA
Found at i:6480 original size:2 final size:2
Alignment explanation
Indices: 6473--6497 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6463 AACTAAATTA
6473 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 A
6498 ACATAGAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7184 original size:25 final size:25
Alignment explanation
Indices: 7115--7237 Score: 71
Period size: 25 Copynumber: 5.2 Consensus size: 25
7105 TAATGAAATT
* * *
7115 TTTATTTATA-TAATAAAAAATATA
1 TTTATTTAAATTAATAAAAATTTTA
* *
7139 ATTATTTAAATTAA-ATTAAATTTTA
1 TTTATTTAAATTAATA-AAAATTTTA
* *
7164 TTTATTTTAATTAATAAAAATATTA
1 TTTATTTAAATTAATAAAAATTTTA
* *
7189 -TT-TTTAAATT--TAAAAAATTAA
1 TTTATTTAAATTAATAAAAATTTTA
* * * *
7210 ATTAATTAAATTTAT-AAAATTTAA
1 TTTATTTAAATTAATAAAAATTTTA
7234 TTTA
1 TTTA
7238 AATCAATTTA
Statistics
Matches: 76, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
21 8 0.11
22 2 0.03
23 14 0.18
24 22 0.29
25 29 0.38
26 1 0.01
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTATTTAAATTAATAAAAATTTTA
Found at i:7190 original size:46 final size:44
Alignment explanation
Indices: 7082--7191 Score: 120
Period size: 46 Copynumber: 2.5 Consensus size: 44
7072 TTTAATTTGA
*
7082 ATAATAAT-AAAATA-TATTTAATTTAATGAAATTTTTATTTAT
1 ATAATAATAAAAATATTATTTAATTAAATGAAATTTTTATTTAT
*
7124 ATAATAA-AAAATATAATTATTTAAATTAAATTAAA-TTTTATTTATT
1 ATAATAATAAAA-AT-ATTATTT-AATTAAATGAAATTTTTATTTA-T
*
7170 TTAATTAATAAAAATATTATTT
1 ATAA-TAATAAAAATATTATTT
7192 TTAAATTTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
42 10 0.18
43 2 0.04
44 1 0.02
45 14 0.25
46 21 0.37
47 5 0.09
48 4 0.07
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (44 bp):
ATAATAATAAAAATATTATTTAATTAAATGAAATTTTTATTTAT
Found at i:7218 original size:23 final size:23
Alignment explanation
Indices: 7192--7235 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
7182 AATATTATTT
7192 TTAAATTTAAAAAATTAAATTAA
1 TTAAATTTAAAAAATTAAATTAA
* *
7215 TTAAATTTATAAAATTTAATT
1 TTAAATTTAAAAAATTAAATT
7236 TAAATCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTAAATTTAAAAAATTAAATTAA
Found at i:7546 original size:14 final size:13
Alignment explanation
Indices: 7514--7546 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
7504 AATCAATCTT
7514 AATT-TTAAAATA
1 AATTATTAAAATA
7526 AATTATTAAAATA
1 AATTATTAAAATA
7539 ATATTATT
1 A-ATTATT
7547 TATTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 9 0.47
14 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTATTAAAATA
Found at i:7551 original size:18 final size:18
Alignment explanation
Indices: 7528--7565 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
7518 TTAAAATAAA
7528 TTATTAAAATAATATTAT
1 TTATTAAAATAATATTAT
*
7546 TTATTAAAATATTATTAT
1 TTATTAAAATAATATTAT
7564 TT
1 TT
7566 TATTCTAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATTAAAATAATATTAT
Found at i:8091 original size:32 final size:33
Alignment explanation
Indices: 8031--8092 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
8021 TGAAAGCATT
* *
8031 ATTTATTTTAGCACTTTCGTTTTGAAAATGGTA
1 ATTTATTTTAGCACTTTCGTATTAAAAATGGTA
8064 ATTT-TTTTAGCATCTTT-GTATTAAAAATG
1 ATTTATTTTAGCA-CTTTCGTATTAAAAATG
8093 TTAAACCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 18 0.69
33 8 0.31
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (33 bp):
ATTTATTTTAGCACTTTCGTATTAAAAATGGTA
Found at i:12515 original size:6 final size:6
Alignment explanation
Indices: 12504--12550 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
12494 AGGTCAAATA
** *
12504 AAATTT AAATTT AAATTT AAATTTT TTATTT AAATTT AAAATT AAAT
1 AAATTT AAATTT AAATTT AAA-TTT AAATTT AAATTT AAATTT AAAT
12551 CATGATTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
6 30 0.88
7 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:12823 original size:17 final size:17
Alignment explanation
Indices: 12792--12838 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
12782 ATTTTAAAAA
*
12792 ATTAAA-AAATATTTAT
1 ATTAAATAATTATTTAT
*
12808 ATTAAATATTTATTTAT
1 ATTAAATAATTATTTAT
*
12825 ATTTAATAATTATT
1 ATTAAATAATTATT
12839 CGAGTTACGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTAAATAATTATTTAT
Found at i:14221 original size:14 final size:14
Alignment explanation
Indices: 14202--14247 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
14192 TATTTAAAAA
14202 ATAATTAAAAAATT
1 ATAATTAAAAAATT
*
14216 ATAATT--AATATT
1 ATAATTAAAAAATT
14228 -T-ATTAAAAAATT
1 ATAATTAAAAAATT
14240 ATAATTAA
1 ATAATTAA
14248 TATTATGTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
10 3 0.12
11 1 0.04
12 10 0.38
13 1 0.04
14 11 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATTAAAAAATT
Found at i:14236 original size:24 final size:24
Alignment explanation
Indices: 14205--14251 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
14195 TTAAAAAATA
14205 ATTAAAAAATTATAATTAATATTT
1 ATTAAAAAATTATAATTAATATTT
14229 ATTAAAAAATTATAATTAATATT
1 ATTAAAAAATTATAATTAATATT
14252 ATGTCCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTAAAAAATTATAATTAATATTT
Found at i:15281 original size:17 final size:17
Alignment explanation
Indices: 15256--15294 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
15246 TATGGTTAAG
15256 TATTAAATAAAAATATA
1 TATTAAATAAAAATATA
* *
15273 TATTTAATATAAATATA
1 TATTAAATAAAAATATA
15290 T-TTAA
1 TATTAA
15295 TTATTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTAAATAAAAATATA
Found at i:15983 original size:2 final size:2
Alignment explanation
Indices: 15976--16005 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15966 ATCAAATCTC
15976 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
16006 TTAACATACA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20361 original size:30 final size:30
Alignment explanation
Indices: 20312--20437 Score: 105
Period size: 30 Copynumber: 4.2 Consensus size: 30
20302 TAAATAAAAA
* *
20312 TAAATTTTAATT-TATATTAAGGAATTATT
1 TAAATTTTAATTAAATATTAAGAAATTATT
*
20341 TACATTTTAATTAAATATTAA-AAATTTATT
1 TAAATTTTAATTAAATATTAAGAAA-TTATT
* * * *
20371 TAAATATAAATTAAAATATTAAGTATTTATT
1 TAAATTTTAATT-AAATATTAAGAAATTATT
* * * *
20402 TTAATGTAAATTAAAAATTAA-AAATTTATT
1 TAAATTTTAATTAAATATTAAGAAA-TTATT
20432 TAAATT
1 TAAATT
20438 CCAGAAAAGT
Statistics
Matches: 77, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
29 14 0.18
30 38 0.49
31 24 0.31
32 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (30 bp):
TAAATTTTAATTAAATATTAAGAAATTATT
Found at i:20391 original size:31 final size:31
Alignment explanation
Indices: 20349--20436 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
20339 TTTACATTTT
20349 AATT-AAATATTAAAAATTTATTTAAATATA
1 AATTAAAATATTAAAAATTTATTTAAATATA
** * *
20379 AATTAAAATATTAAGTATTTATTTTAATGTA
1 AATTAAAATATTAAAAATTTATTTAAATATA
20410 AATTAAAA-ATTAAAAATTTATTTAAAT
1 AATTAAAATATTAAAAATTTATTTAAAT
20437 TCCAGAAAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 20 0.40
31 30 0.60
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (31 bp):
AATTAAAATATTAAAAATTTATTTAAATATA
Found at i:20701 original size:23 final size:22
Alignment explanation
Indices: 20675--20723 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
20665 CGTATGTTTC
20675 ATATCACATTTAAATTATTTTTT
