Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold234
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: 732544
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18906 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:1223 original size:24 final size:24
Alignment explanation
Indices: 1190--1258 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
1180 AAATAATAAT
1190 AATAATAATACAGT-ATAACTTTTA-
1 AATAATAATACA-TAATAA-TTTTAG
*
1214 AGTAATAATACATAATAATTTTAG
1 AATAATAATACATAATAATTTTAG
*
1238 AATAATAATACACAATAATTT
1 AATAATAATACATAATAATTT
1259 CAAAAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
23 6 0.15
24 34 0.85
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.36
Consensus pattern (24 bp):
AATAATAATACATAATAATTTTAG
Found at i:1409 original size:3 final size:3
Alignment explanation
Indices: 1354--1398 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
1344 ACAATACATA
*
1354 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1399 TACAAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3590 original size:20 final size:20
Alignment explanation
Indices: 3547--3590 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
3537 GACAGAGATT
* **
3547 AAACAGAAGAGGAACTAATT
1 AAACAGAAGAAGAACTAAAG
*
3567 AAACAGAAGAAGAAGTAAAG
1 AAACAGAAGAAGAACTAAAG
3587 AAAC
1 AAAC
3591 TCTCACCTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.61, C:0.09, G:0.20, T:0.09
Consensus pattern (20 bp):
AAACAGAAGAAGAACTAAAG
Found at i:3710 original size:29 final size:29
Alignment explanation
Indices: 3677--3733 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
3667 CTCCAATTTC
3677 ACCAGCAGA-GGAAAAAGAACGTTTGGGGA
1 ACCAGCAGAGGGAAAAA-AACGTTTGGGGA
*
3706 ACCAGCAGAGGGGAAAAAACGTTTGGGG
1 ACCAGCAGAGGGAAAAAAACGTTTGGGG
3734 GAGAAGACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.39, C:0.14, G:0.37, T:0.11
Consensus pattern (29 bp):
ACCAGCAGAGGGAAAAAAACGTTTGGGGA
Found at i:4170 original size:13 final size:13
Alignment explanation
Indices: 4154--4184 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4144 TTGGTTAAAA
4154 AATTGGGTTGAGT
1 AATTGGGTTGAGT
*
4167 AATTGGGTTGGGT
1 AATTGGGTTGAGT
4180 AATTG
1 AATTG
4185 AGTTTGGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.39, T:0.39
Consensus pattern (13 bp):
AATTGGGTTGAGT
Found at i:9198 original size:19 final size:19
Alignment explanation
Indices: 9174--9227 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
9164 AATCATATCT
9174 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
9193 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
9212 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
9228 CTTGAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:9464 original size:2 final size:2
Alignment explanation
Indices: 9457--9486 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9447 TATGTGAGTT
9457 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9487 ATCTCTTAAC
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):
TA
Found at i:11592 original size:212 final size:212
Alignment explanation
Indices: 11225--11642 Score: 809
Period size: 212 Copynumber: 2.0 Consensus size: 212
11215 AATTGTATAT
*
11225 TTTGAGATATATTAGTTTTCGTGAAATAAGGTCGGAGTGGATTCAGGTTCCCCTATTCTGACTTT
1 TTTGAGATATATTAGTTTTCGTGAAATAAGGTCGGAGTGGATTCAGGTTCCCCTATTCTAACTTT
11290 GAAAAATCATCAAACAATTTTAAAAAACTATTAAGGATTGCAATTTGTATTTTTAAATTATTAAT
66 GAAAAATCATCAAACAATTTTAAAAAACTATTAAGGATTGCAATTTGTATTTTTAAATTATTAAT
*
11355 GAGTTCATCTTCAAGAGAAACAAACAAAAACATCATCTGAATCTCGTACTAAGAGATAATTAATT
131 GAGTTCATCTTCAAGAGAAACAAACAAAAACATCATCTGAATCCCGTACTAAGAGATAATTAATT
11420 TTTAGTAAAGATTCAGG
196 TTTAGTAAAGATTCAGG
11437 TTTGAGATATATTAGTTTTCGTGAAATAAGGTCGGAGTGGATTCAGGTTCCCCTATTCTAACTTT
1 TTTGAGATATATTAGTTTTCGTGAAATAAGGTCGGAGTGGATTCAGGTTCCCCTATTCTAACTTT
11502 GAAAAATCATCAAACAATTTTAAAAAACTATTAAGGATTGCAATTTGTATTTTTAAATTATTAAT
66 GAAAAATCATCAAACAATTTTAAAAAACTATTAAGGATTGCAATTTGTATTTTTAAATTATTAAT
*
11567 GAGTTTATCTTCAAGAGAAACAAACAAAAACATCATCTGAATCCCGTACTAAGAGATAATTAATT
131 GAGTTCATCTTCAAGAGAAACAAACAAAAACATCATCTGAATCCCGTACTAAGAGATAATTAATT
11632 TTTAGTAAAGA
196 TTTAGTAAAGA
11643 AATGTCGAAG
Statistics
Matches: 203, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
212 203 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (212 bp):
TTTGAGATATATTAGTTTTCGTGAAATAAGGTCGGAGTGGATTCAGGTTCCCCTATTCTAACTTT
GAAAAATCATCAAACAATTTTAAAAAACTATTAAGGATTGCAATTTGTATTTTTAAATTATTAAT
GAGTTCATCTTCAAGAGAAACAAACAAAAACATCATCTGAATCCCGTACTAAGAGATAATTAATT
TTTAGTAAAGATTCAGG
Found at i:11719 original size:7 final size:7
Alignment explanation
Indices: 11707--11733 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
11697 CTGATTGGCT
11707 AAATTAG
1 AAATTAG
11714 AAATTAG
1 AAATTAG
11721 AAATTAG
1 AAATTAG
11728 AAATTA
1 AAATTA
11734 TAAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (7 bp):
AAATTAG
Found at i:12734 original size:3 final size:3
Alignment explanation
Indices: 12720--12753 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