1 ATATCACATTTAAATTA-TTTTT
* * *
20698 ATATTATATTTTAATTATTTTT
1 ATATCACATTTAAATTATTTTT
20720 ATAT
1 ATAT
20724 TATATTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATCACATTTAAATTATTTTT
Found at i:20721 original size:22 final size:23
Alignment explanation
Indices: 20682--20731 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
20672 TTCATATCAC
20682 ATTTAAATTATTTTTTATATTAT
1 ATTTAAATTATTTTTTATATTAT
*
20705 ATTTTAATTA-TTTTTATATTAT
1 ATTTAAATTATTTTTTATATTAT
20727 ATTTA
1 ATTTA
20732 TATCATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
ATTTAAATTATTTTTTATATTAT
Found at i:20725 original size:11 final size:11
Alignment explanation
Indices: 20683--20734 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
20673 TCATATCACA
*
20683 TTTAAATTATTT
1 TTTATATTA-TT
20695 TTTATATTATAT
1 TTTATATTAT-T
20707 TTTA-ATTATT
1 TTTATATTATT
*
20717 TTTATATTATA
1 TTTATATTATT
20728 TTTATAT
1 TTTATAT
20735 CATATAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
10 5 0.14
11 18 0.50
12 13 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTATATTATT
Found at i:20739 original size:11 final size:11
Alignment explanation
Indices: 20695--20739 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
20685 TAAATTATTT
20695 TTTATATTATA
1 TTTATATTATA
*
20706 TTT-TAATTATT
1 TTTAT-ATTATA
20717 TTTATATTATA
1 TTTATATTATA
*
20728 TTTATATCATA
1 TTTATATTATA
20739 T
1 T
20740 AATATAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 1 0.03
11 27 0.93
12 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTATATTATA
Found at i:20905 original size:1 final size:1
Alignment explanation
Indices: 20899--20926 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
20889 ATGTTTAAGG
20899 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
20927 CCTGGTAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:21086 original size:2 final size:2
Alignment explanation
Indices: 21081--21113 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21071 TCATTAAGCT
21081 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
21114 GTATTCTTTG
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:21268 original size:33 final size:34
Alignment explanation
Indices: 21217--21280 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
21207 AGGTTTAACA
*
21217 ATTTTAATTTAAACTTTAAAAATTTAATTAATTT
1 ATTTAAATTTAAACTTTAAAAATTTAATTAATTT
*
21251 ATTTAAATTTAAA-TTTAATAATTTAATTAA
1 ATTTAAATTTAAACTTTAAAAATTTAATTAA
21281 AAAATTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (34 bp):
ATTTAAATTTAAACTTTAAAAATTTAATTAATTT
Found at i:21337 original size:21 final size:22
Alignment explanation
Indices: 21313--21357 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
21303 AATTAATTTG
21313 AATCTAAAATGATTT-AAATTA
1 AATCTAAAATGATTTAAAATTA
* *
21334 AATCTGAAATTATTTAAAATTA
1 AATCTAAAATGATTTAAAATTA
21356 AA
1 AA
21358 AAGATTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (22 bp):
AATCTAAAATGATTTAAAATTA
Found at i:21476 original size:29 final size:29
Alignment explanation
Indices: 21441--21525 Score: 76
Period size: 29 Copynumber: 3.0 Consensus size: 29
21431 AAATTTGATT
21441 AATTTAAATTTAAACTCAAAATAATTAAA
1 AATTTAAATTTAAACTCAAAATAATTAAA
21470 AATTT-AA-TT-AACATC-AAAT-ATT--A
1 AATTTAAATTTAAAC-TCAAAATAATTAAA
*
21493 AATTTAAATGATCTAAACTTAAAATAATTAAA
1 AATTTAAAT--T-TAAACTCAAAATAATTAAA
21525 A
1 A
21526 TTAAAAAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 19
0.69 0.02 0.30
Matches are distributed among these distances:
23 6 0.14
24 2 0.05
25 3 0.07
26 7 0.16
27 5 0.11
28 4 0.09
29 12 0.27
30 3 0.07
32 2 0.05
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.35
Consensus pattern (29 bp):
AATTTAAATTTAAACTCAAAATAATTAAA
Found at i:21552 original size:19 final size:17
Alignment explanation
Indices: 21511--21553 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
21501 TGATCTAAAC
21511 TTAAAATAATTAAAATT
1 TTAAAATAATTAAAATT
**
21528 AAAAAATAATTTTAAAATT
1 TTAAAATAA--TTAAAATT
21547 TTAAAAT
1 TTAAAAT
21554 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 7 0.35
19 13 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAATAATTAAAATT
Found at i:21577 original size:27 final size:25
Alignment explanation
Indices: 21518--21577 Score: 59
Period size: 27 Copynumber: 2.2 Consensus size: 25
21508 AACTTAAAAT
21518 AATTAAAATTAAAAAATAATTTTAA
1 AATTAAAATTAAAAAATAATTTTAA
*
21543 AATTTTAAAATTTAAAATAAT-ATTATTCA
1 AA--TTAAAA-TTAAAA-AATAATT-TTAA
21572 AATTAA
1 AATTAA
21578 TTCGATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
25 2 0.07
27 10 0.34
28 9 0.31
29 8 0.28
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
AATTAAAATTAAAAAATAATTTTAA
Found at i:25727 original size:20 final size:19
Alignment explanation
Indices: 25655--25738 Score: 56
Period size: 20 Copynumber: 4.5 Consensus size: 19
25645 TATTTATGTT
25655 TTTTATTTA-TAATA-TTA
1 TTTTATTTATTAATATTTA
*
25672 TATT-TTTATATAA-A--TA
1 TTTTATTTAT-TAATATTTA
25688 TTTTATTTATTAATAATTTA
1 TTTTATTTATTAAT-ATTTA
25708 TTTTATTTTATGTAAT-TTTA
1 TTTTA-TTTAT-TAATATTTA
*
25728 TATATATTTAT
1 T-TTTATTTAT
25739 ATTCGTGTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
16 12 0.22
17 9 0.17
18 4 0.07
20 17 0.31
21 8 0.15
22 4 0.07
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTTATTTATTAATATTTA
Found at i:26283 original size:20 final size:19
Alignment explanation
Indices: 26241--26284 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
26231 GTGAGGAGAG
* *
26241 AAAAAAAGAAAAGAAAGAG
1 AAAAAAAGAAAACAAAGAA
*
26260 AAAAAAAGAAAAACAAATAA
1 AAAAAAAG-AAAACAAAGAA
26280 AAAAA
1 AAAAA
26285 CTTTTGTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.02
Consensus pattern (19 bp):
AAAAAAAGAAAACAAAGAA
Found at i:26284 original size:19 final size:19
Alignment explanation
Indices: 26237--26276 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
26227 GTTCGTGAGG
*
26237 AGAGAAAAAAAGAAAAGAA
1 AGAGAAAAAAAGAAAACAA
26256 AGAGAAAAAAAGAAAAACAA
1 AGAGAAAAAAAG-AAAACAA
26276 A
1 A
26277 TAAAAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (19 bp):
AGAGAAAAAAAGAAAACAA
Found at i:26928 original size:23 final size:24
Alignment explanation
Indices: 26883--26936 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
26873 TTTGTATCAT
* * *
26883 ATTTATATTATTTTTTATGTTATG
1 ATTTATATTATTCTCTATATTATG
26907 ATTTA-ATTATTCTCTATATTAT-
1 ATTTATATTATTCTCTATATTATG
*
26929 ATTCATAT
1 ATTTATAT
26937 CGTGTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 4 0.16
23 16 0.64
24 5 0.20
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.61
Consensus pattern (24 bp):
ATTTATATTATTCTCTATATTATG
Found at i:27209 original size:29 final size:29
Alignment explanation
Indices: 27153--27209 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
27143 AGTATTATTT
* **
27153 TTATTTATAAAAATATTAAAATTTAATTA
1 TTATTAATAAAAATATTAAAATAAAATTA
27182 TTATTAATAAAAAT-TATAAAATAAAATT
1 TTATTAATAAAAATAT-TAAAATAAAATT
27210 GAAAAGCCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TTATTAATAAAAATATTAAAATAAAATTA
Found at i:27347 original size:4 final size:4
Alignment explanation
Indices: 27338--27391 Score: 53
Period size: 4 Copynumber: 14.2 Consensus size: 4
27328 GAGATGGGAG
* *