12710 ATTATTTATA
12720 AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12754 CATTATCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:13845 original size:20 final size:20
Alignment explanation
Indices: 13755--13832 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
13745 TTGCACATAT
13755 GTGCCTCTGTTTGCACTTTG
1 GTGCCTCTGTTTGCACTTTG
* * *
13775 GTGTCTTTGTATGCACTTTG
1 GTGCCTCTGTTTGCACTTTG
* *
13795 GTGCCTTTGTATGCACTTTG
1 GTGCCTCTGTTTGCACTTTG
13815 GTGCCTCTGTTTGCACTT
1 GTGCCTCTGTTTGCACTT
13833 CGATGTCTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.08, C:0.22, G:0.24, T:0.46
Consensus pattern (20 bp):
GTGCCTCTGTTTGCACTTTG
Found at i:19612 original size:13 final size:13
Alignment explanation
Indices: 19591--19625 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
19581 ACCGTTTTCC
19591 AAAAG-AAGAAAA
1 AAAAGAAAGAAAA
*
19603 GAAAGAAAGAAAA
1 AAAAGAAAGAAAA
19616 AAAAGAAAGA
1 AAAAGAAAGA
19626 GGGACAAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAA
Found at i:22502 original size:20 final size:20
Alignment explanation
Indices: 22479--22524 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
22469 TCCACGCTAC
* *
22479 CGTGTGAACAGGCACGCAGT
1 CGTGTGAACAGGCACACACT
*
22499 CGTGTGAATAGGCACACACT
1 CGTGTGAACAGGCACACACT
22519 CGTGTG
1 CGTGTG
22525 GCCACCCATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.20
Consensus pattern (20 bp):
CGTGTGAACAGGCACACACT
Found at i:23332 original size:24 final size:24
Alignment explanation
Indices: 23300--23361 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
23290 TCGAAGAAGT
* **
23300 TGATAGTAATAGTGTGAGTTATAA
1 TGATAGTAATAGTGTAAACTATAA
*
23324 TGATAGTAATAGTGTAAACTATGA
1 TGATAGTAATAGTGTAAACTATAA
*
23348 TGATAGTGATAGTG
1 TGATAGTAATAGTG
23362 AACTTTGTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (24 bp):
TGATAGTAATAGTGTAAACTATAA
Found at i:29942 original size:33 final size:33
Alignment explanation
Indices: 29905--30035 Score: 163
Period size: 33 Copynumber: 3.8 Consensus size: 33
29895 ATGCATGACT
29905 ACTAGATACATCTACTCTAAATACATTCATTAA
1 ACTAGATACATCTACTCTAAATACATTCATTAA
* * *
29938 ACTAGATACGTCTACTCTAAATACAAGTACATGCATGACT
1 ACTAGATACATCTACTCTAAATAC-A-T---T-CATTA-A
29978 ACTAGATACATCTACTCTAAATACATTCATTAA
1 ACTAGATACATCTACTCTAAATACATTCATTAA
*
30011 ACTAGATACGTCTACTCTAAATACA
1 ACTAGATACATCTACTCTAAATACA
30036 AGTACATGTA
Statistics
Matches: 84, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
33 47 0.56
34 5 0.06
35 2 0.02
38 2 0.02
39 5 0.06
40 23 0.27
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (33 bp):
ACTAGATACATCTACTCTAAATACATTCATTAA
Found at i:30008 original size:73 final size:73
Alignment explanation
Indices: 29889--30043 Score: 310
Period size: 73 Copynumber: 2.1 Consensus size: 73
29879 TGTCCTAGTT
29889 AAGTACATGCATGACTACTAGATACATCTACTCTAAATACATTCATTAAACTAGATACGTCTACT
1 AAGTACATGCATGACTACTAGATACATCTACTCTAAATACATTCATTAAACTAGATACGTCTACT
29954 CTAAATAC
66 CTAAATAC
29962 AAGTACATGCATGACTACTAGATACATCTACTCTAAATACATTCATTAAACTAGATACGTCTACT
1 AAGTACATGCATGACTACTAGATACATCTACTCTAAATACATTCATTAAACTAGATACGTCTACT
30027 CTAAATAC
66 CTAAATAC
30035 AAGTACATG
1 AAGTACATG
30044 TAAGTAATGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 82 1.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (73 bp):
AAGTACATGCATGACTACTAGATACATCTACTCTAAATACATTCATTAAACTAGATACGTCTACT
CTAAATAC
Found at i:32121 original size:32 final size:31
Alignment explanation
Indices: 32085--32197 Score: 94
Period size: 32 Copynumber: 3.7 Consensus size: 31
32075 TAATCATTTT
32085 AATATTAAATTAATATAATACTTATCAAGATA
1 AATATTAAATTAATATAATA-TTATCAAGATA
* *
32117 AATATTAGATTAAATTTAATA-T-T-AA-AT-
1 AATATTAAATT-AATATAATATTATCAAGATA
* *
32144 -CTATTAAATTAATAAAATATTATCAAGATA
1 AATATTAAATTAATATAATATTATCAAGATA
* * *
32174 AGTATTTAATTTAATTTAATATTA
1 AATA-TTAAATTAATATAATATTA
32198 AATCTATTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
25 7 0.11
26 9 0.14
27 1 0.02
28 4 0.06
29 4 0.06
30 1 0.02
31 3 0.05
32 26 0.41
33 8 0.13
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (31 bp):
AATATTAAATTAATATAATATTATCAAGATA
Found at i:32191 original size:57 final size:58
Alignment explanation
Indices: 32087--32214 Score: 197
Period size: 57 Copynumber: 2.2 Consensus size: 58
32077 ATCATTTTAA
*
32087 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATC
1 TATTAAATTAATAAAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATC
* *
32145 TATTAAATTAATAAAATA-TTATCAAGATAAGTATTTA-ATTTAATTTAATATTAAATC
1 TATTAAATTAATAAAATACTTATCAAGATAAATA-TTAGATTAAATTTAATATTAAATC
*
32202 TATTAAAATAATA
1 TATTAAATTAATA
32215 TTATTTTTGG
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
57 45 0.69
58 20 0.31
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (58 bp):
TATTAAATTAATAAAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATC
Found at i:36498 original size:40 final size:40
Alignment explanation
Indices: 36454--36660 Score: 234