27338 AGAA AGAA AGAA AGAA AGAA TG-G AGAA A-AA A-AA A-AA AGAAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG-AA AGAA
27383 AGAA AGAA A
1 AGAA AGAA A
27392 AAGAAGGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
3 10 0.23
4 29 0.67
5 4 0.09
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:28602 original size:12 final size:12
Alignment explanation
Indices: 28585--28609 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28575 TTAGGGGTAG
28585 GAAAGAAAGGAA
1 GAAAGAAAGGAA
28597 GAAAGAAAGGAA
1 GAAAGAAAGGAA
28609 G
1 G
28610 GAGAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (12 bp):
GAAAGAAAGGAA
Found at i:28610 original size:16 final size:15
Alignment explanation
Indices: 28585--28623 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
28575 TTAGGGGTAG
28585 GAAAGAAAGGAAGAAA
1 GAAAGAAAGG-AGAAA
*
28601 GAAAGGAAGGAGAAA
1 GAAAGAAAGGAGAAA
*
28616 AAAAGAAA
1 GAAAGAAA
28624 AAGAAAAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (15 bp):
GAAAGAAAGGAGAAA
Found at i:28630 original size:11 final size:10
Alignment explanation
Indices: 28613--28649 Score: 56
Period size: 11 Copynumber: 3.5 Consensus size: 10
28603 AAGGAAGGAG
28613 AAAAAAAGAA
1 AAAAAAAGAA
28623 AAAGAAAAGATA
1 AAA-AAAAGA-A
28635 AAAAAAAGAA
1 AAAAAAAGAA
28645 AAAAA
1 AAAAA
28650 TTTATATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.36
11 12 0.48
12 4 0.16
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:29618 original size:8 final size:8
Alignment explanation
Indices: 29589--29667 Score: 90
Period size: 8 Copynumber: 9.6 Consensus size: 8
29579 TATTTTTGTC
29589 AAAAAAGA
1 AAAAAAGA
*
29597 AAGAAAAAA
1 AA-AAAAGA
29606 GAAAAAAG-
1 -AAAAAAGA
29614 AAAAAAGA
1 AAAAAAGA
29622 AAAAAAGA
1 AAAAAAGA
29630 AAAAAA-A
1 AAAAAAGA
*
29637 GAAAGAAGA
1 -AAAAAAGA
29646 AAAAAAGA
1 AAAAAAGA
29654 AAAAAAGA
1 AAAAAAGA
29662 GAAAAA
1 -AAAAA
29668 CTTATGTATT
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
7 8 0.13
8 36 0.59
9 15 0.25
10 2 0.03
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:29627 original size:24 final size:23
Alignment explanation
Indices: 29589--29667 Score: 104
Period size: 24 Copynumber: 3.3 Consensus size: 23
29579 TATTTTTGTC
29589 AAAAAAGAAAGAAAAAAGAAAAAAG
1 AAAAAAGAAA-AAAAAA-AAAAAAG
29614 AAAAAAGAAAAAAAGAAAAAAAAG
1 AAAAAAGAAAAAAA-AAAAAAAAG
* *
29638 AAAGAAGAAAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAAAAAAAAAG
29661 AGAAAAA
1 A-AAAAA
29668 CTTATGTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
23 9 0.18
24 28 0.57
25 12 0.24
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAAAAAAAAAAAAAAG
Found at i:29666 original size:7 final size:7
Alignment explanation
Indices: 29596--29658 Score: 81
Period size: 7 Copynumber: 8.4 Consensus size: 7
29586 GTCAAAAAAG
29596 AAAGAAA
1 AAAGAAA
29603 AAAGAAA
1 AAAGAAA
29610 AAAGAAA
1 AAAGAAA
29617 AAAGAAAA
1 AAAG-AAA
29625 AAAGAAAAA
1 AAAG--AAA
29634 AAAGAAA
1 AAAGAAA
*
29641 GAAGAAAA
1 AAAG-AAA
29649 AAAGAAA
1 AAAGAAA
29656 AAA
1 AAA
29659 AGAGAAAAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
7 30 0.59
8 13 0.25
9 8 0.16
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:29667 original size:1 final size:1
Alignment explanation
Indices: 29589--29659 Score: 52
Period size: 1 Copynumber: 71.0 Consensus size: 1
29579 TATTTTTGTC
* * * * * * * * * *
29589 AAAAAAGAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAAGAAAAAAAAGAAAGAAGAAAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29654 AAAAAA
1 AAAAAA
29660 GAGAAAAACT
Statistics
Matches: 50, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (1 bp):
A
Found at i:30461 original size:27 final size:25
Alignment explanation
Indices: 30400--30537 Score: 91
Period size: 28 Copynumber: 5.2 Consensus size: 25
30390 TAATTATTTA
* * *
30400 TTTAT-TTATATTTTGATATTGACAT
1 TTTATATTATTTTTTAATATT-ATAT
30425 GTTTATATTATTTTTGTATCATATTATAT
1 -TTTATATTATTTTT-TA--ATATTATAT
30454 TTTA-ATTATTTTTTAATATTATAT
1 TTTATATTATTTTTTAATATTATAT
* * *
30478 TTATATTTTATTTTAATTTATCTTATAT
1 TT-TATATTATTTT--TTAATATTATAT
* *
30506 TTTATATAAATTTTTTATATAATTAAAT
1 TTTATAT-TATTTTTTA-AT-ATTATAT
30534 TTTA
1 TTTA
30538 AATTTAAATT
Statistics
Matches: 90, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
24 11 0.12
25 2 0.02
26 16 0.18
27 22 0.24
28 31 0.34
29 3 0.03
30 5 0.06
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (25 bp):
TTTATATTATTTTTTAATATTATAT
Found at i:30496 original size:11 final size:11
Alignment explanation
Indices: 30451--30510 Score: 52
Period size: 12 Copynumber: 5.3 Consensus size: 11
30441 TATCATATTA
30451 TATTTTAATTAT
1 TATTTTAATT-T
*
30463 T-TTTTAATAT
1 TATTTTAATTT
30473 TATATTTATATTT
1 TAT-TTTA-ATTT
30486 TATTTTAA-TT
1 TATTTTAATTT
*
30496 TATCTTATATTT
1 TATTTTA-ATTT
30508 TAT
1 TAT
30511 ATAAATTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
10 10 0.25
11 10 0.25
12 14 0.35
13 6 0.15
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTTTAATTT
Found at i:30506 original size:22 final size:24
Alignment explanation
Indices: 30464--30510 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
30454 TTTAATTATT
*
30464 TTTTAATATTATATTTATATTTTA
1 TTTTAATATTATACTTATATTTTA
30488 TTTTAAT-TTAT-CTTATATTTTA
1 TTTTAATATTATACTTATATTTTA
30510 T
1 T
30511 ATAAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 4 0.18
24 7 0.32
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTAATATTATACTTATATTTTA
Found at i:30511 original size:35 final size:35
Alignment explanation
Indices: 30445--30512 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
30435 TTTTTGTATC
* *
30445 ATATTATATTTTAATTATTTTTTAATATTATATTT
1 ATATTATATTTTAATTATATCTTAATATTATATTT
* *
30480 ATATTTTATTTTAATT-TATCTTATATTTTATAT
1 ATATTATATTTTAATTATATCTTA-ATATTATAT
30513 AAATTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 5 0.18
35 23 0.82
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (35 bp):
ATATTATATTTTAATTATATCTTAATATTATATTT
Found at i:30526 original size:22 final size:22
Alignment explanation
Indices: 30478--30525 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
30468 AATATTATAT
* *
30478 TTATATTTTATTTTAATTTATC
1 TTATATTTTATATAAATTTATC
30500 TTATATTTTATATAAATTT-T-
1 TTATATTTTATATAAATTTATC
30520 TTATAT
1 TTATAT
30526 AATTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.25
21 1 0.04
22 17 0.71
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATATTTTATATAAATTTATC
Found at i:30593 original size:43 final size:40
Alignment explanation
Indices: 30529--30609 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 40
30519 TTTATATAAT
30529 TAAATTTTAAATTTAAATTTATGT-ATTAAATAATTTTAAA
1 TAAATTTTAAATTTAAATTTATGTAATTAAA-AATTTTAAA
* *
30569 TAAATTTTATTAATTATAATTTTATTTAATTAAAAATTTTA
1 TAAATTTTA--AATT-TAAATTTATGTAATTAAAAATTTTA
30610 TAAATATTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
40 9 0.26
42 4 0.11
43 16 0.46
44 6 0.17
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (40 bp):
TAAATTTTAAATTTAAATTTATGTAATTAAAAATTTTAAA
Found at i:30597 original size:16 final size:17
Alignment explanation
Indices: 30570--30610 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
30560 AATTTTAAAT
30570 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