Period size: 40 Copynumber: 5.2 Consensus size: 40
36444 AACAATTGAA
** *
36454 TGAATGCACATAAGTGCGTCTGTTTGTACTCCGGTACCCC
1 TGAATGCACATAAGTGCCCCTGTTTGTACTTCGGTACCCC
* * * * *
36494 TGAATGCACATACGTGCTCCTATTTGTACTTTGGTACCCT
1 TGAATGCACATAAGTGCCCCTGTTTGTACTTCGGTACCCC
* * * * **
36534 TGAATGCATATAAGTTCCCCTGTTTCTACCTCAATACCCC
1 TGAATGCACATAAGTGCCCCTGTTTGTACTTCGGTACCCC
* *
36574 TTAATGCACATAAGTGCCGCTGTTTGTACTTCGGTACCCC
1 TGAATGCACATAAGTGCCCCTGTTTGTACTTCGGTACCCC
* * *
36614 TGAAAGCACATCAGTGCCCCTATTTGTACTTCGGTACCCC
1 TGAATGCACATAAGTGCCCCTGTTTGTACTTCGGTACCCC
*
36654 TAAATGC
1 TGAATGC
36661 CTTTATGTGC
Statistics
Matches: 134, Mismatches: 33, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 134 1.00
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (40 bp):
TGAATGCACATAAGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:43416 original size:40 final size:40
Alignment explanation
Indices: 43318--43405 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
43308 AACAATTGAA
** * * *
43318 TGAATGCACATAAGTGCGTCTGTTTGTACTTCGGTACCCT
1 TGAATGCACATAAGTGCCCCTATTTGTACTTCAGTACCCC
*
43358 TGAATGCACATAAGTGCCCCTATTTGTACTTTAGTACCCC
1 TGAATGCACATAAGTGCCCCTATTTGTACTTCAGTACCCC
43398 TGAATGCA
1 TGAATGCA
43406 TTTACGTGCC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (40 bp):
TGAATGCACATAAGTGCCCCTATTTGTACTTCAGTACCCC
Found at i:47593 original size:6 final size:6
Alignment explanation
Indices: 47582--47613 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
47572 TTGATAATTA
47582 CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT CC
1 CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT CC
47614 ACGATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (6 bp):
CCTCTT
Found at i:48955 original size:22 final size:20
Alignment explanation
Indices: 48904--48956 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
48894 TACAATGACT
*
48904 AAAATTTTAAAATTTAATAA
1 AAAATTTTAAAATTAAATAA
*
48924 AATAA-ATTAATAATTAAAATAA
1 AA-AATTTTAA-AATT-AAATAA
48946 AAAATTTTAAA
1 AAAATTTTAAA
48957 CTTGAATGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
20 6 0.23
21 9 0.35
22 11 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTTTAAAATTAAATAA
Found at i:51814 original size:12 final size:12
Alignment explanation
Indices: 51797--51823 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
51787 TTTTATAACA
51797 TTTTTATATATT
1 TTTTTATATATT
51809 TTTTTATATATT
1 TTTTTATATATT
51821 TTT
1 TTT
51824 AAAATTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTATATATT
Found at i:53917 original size:2 final size:2
Alignment explanation
Indices: 53910--53941 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53900 AATAAGGCCT
53910 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
53942 ATTTTGGGTG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:55962 original size:12 final size:12
Alignment explanation
Indices: 55929--55968 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
55919 AATAATAAAA
*
55929 TTTTAATACTTT
1 TTTTAATAATTT
55941 TTTT-AT-ATTT
1 TTTTAATAATTT
55951 TTTTAATAATTT
1 TTTTAATAATTT
55963 TTTTAA
1 TTTTAA
55969 AAATACGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 7 0.28
11 4 0.16
12 14 0.56
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTAATAATTT
Found at i:57547 original size:19 final size:19
Alignment explanation
Indices: 57518--57707 Score: 86
Period size: 22 Copynumber: 9.4 Consensus size: 19
57508 TATAGTTTGG
*
57518 ATTAGAATTTTGTATGAAT
1 ATTATAATTTTGTATGAAT
*
57537 ATTCTAATTTTTTTGTATGAAT
1 ATTATAA---TTTTGTATGAAT
* *
57559 ATTGTAATTTTTTATGAAT
1 ATTATAATTTTGTATGAAT
*
57578 ATTATAATTATTTTAT--A-
1 ATTATAATT-TTGTATGAAT
*
57595 ATTA-AA-TTTGTATTTATAAT
1 ATTATAATTTTGTA--T-GAAT
*
57615 TTTGCATTAGTATTTTGTATGAAT
1 ATT--A-TA--ATTTTGTATGAAT
*
57639 ATTGTAATTTTTTGTATGAAT
1 ATTATAA--TTTTGTATGAAT
*
57660 -TTGTAATTTTGTATGAAT
1 ATTATAATTTTGTATGAAT
*
57678 ATTGTAATTTTTTTGTATGAAT
1 ATTATAA---TTTTGTATGAAT
*
57700 ATTGTAAT
1 ATTATAAT
57708 ATTATAATTT
Statistics
Matches: 138, Mismatches: 10, Indels: 46
0.71 0.05 0.24
Matches are distributed among these distances:
14 4 0.03
15 1 0.01
16 3 0.02
17 4 0.03
18 13 0.09
19 33 0.24
20 14 0.10
21 14 0.10
22 38 0.28
24 6 0.04
25 1 0.01
26 1 0.01
27 6 0.04
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.56
Consensus pattern (19 bp):
ATTATAATTTTGTATGAAT
Found at i:57652 original size:21 final size:21
Alignment explanation
Indices: 57627--57755 Score: 156
Period size: 21 Copynumber: 6.0 Consensus size: 21
57617 TGCATTAGTA
57627 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
57648 TTTTGTATGAAT-TTGTAA--
1 TTTTGTATGAATATTGTAATT
57666 TTTTGTATGAATATTGTAATTT
1 TTTTGTATGAATATTGTAA-TT
57688 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-A-T-T
* *
57713 AATTTTATATGAATATTGCAATT
1 --TTTTGTATGAATATTGTAATT
57736 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
57756 ATTGTAATTT
Statistics
Matches: 95, Mismatches: 4, Indels: 18
0.81 0.03 0.15