30585 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
30602 AAATTTTAT
1 AAATTTTAT
30611 AAATATTACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:31953 original size:16 final size:16
Alignment explanation
Indices: 31934--32023 Score: 51
Period size: 16 Copynumber: 5.4 Consensus size: 16
31924 TATATAATAA
31934 TTATATTTTAAATATT
1 TTATATTTTAAATATT
31950 TTATATTTATATAA-ATT
1 TTATATTT-TA-AATATT
** *
31967 TTGATACATT-AATAAT
1 TT-ATATTTTAAATATT
31983 TTATATTATATAAAT-TT
1 TTATATT-T-TAAATATT
* *
32000 TAAAATATTTAAATATT
1 TTATAT-TTTAAATATT
32017 TATATAT
1 T-TATAT
32024 ATATTTTTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 18
0.66 0.12 0.22
Matches are distributed among these distances:
15 5 0.09
16 18 0.33
17 18 0.33
18 13 0.24
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (16 bp):
TTATATTTTAAATATT
Found at i:32025 original size:32 final size:33
Alignment explanation
Indices: 31940--32027 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 33
31930 ATAATTATAT
* *
31940 TTTAAATATTTTATATTTATATAAATTTTGATACA
1 TTTAAATA-TTTATA-TTATATAAATTTTAAAACA
*
31975 -TT-AATAATTTATATTATATAAATTTTAAAATA
1 TTTAAAT-ATTTATATTATATAAATTTTAAAACA
32007 TTTAAATATTTATATATATAT
1 TTTAAATATTTATAT-TATAT
32028 TTTTGTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
32 16 0.35
33 19 0.41
34 11 0.24
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (33 bp):
TTTAAATATTTATATTATATAAATTTTAAAACA
Found at i:32380 original size:17 final size:18
Alignment explanation
Indices: 32354--32400 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
32344 AATCTTGAAT
*
32354 TTAAAGAAAATA-ATTTA
1 TTAAATAAAATATATTTA
* *
32371 TTAAATAAAAAATATTTT
1 TTAAATAAAATATATTTA
32389 TTAAAATAAAAT
1 TT-AAATAAAAT
32401 TTTAACAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 10 0.42
18 6 0.25
19 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
TTAAATAAAATATATTTA
Found at i:32387 original size:18 final size:20
Alignment explanation
Indices: 32360--32399 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
32350 GAATTTAAAG
32360 AAAATAATTTATT-AAATAA
1 AAAATAATTTATTAAAATAA
*
32379 AAAAT-ATTTTTTAAAATAA
1 AAAATAATTTATTAAAATAA
32398 AA
1 AA
32400 TTTTAACAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATAATTTATTAAAATAA
Found at i:32552 original size:2 final size:2
Alignment explanation
Indices: 32545--32574 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
32535 ACAAAATTTA
32545 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
32575 TTAGAACTCA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36181 original size:5 final size:5
Alignment explanation
Indices: 36120--36162 Score: 79
Period size: 5 Copynumber: 8.8 Consensus size: 5
36110 CTCTTTCGAC
36120 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA -TTAA TTTA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
36163 TATAATATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 33 0.89
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:36781 original size:20 final size:20
Alignment explanation
Indices: 36758--36796 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
36748 TTTGTAATAT
36758 TAAATAAATAATAAATATAG
1 TAAATAAATAATAAATATAG
*
36778 TAAATAATTAATAAATATA
1 TAAATAAATAATAAATATA
36797 TATTTTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
TAAATAAATAATAAATATAG
Found at i:37159 original size:18 final size:18
Alignment explanation
Indices: 37138--37178 Score: 68
Period size: 16 Copynumber: 2.4 Consensus size: 18
37128 AAACGTATAT
37138 AAAATTATAAAAGTGTAC
1 AAAATTATAAAAGTGTAC
37156 AAAA-T-TAAAAGTGTAC
1 AAAATTATAAAAGTGTAC
37172 AAAATTA
1 AAAATTA
37179 ACTTATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 15 0.71
17 2 0.10
18 4 0.19
ACGTcount: A:0.59, C:0.05, G:0.10, T:0.27
Consensus pattern (18 bp):
AAAATTATAAAAGTGTAC
Found at i:37166 original size:16 final size:16
Alignment explanation
Indices: 37145--37179 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
37135 TATAAAATTA
37145 TAAAAGTGTACAAAAT
1 TAAAAGTGTACAAAAT
37161 TAAAAGTGTACAAAAT
1 TAAAAGTGTACAAAAT
37177 TAA
1 TAA
37180 CTTATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (16 bp):
TAAAAGTGTACAAAAT
Found at i:37425 original size:15 final size:16
Alignment explanation
Indices: 37405--37437 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
37395 TATATAAAAA
37405 ATTAAAT-ATATTTAT
1 ATTAAATAATATTTAT
37420 ATTAAATACATATTTAT
1 ATTAAATA-ATATTTAT
37437 A
1 A
37438 ATTGATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTAAATAATATTTAT
Found at i:37567 original size:28 final size:27
Alignment explanation
Indices: 37512--37567 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
37502 TTACTTTGTA
*
37512 TTTGTCAAAAATAGTGGATTTTTTTTG
1 TTTGTCAAAAATAGTGGATTTTATTTG
*
37539 TTTGTCAAAAATTGT-GACTTGTTATTTG
1 TTTGTCAAAAATAGTGGA-TT-TTATTTG
37567 T
1 T
37568 CAAAATTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 2 0.08
27 16 0.64
28 7 0.28
ACGTcount: A:0.25, C:0.05, G:0.18, T:0.52
Consensus pattern (27 bp):
TTTGTCAAAAATAGTGGATTTTATTTG
Found at i:37588 original size:51 final size:53
Alignment explanation
Indices: 37478--37588 Score: 129
Period size: 51 Copynumber: 2.1 Consensus size: 53
37468 AAAAGCCACC
* * *
37478 ATTTGTGTTTGTCAAAAATGATAGTTACTTTGTATTTGTCAAAAATAGTGGATT
1 ATTTTTGTTTGTCAAAAAT-ATAGTGACTTTGTATTTGTCAAAAATAGTGGATA
* * *
37532 TTTTTTGTTTGTCAAAAAT-T-GTGAC-TTGTTATTTGTCAAAATTAGTGGCTA
1 ATTTTTGTTTGTCAAAAATATAGTGACTTTG-TATTTGTCAAAAATAGTGGATA
37583 ATTTTT
1 ATTTTT
37589 ATTGCAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
50 3 0.06
51 28 0.57
52 1 0.02
54 17 0.35
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.49
Consensus pattern (53 bp):
ATTTTTGTTTGTCAAAAATATAGTGACTTTGTATTTGTCAAAAATAGTGGATA
Found at i:42101 original size:26 final size:27
Alignment explanation
Indices: 42045--42101 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
42035 AAAAGCTATC
* *
42045 CTTTGTATTTATCAAAAATAGTGGTTA
1 CTTTGTATTTATCAAAAATAGTAGATA
42072 CTTTGTATTTATCAAAAATAGTAGAT-
1 CTTTGTATTTATCAAAAATAGTAGATA
42098 CTTT
1 CTTT
42102 TTTTGTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (27 bp):
CTTTGTATTTATCAAAAATAGTAGATA
Found at i:42357 original size:22 final size:21
Alignment explanation
Indices: 42315--42357 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
42305 ATCTTTAGTG
** *
42315 TTTTATTTTTTCTTTTATTAT
1 TTTTATTTTTTCAATAATTAT
42336 TTTTATTTTTTCAATAACTTAT
1 TTTTATTTTTTCAATAA-TTAT
42358 AAGTGAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTATTTTTTCAATAATTAT
Found at i:42896 original size:16 final size:18
Alignment explanation
Indices: 42875--42915 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
42865 ATAATTTAAG
*
42875 TAAATTATATTT-GAA-T
1 TAAATTATATTTAAAAGT
42891 TAAATT-TATTTAAAAGT
1 TAAATTATATTTAAAAGT
42908 TAAATTAT
1 TAAATTAT
42916 TTATTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.24
16 8 0.38
17 7 0.33
18 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
TAAATTATATTTAAAAGT
Found at i:43449 original size:18 final size:17
Alignment explanation
Indices: 43426--43482 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 17
43416 ATGTTTATGA
43426 TTAATATAAAATAAGTTT
1 TTAATATAAAATAA-TTT
*
43444 TTAATATATTAATATATTT
1 TTAATATA-AAATA-ATTT
*
43463 TAAATAGTAAAATAATTT
1 TTAATA-TAAAATAATTT
43481 TT
1 TT
43483 TATTTAAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 13 0.41
19 16 0.50
20 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (17 bp):
TTAATATAAAATAATTT
Found at i:43521 original size:38 final size:38
Alignment explanation
Indices: 43463--43562 Score: 105
Period size: 39 Copynumber: 2.6 Consensus size: 38
43453 TAATATATTT
* * *
43463 TAAATAGTAAAATAATTTTTTATTT-AAGTTAATTTTAA
1 TAAATAATAAAATTA-TTTTTATTTAAAGTTAATTATAA
*
43501 GTAAATAATAAAATTATTTTTATTTAAATTTAATTATAA
1 -TAAATAATAAAATTATTTTTATTTAAAGTTAATTATAA
* *
43540 AAAATATATAAAA-TATTTATATT
1 TAAATA-ATAAAATTATTTTTATT
43563 GATTATATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
38 23 0.43
39 30 0.57
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (38 bp):
TAAATAATAAAATTATTTTTATTTAAAGTTAATTATAA
Found at i:43579 original size:357 final size:359
Alignment explanation
Indices: 43146--43876 Score: 1193
Period size: 357 Copynumber: 2.0 Consensus size: 359
43136 AATTATTATT
43146 TAAATAATAAAAATATTTTTATTTAAATTTAATTATAAAAATATATAAAATATTTATACTGATTA
1 TAAATAATAAAAATATTTTTATTTAAATTTAATTATAAAAATATATAAAATATTTATACTGATTA
* *
43211 TATAATTTTTAATTGAGTTAGTATTATAATTTAATGAAATATTAATTTATTCAATGAAATTATTT
66 TATAATTTTTAACTGAGTTAGTATTACAATTTAATGAAATATTAATTTATTCAATGAAATTATTT
* * *
43276 AATAATTTATTAAAATAATAACAATAAGACCATTATGTATTTTTTATATTTAAAAAATTTACTCA
131 AAAAATTTATTAAAATAATAACAATAAGACCATGATGTATTTTTTATATTTAAAAAAATTACTCA
*
43341 CT-TGTGT-CTGAACTA-TTTTTTCTCTTTTAAAACATCTTTAGTCAATTTTTTTTCTTGGCCCA
196 CTCTGTCTACTGAACTATTTTTTTCTCTTTTAAAACATCTTTAGTCAA-TTTTTTTCTTGGCCCA
* *
43403 CGTGGT-GACCAAAATGTTTATGATTAATATAAAATAAGTTTTTAATATATTAATATATTTTAAA
260 CGTGGTGGACCAAAATGTTTATGATTAATATAAAATAAATTTTTAATATATTAATACATTTTAAA
*
43467 TAGTAAAATAA-TTTTTTATTTAAGTTAATTTTAAG
325 TAGTAAAATAATTTTTTTATTCAA-TTAATTTTAAG
* *
43502 TAAATAATAAAATTATTTTTATTTAAATTTAATTATAAAAAATATATAAAATATTTATATTGATT
1 TAAATAATAAAAATATTTTTATTTAAATTTAATTAT-AAAAATATATAAAATATTTATACTGATT
43567 ATATAATTTTTAACTGAGTTAGTATTACAATTTAATGAAATATTAATTTATTCAATGAAATTATT
65 ATATAATTTTTAACTGAGTTAGTATTACAATTTAATGAAATATTAATTTATTCAATGAAATTATT
*
43632 TAAAAATTTATTAAAATAATAACAATAAGATCATGATGTATTTTTTATATTTAAAAAAATTACTC
130 TAAAAATTTATTAAAATAATAACAATAAGACCATGATGTATTTTTTATATTTAAAAAAATTACTC
43697 ACTCGTGTCTAACAAACTGAACTATTTTTTTTCTCTTTTAAAACATCTTTAGTCAATTTTTTTCT
195 ACTC-TGTCT-----ACTGAACTA-TTTTTTTCTCTTTTAAAACATCTTTAGTCAATTTTTTTCT
*
43762 TTGCCCACGTGGTGGACCAAAATGTTTATGATTAATATAAAATAAATTTTTAATATATTAATACA
253 TGGCCCACGTGGTGGACCAAAATGTTTATGATTAATATAAAATAAATTTTTAATATATTAATACA
* *
43827 TTTTAAATAGTAAAATAATTTTTTTATTCGATTAATTTTGAG
318 TTTTAAATAGTAAAATAATTTTTTTATTCAATTAATTTTAAG
*
43869 CAAATAAT
1 TAAATAAT
43877 TTTTTATTTG
Statistics
Matches: 346, Mismatches: 16, Indels: 15
0.92 0.04 0.04
Matches are distributed among these distances:
356 35 0.10
357 154 0.45
359 4 0.01
365 8 0.02
366 21 0.06
367 114 0.33
368 10 0.03
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (359 bp):
TAAATAATAAAAATATTTTTATTTAAATTTAATTATAAAAATATATAAAATATTTATACTGATTA
TATAATTTTTAACTGAGTTAGTATTACAATTTAATGAAATATTAATTTATTCAATGAAATTATTT
AAAAATTTATTAAAATAATAACAATAAGACCATGATGTATTTTTTATATTTAAAAAAATTACTCA
CTCTGTCTACTGAACTATTTTTTTCTCTTTTAAAACATCTTTAGTCAATTTTTTTCTTGGCCCAC
GTGGTGGACCAAAATGTTTATGATTAATATAAAATAAATTTTTAATATATTAATACATTTTAAAT
AGTAAAATAATTTTTTTATTCAATTAATTTTAAG
Found at i:43829 original size:19 final size:18
Alignment explanation
Indices: 43793--43849 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
43783 ATGTTTATGA
43793 TTAATATAAAATAAATTT
1 TTAATATAAAATAAATTT
* *
43811 TTAATATATTAATACATTT
1 TTAATATA-AAATAAATTT
*
43830 TAAATAGTAAAAT-AATTT
1 TTAATA-TAAAATAAATTT
43848 TT
1 TT
43850 TTATTCGATT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
18 13 0.42
19 16 0.52
20 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATATAAAATAAATTT
Found at i:44408 original size:60 final size:57
Alignment explanation
Indices: 44273--44408 Score: 145
Period size: 57 Copynumber: 2.3 Consensus size: 57
44263 ATTTATGTTT
* *
44273 TTATATTATATTTATATATATTATTATGTTATAATTAAATTTAAAATATTTTATATA
1 TTATATTATATTTATATATATAATAATGTTATAATTAAATTTAAAATATTTTATATA
*
44330 TT-TATATAAATTTA-ATATATTAATAAT-TTATATATGATAAATATTAAAATATATATT-TATA
1 TTATAT-TATATTTATATATA-TAATAATGTTATA-AT--TAAAT-TTAAAATAT-T-TTATATA
44391 TTATATTATATTTATATA
1 TTATATTATATTTATATA
44409 ATAGTACCTA
Statistics
Matches: 65, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
56 13 0.20
57 16 0.25
59 5 0.08
60 9 0.14
61 14 0.22
62 8 0.12
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (57 bp):
TTATATTATATTTATATATATAATAATGTTATAATTAAATTTAAAATATTTTATATA
Found at i:48358 original size:2 final size:2
Alignment explanation
Indices: 48346--48375 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
48336 GCTAGGCAAA
48346 AT AT GAT 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 A
48376 GATGAACCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:49531 original size:47 final size:47
Alignment explanation
Indices: 49462--49555 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
49452 CCTGGAAAAA
* *
49462 CGTGCATAGGGCCAACTTTGGACGCCATTGTTTTGGAGTCGTGAGGC
1 CGTGCAAAGGGCCAACTTTGGACGCCATTATTTTGGAGTCGTGAGGC
49509 CGTGCAAAGGGCCAACTTTGGACGCCATTATTTTGGAGTCGTGAGGC
1 CGTGCAAAGGGCCAACTTTGGACGCCATTATTTTGGAGTCGTGAGGC
49556 TGAGATTCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.27
Consensus pattern (47 bp):
CGTGCAAAGGGCCAACTTTGGACGCCATTATTTTGGAGTCGTGAGGC
Found at i:49860 original size:17 final size:17
Alignment explanation
Indices: 49838--49883 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
49828 AGTAAAATTA
49838 AATTAAAAATATATATT
1 AATTAAAAATATATATT
*
49855 AATTAAATAAT-T-TTTT
1 AATTAAA-AATATATATT
*
49871 AAATAAAAATATA
1 AATTAAAAATATA
49884 ATTTCGAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.12
16 10 0.42
17 8 0.33
18 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTAAAAATATATATT
Found at i:50517 original size:11 final size:10
Alignment explanation
Indices: 50496--50558 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
50486 AAAGATATAA
50496 ATATA-AAAT
1 ATATATAAAT
50505 ATGATATAAAT
1 AT-ATATAAAT
50516 ATATTATAAAT
1 ATA-TATAAAT
50527 -TAT-T-AAT
1 ATATATAAAT
50534 ATAT-TAAAAT
1 ATATAT-AAAT
*
50544 TTATATAAAT
1 ATATATAAAT
50554 ATATA
1 ATATA
50559 ATATTTTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
7 3 0.07
8 5 0.11
9 3 0.07
10 20 0.44
11 14 0.31
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (10 bp):
ATATATAAAT
Found at i:50566 original size:20 final size:20
Alignment explanation
Indices: 50490--50561 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 20
50480 AAAATTAAAG
* *
50490 ATATAAATATA-AA-ATATG
1 ATATAAATATATAATAAATT
*
50508 ATATAAATATATTATAAATT
1 ATATAAATATATAATAAATT
*
50528 AT-T-AATATATTAA-AATTT
1 ATATAAATATA-TAATAAATT
50546 ATATAAATATATAATA
1 ATATAAATATATAATA
50562 TTTTAAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
18 23 0.53
19 8 0.19
20 12 0.28
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (20 bp):
ATATAAATATATAATAAATT