Matches are distributed among these distances:
18 12 0.13
19 6 0.06
20 6 0.06
21 30 0.32
22 17 0.18
23 2 0.02
24 4 0.04
25 2 0.02
26 1 0.01
27 15 0.16
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:57726 original size:27 final size:26
Alignment explanation
Indices: 57663--57879 Score: 177
Period size: 27 Copynumber: 8.9 Consensus size: 26
57653 TATGAATTTG
57663 TAATTTTGTATGAATATTGT-A-ATT
1 TAATTTTGTATGAATATTGTAATATT
57687 T--TTTTGTATGAATATTGTAATATT
1 TAATTTTGTATGAATATTGTAATATT
* *
57711 ATAATTTTATATGAATATTG-CA-A-T
1 -TAATTTTGTATGAATATTGTAATATT
57735 T--TTTTGTATGAATATTGTAATATT
1 TAATTTTGTATGAATATTGTAATATT
* * *
57759 GTAATTTTGTATGAATATTATAATGTC
1 -TAATTTTGTATGAATATTGTAATATT
*
57786 GAGATATATTG--T-AATATTGT-A-A-T
1 TA-AT-T-TTGTATGAATATTGTAATATT
57809 T--TTTTGTATGAATATTGTAAT-TT
1 TAATTTTGTATGAATATTGTAATATT
*
57832 T--TTTTGTATGAATATTGTCATATT
1 TAATTTTGTATGAATATTGTAATATT
57856 GTAATTTTGTATGAATATTGTAAT
1 -TAATTTTGTATGAATATTGTAAT
57880 GTCGAGATAT
Statistics
Matches: 155, Mismatches: 14, Indels: 45
0.72 0.07 0.21
Matches are distributed among these distances:
18 3 0.02
19 1 0.01
20 2 0.01
21 23 0.15
22 19 0.12
23 24 0.15
24 8 0.05
25 5 0.03
26 9 0.06
27 57 0.37
28 1 0.01
29 3 0.02
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.53
Consensus pattern (26 bp):
TAATTTTGTATGAATATTGTAATATT
Found at i:57769 original size:97 final size:96
Alignment explanation
Indices: 57660--57932 Score: 340
Period size: 97 Copynumber: 2.8 Consensus size: 96
57650 TTGTATGAAT
* *
57660 TTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGA-ATATTGTAATATTATAA-TTTTATAT
1 TTGTAATTTTGTATGAATATTGTAA--TTGTCG-A-GATATATTGTAATATTATAATTTTTATAT
57723 GAATATTGCAA-TTTTTTGTATGAATATTGTAATA
62 GAATATTGCAATTTTTTTGTATGAATATTGTAATA
* * *
57757 TTGTAATTTTGTATGAATATTATAA-TGTCGAGATATATTGTAATATTGTAATTTTTTGTATGAA
1 TTGTAATTTTGTATGAATATTGTAATTGTCGAGATATATTGTAATATTATAA-TTTTTATATGAA
* *
57821 TATTGTAATTTTTTTTGTATGAATATTGTCATA
65 TATTGCAA-TTTTTTTGTATGAATATTGTAATA
* * *
57854 TTGTAATTTTGTATGAATATTGTAA-TGTCGAGATATATTATAATATTGTAATTTTTTGTATGAA
1 TTGTAATTTTGTATGAATATTGTAATTGTCGAGATATATTGTAATATTATAA-TTTTTATATGAA
* *
57918 TATTGTAATTATTTT
65 TATTGCAATTTTTTT
57933 ATAATTAATT
Statistics
Matches: 161, Mismatches: 10, Indels: 11
0.88 0.05 0.06
Matches are distributed among these distances:
92 2 0.01
93 17 0.11
94 3 0.02
95 17 0.11
96 6 0.04
97 116 0.72
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (96 bp):
TTGTAATTTTGTATGAATATTGTAATTGTCGAGATATATTGTAATATTATAATTTTTATATGAAT
ATTGCAATTTTTTTGTATGAATATTGTAATA
Found at i:57777 original size:19 final size:19
Alignment explanation
Indices: 57523--57761 Score: 126
Period size: 19 Copynumber: 12.5 Consensus size: 19
57513 TTTGGATTAG
*
57523 AATTTTGTATGAATATTCT
1 AATTTTGTATGAATATTGT
57542 AATTTTTTTGTATGAATATTGT
1 AA---TTTTGTATGAATATTGT
* *
57564 AATTTTTTATGAATATTAT
1 AATTTTGTATGAATATTGT
*
57583 AATTATTTTAT-AATTAAATTTGT
1 AATT-TTGTATGAA-T--A-TTGT
* * * *
57606 -ATTTATAATTTTGCAT-TAGT
1 AATTT-T--GTATGAATATTGT
57626 -ATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
57644 AATTTTTTGTATGAAT-TTGT
1 AA--TTTTGTATGAATATTGT
57664 AATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
57683 AATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
* *
57697 AATATTG--T-AATATTAT
1 AATTTTGTATGAATATTGT
* *
57713 AATTTTATATGAATATTGC
1 AATTTTGTATGAATATTGT
57732 AATTTTTTGTATGAATATTGT
1 AA--TTTTGTATGAATATTGT
*
57753 AATATTGTA
1 AATTTTGTA
57762 ATTTTGTATG
Statistics
Matches: 172, Mismatches: 21, Indels: 54
0.70 0.09 0.22
Matches are distributed among these distances:
13 1 0.01
14 7 0.04
15 3 0.02
16 7 0.04
17 5 0.03
18 19 0.11
19 49 0.28
20 20 0.12
21 30 0.17
22 23 0.13
23 3 0.02
24 4 0.02
25 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.55
Consensus pattern (19 bp):
AATTTTGTATGAATATTGT
Found at i:57823 original size:21 final size:22
Alignment explanation
Indices: 57798--57932 Score: 116
Period size: 21 Copynumber: 5.8 Consensus size: 22
57788 GATATATTGT
57798 AATATTGTAATT-TTTTGTATG
1 AATATTGTAATTATTTTGTATG
*
57819 AATATTGTAATTTTTTTTGTATG
1 AATATTGTAA-TTATTTTGTATG
57842 AATATTGTCATATTGTAATTTTGTATG
1 AATATTGT-A-A-T-T-ATTTTGTATG
*
57869 AATATTGTAATGTCGAGATATAT-TAT-
1 AATATTGTAAT-T----AT-TTTGTATG
57895 AATATTGTAATT-TTTTGTATG
1 AATATTGTAATTATTTTGTATG
57916 AATATTGTAATTATTTT
1 AATATTGTAATTATTTT
57933 ATAATTAATT
Statistics
Matches: 97, Mismatches: 4, Indels: 25
0.77 0.03 0.20
Matches are distributed among these distances:
19 2 0.02
20 4 0.04
21 22 0.23
22 6 0.06
23 17 0.18
24 4 0.04
25 5 0.05
26 13 0.13
27 22 0.23
28 2 0.02
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.54
Consensus pattern (22 bp):
AATATTGTAATTATTTTGTATG
Found at i:57924 original size:47 final size:45
Alignment explanation
Indices: 57660--57926 Score: 234
Period size: 48 Copynumber: 5.6 Consensus size: 45
57650 TTGTATGAAT
* *
57660 TTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGA-ATATTGTAATA
1 TTGTAATTTTGTATGAATATTGTAA---TGTCG-A-GATATATTGTAATA
* * * * *
57709 TTATAATTTTATATGAATATTGCAATTTTTTGTATGA-ATATTGTAATA
1 TTGTAATTTTGTATGAATATTGTAA--TGTCG-A-GATATATTGTAATA
*
57757 TTGTAATTTTGTATGAATATTATAATGTCGAGATATATTGTAATA
1 TTGTAATTTTGTATGAATATTGTAATGTCGAGATATATTGTAATA
* * *
57802 TTGTAATTTTTTGTATGAATATTGTAATTTTTTTTGTATGA-ATATTGTCATA
1 TTGTAA--TTTTGTATGAATATTGTAA----TGTCG-A-GATATATTGTAATA
*
57854 TTGTAATTTTGTATGAATATTGTAATGTCGAGATATATTATAATA
1 TTGTAATTTTGTATGAATATTGTAATGTCGAGATATATTGTAATA
57899 TTGTAATTTTTTGTATGAATATTGTAAT
1 TTGTAA--TTTTGTATGAATATTGTAAT
57927 TATTTTATAA
Statistics
Matches: 189, Mismatches: 17, Indels: 26
0.81 0.07 0.11
Matches are distributed among these distances:
44 4 0.02
45 34 0.18
46 6 0.03
47 38 0.20
48 44 0.23
49 22 0.12
50 19 0.10
51 3 0.02
52 17 0.09
53 2 0.01
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.52
Consensus pattern (45 bp):
TTGTAATTTTGTATGAATATTGTAATGTCGAGATATATTGTAATA
Found at i:57987 original size:25 final size:24
Alignment explanation
Indices: 57920--58004 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 24
57910 TGTATGAATA
*
57920 TTGTAATTATTTTATAATTAATTTG
1 TTGTAATTA-TTTAAAATTAATTTG
*
57945 TTAGTAATT-TATATAAATT-ATTGTG
1 TT-GTAATTATTTA-AAATTAATT-TG
*
57970 TGTGTAATTATTTAAAATTTAATTTA
1 T-TGTAATTATTTAAAA-TTAATTTG
57996 TTAGTAATT
1 TT-GTAATT
58005 TAGGATTAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
24 6 0.12
25 19 0.40
26 20 0.42
27 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.55
Consensus pattern (24 bp):
TTGTAATTATTTAAAATTAATTTG
Found at i:58128 original size:36 final size:37
Alignment explanation
Indices: 58066--58145 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 37
58056 CATATAAAGT
58066 TTATAAAAAAATAAAAAATCATTTTATTAAAAGTTTAA
1 TTAT-AAAAAATAAAAAATCATTTTATTAAAAGTTTAA
*
58104 TTATAAAAAATTAAAAATCA-TTTATTAAAAGTTTAA
1 TTATAAAAAATAAAAAATCATTTTATTAAAAGTTTAA
58140 TTATAA
1 TTATAA
58146 CTGACTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
36 22 0.54
37 15 0.37
38 4 0.10
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (37 bp):
TTATAAAAAATAAAAAATCATTTTATTAAAAGTTTAA
Found at i:58757 original size:260 final size:259
Alignment explanation
Indices: 58264--58781 Score: 892
Period size: 260 Copynumber: 2.0 Consensus size: 259
58254 TGATTTTTTG
* * *
58264 AAACAAATTAAATGAATTCATTTTTTAATTGCAGATTTGTAGGAAATGGGTTCTCTGATTAATAA
1 AAACAAATTAAATGAATTCATTTTTTAATTGCAGATTTGCAGGAAATGAGTTCTCTAATTAATAA
*
58329 TAATAATCACATATCAAGTACAATTAATGAGATGGTAATAAAATTTTTATTTGATACTCATGTTA
66 TAATAATCACATATCAAGTACAATTAATGAGATGGTAATAAAATGTTTATTTGATACTCATGTTA
*
58394 TTTGCTGAATTAAATTATATTGTATTAACTATTTTGCTAATTTAATAATGTCAGGGTCCGTACCG
131 TTTGCTGAATTAAATTATATTGTATTAACTATTTTGCTAATTTAATAATGCCAGGGTCCGTACCG
* *
58459 CATATTGAGTGGCCATGTTAATAGTGTAGGGTTTCAGCCAGATGAACGCCTAATCCCATACTTT
196 CATATTGAGGGGCCATGTTAATAGTGTAGGGTTTCAGCCAGATGAACGCCTAATACCATACTTT
* * *
58523 AAACAAATTAACTGAATTCATTTTTTTGATTGTAGATTTGCAGGAAATGAGTTCTCTAATTAATA
1 AAACAAATTAAATGAATTCA-TTTTTTAATTGCAGATTTGCAGGAAATGAGTTCTCTAATTAATA
* *
58588 ATAATAATCACATATCAAGTACTATTAATGAGATGGTAATAAAATGTTTATTTGATATTCATGTT
65 ATAATAATCACATATCAAGTACAATTAATGAGATGGTAATAAAATGTTTATTTGATACTCATGTT
*
58653 ATTTGTTGAATTAAATTATATTGTATTAACTATTTTGCTAATTTAATAATGCCAGGGTCCGTACC
130 ATTTGCTGAATTAAATTATATTGTATTAACTATTTTGCTAATTTAATAATGCCAGGGTCCGTACC
* *
58718 GCGTATTGAGGGGCCGTGTTAATAGTGTAGGGTTTCAGCCAGATGAACGCCTAATACCATACTT
195 GCATATTGAGGGGCCATGTTAATAGTGTAGGGTTTCAGCCAGATGAACGCCTAATACCATACTT
58782 AGAGTTAGCC
Statistics
Matches: 243, Mismatches: 15, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
259 19 0.08
260 224 0.92
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (259 bp):
AAACAAATTAAATGAATTCATTTTTTAATTGCAGATTTGCAGGAAATGAGTTCTCTAATTAATAA
TAATAATCACATATCAAGTACAATTAATGAGATGGTAATAAAATGTTTATTTGATACTCATGTTA
TTTGCTGAATTAAATTATATTGTATTAACTATTTTGCTAATTTAATAATGCCAGGGTCCGTACCG
CATATTGAGGGGCCATGTTAATAGTGTAGGGTTTCAGCCAGATGAACGCCTAATACCATACTTT
Found at i:60341 original size:28 final size:27
Alignment explanation
Indices: 60276--60342 Score: 116
Period size: 27 Copynumber: 2.4 Consensus size: 27
60266 CATATTTATG
60276 TAATGATTTTTTTATGTAAATAAAATTA
1 TAATG-TTTTTTTATGTAAATAAAATTA
*
60304 TAATGGTTTTTTATGTAAATAAAATTA
1 TAATGTTTTTTTATGTAAATAAAATTA
60331 TAATGTTTTTTT
1 TAATGTTTTTTT
60343 TATTTTACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
27 32 0.86
28 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (27 bp):
TAATGTTTTTTTATGTAAATAAAATTA
Found at i:63364 original size:21 final size:22
Alignment explanation
Indices: 63315--63394 Score: 101
Period size: 21 Copynumber: 3.6 Consensus size: 22
63305 TACCTTATTT
*
63315 TTTTCTTAT-TTTCCTTCCTTC
1 TTTTCTTCTGTTTCCTTCCTTC
63336 TTTTCTTCT-TTTCCTTCCTTC
1 TTTTCTTCTGTTTCCTTCCTTC
* *
63357 TTTTCTTCTGCTTCCTTCTTTC
1 TTTTCTTCTGTTTCCTTCCTTC
63379 TTATTTCTTCTGTTTC
1 -T-TTTCTTCTGTTTC
63395 TCTAGTAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
21 29 0.56
22 10 0.19
23 1 0.02
24 12 0.23