Found at i:50580 original size:20 final size:18
Alignment explanation
Indices: 50511--50579 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 18
50501 AAATATGATA
50511 TAAATATATTATAAATTAT
1 TAAATATATTATAAATT-T
50530 T-AATATATTA-AAATTT
1 TAAATATATTATAAATTT
50546 ATATAA-ATA-TATAATATTT
1 -TA-AATATATTATAA-ATTT
50565 TAAATATAATTATAA
1 TAAATAT-ATTATAA
50580 TGTATAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
16 1 0.02
17 10 0.24
18 18 0.43
19 8 0.19
20 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAATATATTATAAATTT
Found at i:50597 original size:23 final size:23
Alignment explanation
Indices: 50566--50621 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
50556 ATAATATTTT
50566 AAATATAATTATA-ATGTATAAAA
1 AAATATAATTATAGAT-TATAAAA
* * *
50589 AAATTTAATTTTAGATTATAAAT
1 AAATATAATTATAGATTATAAAA
50612 AAATA-AATTA
1 AAATATAATTA
50622 GGCTATGCCC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 4 0.15
23 21 0.78
24 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
AAATATAATTATAGATTATAAAA
Found at i:53167 original size:30 final size:30
Alignment explanation
Indices: 53126--53219 Score: 125
Period size: 30 Copynumber: 3.1 Consensus size: 30
53116 AAAAAACTAA
* *
53126 TATCACTTAGATTAAGGACTAGTACACCAC
1 TATCCCTTAGATTAAGGACTAGTGCACCAC
* *
53156 TATCCCTTAGATTAAAGACTAGTGCATCAC
1 TATCCCTTAGATTAAGGACTAGTGCACCAC
* * *
53186 TATTCCTTAAATTAAGGACTAATGCACCAC
1 TATCCCTTAGATTAAGGACTAGTGCACCAC
53216 TATC
1 TATC
53220 TAATTTAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (30 bp):
TATCCCTTAGATTAAGGACTAGTGCACCAC
Found at i:56757 original size:21 final size:21
Alignment explanation
Indices: 56731--56770 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
56721 GTACATATAC
*
56731 CTGCAGGTTTCTTCAGGTTTG
1 CTGCAGGTTTCTCCAGGTTTG
56752 CTGCAGGTTTCTCCAGGTT
1 CTGCAGGTTTCTCCAGGTT
56771 GCTAAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.23, G:0.28, T:0.40
Consensus pattern (21 bp):
CTGCAGGTTTCTCCAGGTTTG
Found at i:56760 original size:11 final size:10
Alignment explanation
Indices: 56731--56770 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
56721 GTACATATAC
56731 CTGCAGGTTT
1 CTGCAGGTTT
*
56741 CTTCAGGTTT
1 CTGCAGGTTT
56751 GCTGCAGGTTT
1 -CTGCAGGTTT
*
56762 CTCCAGGTT
1 CTGCAGGTT
56771 GCTAAAGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.10, C:0.23, G:0.28, T:0.40
Consensus pattern (10 bp):
CTGCAGGTTT
Found at i:57169 original size:31 final size:31
Alignment explanation
Indices: 57134--57229 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
57124 AACAATGAAG
57134 GCTGACTGAATGAAATAAATCAGTAATAAAA
1 GCTGACTGAATGAAATAAATCAGTAATAAAA
** * * *
57165 GCTGATCT-AACAAAATCAATCAGTAATGAAG
1 GCTGA-CTGAATGAAATAAATCAGTAATAAAA
*
57196 GCTGACTGAATGAAATAAATCAGTGATAAAA
1 GCTGACTGAATGAAATAAATCAGTAATAAAA
57227 GCT
1 GCT
57230 AATTCAAAGA
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
30 2 0.04
31 48 0.92
32 2 0.04
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (31 bp):
GCTGACTGAATGAAATAAATCAGTAATAAAA
Found at i:57204 original size:62 final size:62
Alignment explanation
Indices: 57107--57229 Score: 219
Period size: 62 Copynumber: 2.0 Consensus size: 62
57097 GCAGCCAATT
57107 ATCTAACAAAATCAATCAACAATGAAGGCTGACTGAATGAAATAAATCAGTAATAAAAGCTG
1 ATCTAACAAAATCAATCAACAATGAAGGCTGACTGAATGAAATAAATCAGTAATAAAAGCTG
** *
57169 ATCTAACAAAATCAATCAGTAATGAAGGCTGACTGAATGAAATAAATCAGTGATAAAAGCT
1 ATCTAACAAAATCAATCAACAATGAAGGCTGACTGAATGAAATAAATCAGTAATAAAAGCT
57230 AATTCAAAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.49, C:0.14, G:0.15, T:0.22
Consensus pattern (62 bp):
ATCTAACAAAATCAATCAACAATGAAGGCTGACTGAATGAAATAAATCAGTAATAAAAGCTG
Found at i:57284 original size:22 final size:22
Alignment explanation
Indices: 57242--57283 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
57232 TTCAAAGAGA
57242 AAAAGAATCCCAGAATTTTTTC
1 AAAAGAATCCCAGAATTTTTTC
*
57264 AAAAGAATTCCA-AATTTTTT
1 AAAAGAATCCCAGAATTTTTT
57284 TTAGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (22 bp):
AAAAGAATCCCAGAATTTTTTC
Found at i:57509 original size:30 final size:30
Alignment explanation
Indices: 57470--57558 Score: 133
Period size: 30 Copynumber: 3.0 Consensus size: 30
57460 ATTTAAATCT
* *
57470 CTTAAATTAAAGACTAGTGCACCACTATTC
1 CTTAAATTAAGGACTAGTGCACCACTATCC
*
57500 CTTAGATTAAGGACTAGTGCACCACTATCC
1 CTTAAATTAAGGACTAGTGCACCACTATCC
* *
57530 CTTAAATTAAGGACTAATGCATCACTATC
1 CTTAAATTAAGGACTAGTGCACCACTATC
57559 TAATTCAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (30 bp):
CTTAAATTAAGGACTAGTGCACCACTATCC
Found at i:58868 original size:17 final size:16
Alignment explanation
Indices: 58821--58870 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
58811 TTATTTATTC
58821 TTATCCTAAATAAATA
1 TTATCCTAAATAAATA
*
58837 TT-TACTCAAATTAAATA
1 TTATCCT-AAA-TAAATA
58854 TATATCCTAAATAAATA
1 T-TATCCTAAATAAATA
58871 CAAAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 3 0.11
16 5 0.18
17 13 0.46
18 4 0.14
19 3 0.11
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (16 bp):
TTATCCTAAATAAATA
Found at i:63413 original size:21 final size:21
Alignment explanation
Indices: 63389--63477 Score: 90
Period size: 21 Copynumber: 4.2 Consensus size: 21
63379 TACAATACCT
*
63389 ACCTACAGTACCCCAAATAGA
1 ACCTACAGTACCTCAAATAGA
*
63410 ACCTACAGTACCTC-AATCAAA
1 ACCTACAGTACCTCAAAT-AGA
** *
63431 ACCTATGGTACCTCAAATAGC
1 ACCTACAGTACCTCAAATAGA
* * *
63452 ACCTACAGCACCTCAAACAGC
1 ACCTACAGTACCTCAAATAGA
63473 ACCTA
1 ACCTA
63478 TTTATGATAT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
20 3 0.05
21 50 0.89
22 3 0.05
ACGTcount: A:0.39, C:0.35, G:0.09, T:0.17
Consensus pattern (21 bp):
ACCTACAGTACCTCAAATAGA
Found at i:66589 original size:3 final size:3
Alignment explanation
Indices: 66583--66615 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
66573 TTGCTGGCCT
66583 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
66616 AGCGTGCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
TGC
Found at i:67026 original size:24 final size:23
Alignment explanation
Indices: 66977--67028 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
66967 TTTTGAAGGG
*
66977 ATTTTTTTAAAATTTTTATCGATA
1 ATTTTTTT-AAATTTTTATCAATA
67001 ATTTTTTT-AATTTTTATCTAATTA
1 ATTTTTTTAAATTTTTATC-AA-TA
67025 ATTT
1 ATTT
67029 ATGATATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 10 0.40
23 1 0.04
24 14 0.56
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (23 bp):
ATTTTTTTAAATTTTTATCAATA
Found at i:67029 original size:20 final size:21
Alignment explanation
Indices: 66987--67029 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
66977 ATTTTTTTAA
**
66987 AATTTTTATCGATAATTTTTTT
1 AATTTTTATC-ATAATTAATTT
67009 AATTTTTATC-TAATTAATTT
1 AATTTTTATCATAATTAATTT
67029 A
1 A
67030 TGATATTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
22 10 0.53
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (21 bp):
AATTTTTATCATAATTAATTT
Found at i:67117 original size:19 final size:20
Alignment explanation
Indices: 67095--67151 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
67085 AAAATCATAC
67095 TAATTAAATTAA-A-TTATGT
1 TAATTAAATTAATATTTAT-T
67114 TAATTAAATTAATATTTATT