ACGTcount: A:0.03, C:0.29, G:0.03, T:0.66
Consensus pattern (22 bp):
TTTTCTTCTGTTTCCTTCCTTC
Found at i:63506 original size:27 final size:27
Alignment explanation
Indices: 63446--63511 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
63436 AAAATCAGAG
*
63446 CATTGGCGCCTCTCAGTATGGCACCAA
1 CATTGGCGCCTCCCAGTATGGCACCAA
* * *
63473 TAATGGCGCCTCCCAG-ATAGGCACCAC
1 CATTGGCGCCTCCCAGTAT-GGCACCAA
63500 CATTGGCGCCTC
1 CATTGGCGCCTC
63512 TAATACTATG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 2 0.06
27 30 0.94
ACGTcount: A:0.21, C:0.36, G:0.23, T:0.20
Consensus pattern (27 bp):
CATTGGCGCCTCCCAGTATGGCACCAA
Found at i:68245 original size:9 final size:10
Alignment explanation
Indices: 68211--68251 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
68201 AAAATATCAT
68211 ATTAATTTTA
1 ATTAATTTTA
68221 ATTAATTTTA
1 ATTAATTTTA
*
68231 ATTAA-TTTG
1 ATTAATTTTA
68240 ATTAA-TTTA
1 ATTAATTTTA
68249 ATT
1 ATT
68252 TTACTTTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
ATTAATTTTA
Found at i:69858 original size:9 final size:9
Alignment explanation
Indices: 69846--69870 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
69836 TAAGGTTGCA
69846 CGAGTCGCC
1 CGAGTCGCC
69855 CGAGTCGCC
1 CGAGTCGCC
69864 CGAGTCG
1 CGAGTCG
69871 ACTGTGGACC
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:0.12, C:0.40, G:0.36, T:0.12
Consensus pattern (9 bp):
CGAGTCGCC
Found at i:74024 original size:18 final size:19
Alignment explanation
Indices: 73997--74034 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
73987 AATAGCAAGA
*
73997 GAAAAGCAG-AGAAAAAAG
1 GAAAAACAGAAGAAAAAAG
74015 GAAAAACAGAAAGAAAAAAG
1 GAAAAACAG-AAGAAAAAAG
74035 AAATTTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.71, C:0.05, G:0.24, T:0.00
Consensus pattern (19 bp):
GAAAAACAGAAGAAAAAAG
Found at i:74904 original size:3 final size:3
Alignment explanation
Indices: 74898--74954 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
74888 TACTACTACC
74898 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
74946 ATT ATT ATT
1 ATT ATT ATT
74955 TTTANNNNNN
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:81606 original size:15 final size:15
Alignment explanation
Indices: 81586--81615 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
81576 CTATGCATGC
*
81586 AAAATATAAAAGACA
1 AAAATACAAAAGACA
81601 AAAATACAAAAGACA
1 AAAATACAAAAGACA
81616 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.10, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAATACAAAAGACA
Found at i:82295 original size:21 final size:21
Alignment explanation
Indices: 82245--82300 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
82235 AATAACTAAC
82245 TAATCTTAATTAA-C-TAAAT
1 TAATCTTAATTAATCATAAAT
82264 TAA-CTTTAATTAATCATATAA-
1 TAATC-TTAATTAATCATA-AAT
82285 TAATCTTAATTAATCA
1 TAATCTTAATTAATCA
82301 AAGATAGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 1 0.03
19 11 0.34
20 1 0.03
21 16 0.50
22 3 0.09
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATCTTAATTAATCATAAAT
Found at i:101096 original size:23 final size:23
Alignment explanation
Indices: 101066--101111 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
101056 ATCATGAATA
101066 TATTTTTTAATTTATTAAATAAT
1 TATTTTTTAATTTATTAAATAAT
*
101089 TATTTTTTAATTTATTAATTAAT
1 TATTTTTTAATTTATTAAATAAT
101112 GTAAAATAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTTTTTAATTTATTAAATAAT
Found at i:101930 original size:19 final size:19
Alignment explanation
Indices: 101906--101943 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
101896 GTAAAAGAGA
101906 TTAGCATGACCCACTTATC
1 TTAGCATGACCCACTTATC
101925 TTAGCATGACCCACTTATC
1 TTAGCATGACCCACTTATC
101944 ACGTCAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.32
Consensus pattern (19 bp):
TTAGCATGACCCACTTATC
Found at i:104075 original size:54 final size:54
Alignment explanation
Indices: 103971--104076 Score: 122
Period size: 54 Copynumber: 2.0 Consensus size: 54
103961 AAAATTCAAC
** * * * * ** *
103971 AAATTTGGCACTCAATGTTTACAAAATTTTTCATTTTAGTTTTAATTCTAAACA
1 AAATTTGGCACTCAATAATTACAAAATCTATCAATTTAATCCTAACTCTAAACA
*
104025 AAATTTGGCCCTCAATAATTACAAAATCTATCAATTTAATCCTAACTCTAAA
1 AAATTTGGCACTCAATAATTACAAAATCTATCAATTTAATCCTAACTCTAAA
104077 AATTTTAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 42 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (54 bp):
AAATTTGGCACTCAATAATTACAAAATCTATCAATTTAATCCTAACTCTAAACA
Found at i:108151 original size:50 final size:50
Alignment explanation
Indices: 108071--108324 Score: 274
Period size: 50 Copynumber: 4.8 Consensus size: 50
108061 ATTTGGGTAA
* * *
108071 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCATCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGACACG
*
108121 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCTGGGAAATGGCGTTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGG--A---C------ATGGCGTTGGCACCGACACG
*
108182 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGACACG
* * * * * *