1 TAATTAAATTAATATTTATT
*
67134 TAATTATAAATAATATTT
1 TAATTA-AATTAATATTT
67152 TTATATGTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 12 0.35
20 8 0.24
21 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TAATTAAATTAATATTTATT
Found at i:70017 original size:12 final size:12
Alignment explanation
Indices: 70000--70029 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
69990 TAAAATTAAA
*
70000 TTTTATTTTATT
1 TTTTATTTAATT
70012 TTTTATTTAATT
1 TTTTATTTAATT
70024 TTTTAT
1 TTTTAT
70030 AATATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTATTTAATT
Found at i:72399 original size:11 final size:12
Alignment explanation
Indices: 72357--72401 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
72347 ATTTTTTTTA
72357 AAAT-TTAATTAT
1 AAATATTAA-TAT
72369 AAATA-T-ATAT
1 AAATATTAATAT
72379 AAATATTAATAT
1 AAATATTAATAT
72391 AAA-ATTAATAT
1 AAATATTAATAT
72402 TTGAATACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 8 0.27
11 10 0.33
12 12 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AAATATTAATAT
Found at i:73569 original size:8 final size:8
Alignment explanation
Indices: 73556--73603 Score: 60
Period size: 8 Copynumber: 6.0 Consensus size: 8
73546 ACACACACAC
73556 ATATACAT
1 ATATACAT
*
73564 ACATACAT
1 ATATACAT
*
73572 ATATATAT
1 ATATACAT
*
73580 ATATATAT
1 ATATACAT
73588 ATATACAT
1 ATATACAT
*
73596 ACATACAT
1 ATATACAT
73604 TTTTCCACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATACAT
Found at i:74230 original size:2 final size:2
Alignment explanation
Indices: 74223--74254 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
74213 AGGAAACATA
74223 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
74255 CAATTATTTC
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:75463 original size:22 final size:19
Alignment explanation
Indices: 75419--75468 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 19
75409 GTTATTTTAA
*
75419 AATTAAATAAAAATATTGT
1 AATTAAATAAAAAAATTGT
75438 -ATTAAATGAAAAAAATATGAT
1 AATTAAAT-AAAAAAAT-TG-T
75459 AATTAAATAA
1 AATTAAATAA
75469 TTCAGAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 7 0.27
19 7 0.27
20 2 0.08
21 3 0.12
22 7 0.27
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (19 bp):
AATTAAATAAAAAAATTGT
Found at i:79284 original size:5 final size:5
Alignment explanation
Indices: 79274--79332 Score: 73
Period size: 5 Copynumber: 11.0 Consensus size: 5
79264 TCTCTAATAT
79274 ATAAA ATAAA ATAAA ATAAA ATAAAA ATAAAA ATAAAA ATAAA CATAAA
1 ATAAA ATAAA ATAAA ATAAA AT-AAA AT-AAA AT-AAA ATAAA -ATAAA
*
79323 ATATA ATAAA
1 ATAAA ATAAA
79333 TTATTAATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
5 28 0.56
6 22 0.44
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:79302 original size:6 final size:6
Alignment explanation
Indices: 79276--79333 Score: 68
Period size: 6 Copynumber: 9.8 Consensus size: 6
79266 TCTAATATAT
*
79276 AAAAT- AAAAT- AAAAT- AAAATA AAAATA AAAATA AAAATA AACATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
79321 AAATATA ATAAAT
1 AAA-ATA A-AAAT
79334 TATTAATATG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
5 15 0.31
6 25 0.52
7 6 0.12
8 2 0.04
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:79415 original size:12 final size:12
Alignment explanation
Indices: 79408--79471 Score: 78
Period size: 12 Copynumber: 5.3 Consensus size: 12
79398 TATTTTTTTC
79408 CTTTTTTTCTTT
1 CTTTTTTTCTTT
79420 CTTTTTTTCTTT
1 CTTTTTTTCTTT
79432 -TTTTTCTTCTTT
1 CTTTTT-TTCTTT
*
79444 CTTTTTTT-TTC
1 CTTTTTTTCTTT
*
79455 CTTTCTTTTCCTT
1 CTTT-TTTTCTTT
79468 CTTT
1 CTTT
79472 CTTAGCCTGC
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
11 11 0.24
12 24 0.53
13 10 0.22
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
CTTTTTTTCTTT
Found at i:79422 original size:4 final size:4
Alignment explanation
Indices: 79408--79474 Score: 50
Period size: 4 Copynumber: 16.8 Consensus size: 4
79398 TATTTTTTTC
* * *
79408 CTTT TTTT CTTT CTTT TTTT CTTT -TTT TTCTT CTTT CTTT -TTT -TTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT-TT CTTT CTTT CTTT CTTT
*
79454 CCTTT CTTTT CCTT CTTT CTT
1 -CTTT C-TTT CTTT CTTT CTT
79475 AGCCTGCTGA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
3 9 0.18
4 32 0.63
5 10 0.20
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
CTTT
Found at i:79426 original size:20 final size:19
Alignment explanation
Indices: 79401--79463 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 19
79391 ATACATATAT
79401 TTTTTTCCTTTTTTTCTTTC
1 TTTTTT-CTTTTTTTCTTTC
79421 TTTTTTTCTTTTTTT-TCTTC
1 -TTTTTTCTTTTTTTCT-TTC
*
79441 TTTCTTT-TTTTTTCCTTTC
1 TTT-TTTCTTTTTTTCTTTC
79460 TTTT
1 TTTT
79464 CCTTCTTTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
18 1 0.03
19 16 0.42
20 15 0.39
21 6 0.16
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTTCTTTTTTTCTTTC
Found at i:79426 original size:21 final size:20
Alignment explanation
Indices: 79400--79463 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
79390 AATACATATA
79400 TTTTTTTCCTTTTTTTCTTTC
1 TTTTTTT-CTTTTTTTCTTTC
79421 TTTTTTTCTTTTTTT-TCTTC
1 TTTTTTTCTTTTTTTCT-TTC
* *
79441 TTTCTTT-TTTTTTCCTTTC
1 TTTTTTTCTTTTTTTCTTTC
79460 TTTT
1 TTTT
79464 CCTTCTTTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
19 13 0.34
20 18 0.47
21 7 0.18
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTTTCTTTTTTTCTTTC
Found at i:79437 original size:17 final size:16
Alignment explanation
Indices: 79400--79463 Score: 64
Period size: 16 Copynumber: 4.2 Consensus size: 16
79390 AATACATATA
79400 TTTTTTTC--CTTT-T
1 TTTTTTTCTTCTTTCT
* *
79413 TTTCTTTCTTTTTTTCT
1 TTTTTTTC-TTCTTTCT
79430 TTTTTTTCTTCTTTCT
1 TTTTTTTCTTCTTTCT
*
79446 TTTTTTT-TCCTTTCT
1 TTTTTTTCTTCTTTCT
79461 TTT
1 TTT
79464 CCTTCTTTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
13 7 0.17
15 10 0.24
16 17 0.40
17 8 0.19
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTCTTCTTTCT
Found at i:79444 original size:28 final size:28
Alignment explanation
Indices: 79403--79474 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 28
79393 ACATATATTT
* *
79403 TTTTCCTTTTTTTCTTTCTTTTTTTCTTT-
1 TTTTCC-TTCTTTCTTT-TTTTTTCCTTTC
*
79432 TTTTTCTTCTTTCTTTTTTTTTCCTTTC
1 TTTTCCTTCTTTCTTTTTTTTTCCTTTC
79460 TTTTCCTTCTTTCTT
1 TTTTCCTTCTTTCTT
79475 AGCCTGCTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 10 0.26
28 23 0.61
29 5 0.13
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (28 bp):
TTTTCCTTCTTTCTTTTTTTTTCCTTTC
Found at i:79469 original size:24 final size:23
Alignment explanation
Indices: 79400--79471 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 23
79390 AATACATATA
79400 TTTTTTTCCTTTTTTTCTTTCTT
1 TTTTTTTCCTTTTTTTCTTTCTT
*
79423 TTTTTCTT-TTTTTTCTTCTTTCTT
1 TTTTT-TTCCTTTTT-TTCTTTCTT
*
79447 TTTTTTTCCTTTCTTTTCCTTCTT
1 TTTTTTTCCTTT-TTTTCTTTCTT
79471 T
1 T
79472 CTTAGCCTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 12 0.29
24 28 0.67
25 2 0.05
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTTTCCTTTTTTTCTTTCTT
Found at i:79471 original size:9 final size:10
Alignment explanation
Indices: 79403--79471 Score: 51
Period size: 9 Copynumber: 7.3 Consensus size: 10
79393 ACATATATTT
79403 TTTTCCTTT-
1 TTTTCCTTTC
79412 TTTT-CTTTC