108232 AGATGTCCCTTATAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGACACG
** *
108282 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
108325 TGTTATTATC
Statistics
Matches: 177, Mismatches: 15, Indels: 23
0.82 0.07 0.11
Matches are distributed among these distances:
50 92 0.52
51 34 0.19
52 1 0.01
55 1 0.01
56 1 0.01
59 1 0.01
61 47 0.27
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGACACG
Found at i:108179 original size:61 final size:61
Alignment explanation
Indices: 108101--108216 Score: 223
Period size: 61 Copynumber: 1.9 Consensus size: 61
108091 TGTCTAGGAC
*
108101 ATGGCGTTGGCATCGAGACGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCTGGGAA
1 ATGGCGTTGGCACCGAGACGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCTGGGAA
108162 ATGGCGTTGGCACCGAGACGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
1 ATGGCGTTGGCACCGAGACGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
108217 GTTGGCACCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.24, C:0.22, G:0.35, T:0.19
Consensus pattern (61 bp):
ATGGCGTTGGCACCGAGACGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCTGGGAA
Found at i:108248 original size:111 final size:112
Alignment explanation
Indices: 108071--108271 Score: 332
Period size: 111 Copynumber: 1.8 Consensus size: 112
108061 ATTTGGGTAA
* * *
108071 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCATCGAGACGAGAGGTCCCATGTAA
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGACACGAGAGGTCCCATATAA
108136 GACCATGTCTGGGACATGGC-TGGGAAATGGCGTTGGCACCGAGACG
66 GACCATGTCTGGGACATGGCATGGGAAATGGCGTTGGCACCGAGACG
* * * *
108182 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGACATGAGATGTCCCTTATAA
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGACACGAGAGGTCCCATATAA
108247 GACCATGTCTGGGACATGGCATGGG
66 GACCATGTCTGGGACATGGCATGGG
108272 CACCGACATG
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
111 78 0.95
112 4 0.05
ACGTcount: A:0.25, C:0.22, G:0.33, T:0.20
Consensus pattern (112 bp):
AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGACACGAGAGGTCCCATATAA
GACCATGTCTGGGACATGGCATGGGAAATGGCGTTGGCACCGAGACG
Found at i:111624 original size:3 final size:3
Alignment explanation
Indices: 111616--111677 Score: 88
Period size: 3 Copynumber: 20.7 Consensus size: 3
111606 GATATACCTT
* * *
111616 TTA TTA TTA TTA TTA TTA TTG TTG TTA TTA TTA TTA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
111664 TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TT
111678 TTGTACATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:111643 original size:21 final size:21
Alignment explanation
Indices: 111619--111681 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
111609 ATACCTTTTA
111619 TTATTATTATTATTATTGTTG
1 TTATTATTATTATTATTGTTG
*
111640 TTATTATTATTATTATTGTTA
1 TTATTATTATTATTATTGTTG
*
111661 TTATTATTGTTATTATT-TTG
1 TTATTATTATTATTATTGTTG
111681 T
1 T
111682 ACATTAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 3 0.08
21 36 0.92
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (21 bp):
TTATTATTATTATTATTGTTG
Found at i:113274 original size:16 final size:16
Alignment explanation
Indices: 113253--113294 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
113243 TGAACCTTAG
113253 GAACTTGCCCTAGGTA
1 GAACTTGCCCTAGGTA
113269 GAACTTGCCCTAGGTA
1 GAACTTGCCCTAGGTA
113285 GAACTATGCC
1 GAACT-TGCC
113295 AAACCCTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (16 bp):
GAACTTGCCCTAGGTA
Found at i:118121 original size:24 final size:24
Alignment explanation
Indices: 118063--118121 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
118053 ATTAAGCACG
118063 AGGATGA-AAGCTGACCTAGGGTTA
1 AGGATGACAA-CTGACCTAGGGTTA
*
118087 AGGA-GAGCAACTGACTTAGGGTTA
1 AGGATGA-CAACTGACCTAGGGTTA
118111 AGGATGACAAC
1 AGGATGACAAC
118122 CACCCTAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 2 0.06
24 25 0.81
25 4 0.13
ACGTcount: A:0.36, C:0.14, G:0.32, T:0.19
Consensus pattern (24 bp):
AGGATGACAACTGACCTAGGGTTA
Found at i:121236 original size:71 final size:71
Alignment explanation
Indices: 121068--121244 Score: 248
Period size: 71 Copynumber: 2.5 Consensus size: 71
121058 AAATCTAGTA
* * * * *
121068 CGTGTCGCGACACAGATACCCCTTTATTTCTACACGCAACTTTGAAGTATTAAAATTTGAAAATA
1 CGTGTCGCGACACAGGTACCCCTGTGTTGCGACACGCAACTTTGAAGTATTAAAATTTGAAAATA
121133 ACAGGC
66 ACAGGC
* *
121139 CGTGTCGTGACACAGGTACCCCTGTGTTGTGACACGCAACTTTGAAGTATTAAAATTTGAAAATA
1 CGTGTCGCGACACAGGTACCCCTGTGTTGCGACACGCAACTTTGAAGTATTAAAATTTGAAAATA
*
121204 CCAGGC
66 ACAGGC
* *
121210 CGTGTTGCGACATAGGT-CCCCTTGTGTTGCGACAC
1 CGTGTCGCGACACAGGTACCCC-TGTGTTGCGACAC
121245 ATTACTTCGA
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
70 4 0.04
71 89 0.96
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (71 bp):
CGTGTCGCGACACAGGTACCCCTGTGTTGCGACACGCAACTTTGAAGTATTAAAATTTGAAAATA
ACAGGC
Found at i:129345 original size:16 final size:17
Alignment explanation
Indices: 129326--129370 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