1 TTTTCCTTTC
79421 TTTT--TTTC
1 TTTTCCTTTC
*
79429 TTTT-TTTTC
1 TTTTCCTTTC
* *
79438 TTCTTTCTTTTT
1 -T-TTTCCTTTC
79450 TTTTCCTTTC
1 TTTTCCTTTC
79460 TTTTCC-TTC
1 TTTTCCTTTC
79469 TTT
1 TTT
79472 CTTAGCCTGC
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
8 12 0.23
9 18 0.35
10 14 0.27
11 4 0.08
12 4 0.08
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTCCTTTC
Found at i:80673 original size:2 final size:2
Alignment explanation
Indices: 80666--80703 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
80656 GAACTGATGA
80666 AT AT AT 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 AT AT AT
80704 GGACAATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81456 original size:6 final size:5
Alignment explanation
Indices: 81444--81621 Score: 90
Period size: 5 Copynumber: 36.0 Consensus size: 5
81434 TAAAAATTTA
* *
81444 TATAT TAATAT TATAT T-TA- TATAT TTTAT TATGT TAATAT TATA- TATAT
1 TATAT T-ATAT TATAT TATAT TATAT TATAT TATAT T-ATAT TATAT TATAT
* * * * *
81493 TATTT TATAT T-TAT ATAAAT TTTAA TATAT TA-AT AAT-T TATAT TATA-
1 TATAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT
* *
81540 TATAAT T-TAA AATAT T-TA- TATAT TCATAT TATAT TATATTT TATAT
1 TAT-AT TATAT TATAT TATAT TATAT T-ATAT TATAT TATA--T TATAT
* * *
81586 TATAT TTTAAT TATAT CA-AT TATATT TATAT CATAT
1 TATAT TAT-AT TATAT TATAT TATA-T TATAT TATAT
81622 ATAAAATTAT
Statistics
Matches: 130, Mismatches: 23, Indels: 40
0.67 0.12 0.21
Matches are distributed among these distances:
3 2 0.02
4 28 0.22
5 69 0.53
6 26 0.20
7 5 0.04
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:81462 original size:27 final size:27
Alignment explanation
Indices: 81428--81574 Score: 95
Period size: 29 Copynumber: 5.2 Consensus size: 27
81418 CTTTTTTTTA
*
81428 TATATTTAAAAATTTATATATTAATAT
1 TATATTTAATAATTTATATATTAATAT
* *
81455 TATATTTATATATTTTATTATGTTAATAT
1 TATATTTA-ATAATTTA-TATATTAATAT
* * * *
81484 TATATATATTATTTTATATTTATATAAATTT
1 TATATTTAATAATTTATA--TAT-T-AATAT
81515 TAATATATTAATAA-TT-TATATT-ATA-
1 T-ATAT-TTAATAATTTATATATTAATAT
* *
81540 TATAATTTAAAATATTTATATATTCATAT
1 TAT-ATTTAATA-ATTTATATATTAATAT
81569 TATATT
1 TATATT
81575 ATATTTTATA
Statistics
Matches: 94, Mismatches: 12, Indels: 27
0.71 0.09 0.20
Matches are distributed among these distances:
24 7 0.07
25 4 0.04
26 4 0.04
27 16 0.17
28 20 0.21
29 25 0.27
30 1 0.01
31 7 0.07
32 6 0.06
33 4 0.04
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (27 bp):
TATATTTAATAATTTATATATTAATAT
Found at i:81480 original size:29 final size:28
Alignment explanation
Indices: 81440--81591 Score: 91
Period size: 29 Copynumber: 5.4 Consensus size: 28
81430 TATTTAAAAA
*
81440 TTTA-TATATTAATATTATATTTATATAT
1 TTTATTATATTAATATTATATATAT-TAT
*
81468 TTTATTATGTTAATATTATATATATTAT
1 TTTATTATATTAATATTATATATATTAT
* *
81496 TTTATATTTATATAA-ATTTTAATATATTA-
1 TTTAT-TATAT-TAATATTAT-ATATATTAT
* * * * * *
81525 ATAATTTATATTATATATAATTTAAAATA-
1 TTTA-TTATATTA-ATATTATATATATTAT
*
81554 TTTA-TATATTCATATTATATTATATT-T
1 TTTATTATATTAATATTATA-TATATTAT
*
81581 TATATTATATT
1 TTTATTATATT
81592 TTAATTATAT
Statistics
Matches: 93, Mismatches: 21, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
26 6 0.06
27 13 0.14
28 20 0.22
29 39 0.42
30 15 0.16
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.59
Consensus pattern (28 bp):
TTTATTATATTAATATTATATATATTAT
Found at i:81495 original size:20 final size:18
Alignment explanation
Indices: 81470--81592 Score: 66
Period size: 18 Copynumber: 6.8 Consensus size: 18
81460 TTATATATTT
81470 TATTATGTTAATATTATATA
1 TATTAT-TTAATATT-TATA
*
81490 TATTATTTTATATTTATA
1 TATTATTTAATATTTATA
*
81508 TA-AATTTTAATATATTA-A
1 TATTA-TTTAATAT-TTATA
81526 TA--ATTT-ATA-TTATA
1 TATTATTTAATATTTATA
*
81540 TATAATTTAAAATATTTATA
1 TATTATTT--AATATTTATA
81560 TATTCATATT-ATA-TTATA
1 TATT-AT-TTAATATTTATA
*
81578 TTTTATATT-ATATTT
1 TATTAT-TTAATATTT
81593 TAATTATATC
Statistics
Matches: 86, Mismatches: 5, Indels: 26
0.74 0.04 0.22
Matches are distributed among these distances:
13 3 0.03
14 3 0.03
15 3 0.03
16 7 0.08
17 10 0.12
18 26 0.30
19 16 0.19
20 14 0.16
21 2 0.02
22 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.58
Consensus pattern (18 bp):
TATTATTTAATATTTATA
Found at i:81535 original size:43 final size:43
Alignment explanation
Indices: 81444--81590 Score: 114
Period size: 43 Copynumber: 3.5 Consensus size: 43
81434 TAAAAATTTA
* * * *
81444 TATATTAATATTATATTTATAT--ATTTTATTATGTTAATATTATA
1 TATATT-ATTTTATATTTATATAAATTTTAATATATTAATA--ATT
81488 TATATTATTTTATATTTATATAAATTTTAATATATTAATAATT
1 TATATTATTTTATATTTATATAAATTTTAATATATTAATAATT
* * *
81531 TATATTA-TATATAATT-TA-AAATATTT-ATATATTCAT-A-T
1 TATATTATTTTATATTTATATAAAT-TTTAATATATTAATAATT
81569 TATATTATATTT-TATATTATAT
1 TATATTAT-TTTATAT-TTATAT
81591 TTTAATTATA
Statistics
Matches: 86, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
38 8 0.09
39 3 0.03
40 17 0.20
41 7 0.08
42 7 0.08
43 23 0.27
44 6 0.07
45 15 0.17
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.58
Consensus pattern (43 bp):
TATATTATTTTATATTTATATAAATTTTAATATATTAATAATT
Found at i:81893 original size:16 final size:16
Alignment explanation
Indices: 81874--81904 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
81864 TTTTATTAAT
*
81874 AAAAAAAATTATGTAA
1 AAAAAAAATCATGTAA
81890 AAAAAAAATCATGTA
1 AAAAAAAATCATGTA
81905 TTTGATTATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (16 bp):
AAAAAAAATCATGTAA
Found at i:82222 original size:5 final size:5
Alignment explanation
Indices: 82205--82238 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
82195 AGCTTTTACT
*
82205 ATATA ATACA ATATA ATATA ATATA ATAATA ATA
1 ATATA ATATA ATATA ATATA ATATA AT-ATA ATA
82239 CAGCTGAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (5 bp):
ATATA
Found at i:82394 original size:38 final size:37
Alignment explanation
Indices: 82352--82432 Score: 92
Period size: 38 Copynumber: 2.2 Consensus size: 37
82342 AAAAAATAAT
82352 TTTAATTTAAATTAAATTGAATATAAATATTATT-TTTA
1 TTTAATTTAAATTAAATTG-ATATAAA-ATTATTATTTA
* * * *
82390 TTTAAATTAATTTAATTTGATTTAAAATTATTATTTA
1 TTTAATTTAAATTAAATTGATATAAAATTATTATTTA
*
82427 ATTAAT
1 TTTAAT
82433 AAATTTTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
36 6 0.17
37 14 0.39
38 16 0.44
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (37 bp):
TTTAATTTAAATTAAATTGATATAAAATTATTATTTA
Found at i:82414 original size:20 final size:22
Alignment explanation
Indices: 82389--82429 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
82379 TATTATTTTT
82389 ATTT-AAATTA-ATTTAATTTG
1 ATTTAAAATTATATTTAATTTG
82409 ATTTAAAATTATTATTTAATT
1 ATTTAAAATTA-TATTTAATT
82430 AATAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
23 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTAAAATTATATTTAATTTG
Found at i:82473 original size:25 final size:25
Alignment explanation
Indices: 82422--82473 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
82412 TAAAATTATT
* * *
82422 ATTTAATTAATAAATTTTTATTTAA
1 ATTTAATTAAAAAATATTTATTAAA
82447 ATTTAATTAAAAAAATATTT-TTAAA
1 ATTTAATT-AAAAAATATTTATTAAA
82472 AT
1 AT
82474 AATAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTAATTAAAAAATATTTATTAAA
Done.