129316 TTTTAATTAG
129326 TTTAATTTAATTAATT-
1 TTTAATTTAATTAATTC
129342 TTTAATCTTAA-TAATTC
1 TTTAAT-TTAATTAATTC
129359 TTT-A-TTAATTAA
1 TTTAATTTAATTAA
129371 ACTAATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.15
15 3 0.12
16 12 0.46
17 7 0.27
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAATTTAATTAATTC
Found at i:131721 original size:22 final size:24
Alignment explanation
Indices: 131678--131721 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
131668 TGATAATATG
131678 TTTTGATATAACAAATTAAAGTAT
1 TTTTGATATAACAAATTAAAGTAT
*
131702 TTTTGA-ATAA-AATTTAAAGT
1 TTTTGATATAACAAATTAAAGT
131722 TGAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTAT
Found at i:131845 original size:20 final size:20
Alignment explanation
Indices: 131820--131861 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
131810 CAAACTTTAA
131820 AATCAAGTTAAAA-TTATTTT
1 AATCAAG-TAAAAGTTATTTT
*
131840 AATCAAGTAAAAGTTCTTTT
1 AATCAAGTAAAAGTTATTTT
131860 AA
1 AA
131862 CTAGTCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (20 bp):
AATCAAGTAAAAGTTATTTT
Found at i:132109 original size:13 final size:13
Alignment explanation
Indices: 132091--132154 Score: 83
Period size: 13 Copynumber: 4.9 Consensus size: 13
132081 AGTTCTTCAT
*
132091 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
132104 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
***
132117 TGCTGCGGAAAAG
1 TGCTTTTGAAAAG
*
132130 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
132143 TGCTTTTGAAAA
1 TGCTTTTGAAAA
132155 ATTTGAGCGT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:141639 original size:2 final size:2
Alignment explanation
Indices: 141632--141662 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
141622 AATGTTCAAG
141632 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 T
141663 GACAGAAGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:145554 original size:154 final size:154
Alignment explanation
Indices: 145355--145633 Score: 531
Period size: 154 Copynumber: 1.8 Consensus size: 154
145345 GTCATCACTT
* *
145355 ATGAATTAATTGGCTCCTTAACAAATTTGTATAATGATATAACTAAATCTATTTTACTTAAGTAA
1 ATGAAGTAATTGGATCCTTAACAAATTTGTATAATGATATAACTAAATCTATTTTACTTAAGTAA
145420 TATAATCAAATATGCTATTTAACCAAGTCATGATTTAACAACTTTAATAGTTCATATAATGATAT
66 TATAATCAAATATGCTATTTAACCAAGTCATGATTTAACAACTTTAATAGTTCATATAATGATAT
145485 GACTAAATCTATTTAAGTAATATA
131 GACTAAATCTATTTAAGTAATATA
*
145509 ATGAAGTAATTGGATCCTTAACAAATTTGTATAATGATATGACTAAATCTATTTTACTTAAGTAA
1 ATGAAGTAATTGGATCCTTAACAAATTTGTATAATGATATAACTAAATCTATTTTACTTAAGTAA
145574 TATAATCAAATATGCTATTTAACCAAGTCATGATTTAACAACTTTAATAGTTCATATAAT
66 TATAATCAAATATGCTATTTAACCAAGTCATGATTTAACAACTTTAATAGTTCATATAAT
145634 TAAAACAGAA
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
154 122 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (154 bp):
ATGAAGTAATTGGATCCTTAACAAATTTGTATAATGATATAACTAAATCTATTTTACTTAAGTAA
TATAATCAAATATGCTATTTAACCAAGTCATGATTTAACAACTTTAATAGTTCATATAATGATAT
GACTAAATCTATTTAAGTAATATA
Found at i:148586 original size:174 final size:172
Alignment explanation
Indices: 148384--148766 Score: 495
Period size: 174 Copynumber: 2.2 Consensus size: 172
148374 TCCATCATTC
* * * ** * *
148384 TAATCCACTCCACTACAACTTTAGGGAGATAGGATTTGTTTA-TTTAGTCTGACC-CACTGCAAT
1 TAATCCGCTCCACTACAACTTCAGGGAGATAGGATTCG-CCACTTCAGTCTG-CCTCACTGCAAC
* *
148447 TTCAAGG-GGATAAGACTTGCTTTCTTAAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAAC-C
64 TTC-AGGAGGATAAGACTTGCTTACTT-AGTCTGCTCCACTGCAACTTCAGGGAGATAAG-ACTA
*
148510 GATGTGATCTACTATACAGCAACTTTAGAGAGATAGGATTATTGGCTT
126 GATATGATCTACTAT-CAGCAACTTTAGAGAGATAGGATTATTGGCTT
*
148558 TAATCCGCTCCACTACAACTTCAGGGAGATAAGATTCGCCACCTTCAGTCTGCCTCACTGCAACT
1 TAATCCGCTCCACTACAACTTCAGGGAGATAGGATTCGCCA-CTTCAGTCTGCCTCACTGCAACT
*
148623 TCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCATGGAGATAAGACTAGATA
65 TCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATA
* * * *
148688 TGATCTGCTCTCTGCAACTTTAGGGAGATAGGATTATTGGCTT
130 TGATCTACTATCAGCAACTTTAGAGAGATAGGATTATTGGCTT
* * * *
148731 TCATCTGCTCTACTGCAACTTCAGGGAGATAGGATT
1 TAATCCGCTCCACTACAACTTCAGGGAGATAGGATT
148767 ATTGGCTTTA
Statistics
Matches: 183, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
173 64 0.35
174 82 0.45
175 37 0.20
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (172 bp):
TAATCCGCTCCACTACAACTTCAGGGAGATAGGATTCGCCACTTCAGTCTGCCTCACTGCAACTT
CAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATAT
GATCTACTATCAGCAACTTTAGAGAGATAGGATTATTGGCTT
Found at i:148666 original size:44 final size:46
Alignment explanation
Indices: 148564--148682 Score: 135
Period size: 45 Copynumber: 2.7 Consensus size: 46
148554 GCTTTAATCC
*
148564 GCTCCACTACAACTTCAGG-GAGATAAGA-TTCGCCACCTTCAGTCT
1 GCTCCACTGCAACTTCAGGAG-GATAAGACTTCGCCACCTTCAGTCT
*
148609 GC-CTCACTGCAACTTCAGGAGGATAAGACTT-GCTTA-CTT-AGTCT
1 GCTC-CACTGCAACTTCAGGAGGATAAGACTTCGC-CACCTTCAGTCT
148653 GCTCCACTGCAACTTCATGGA-GATAAGACT
1 GCTCCACTGCAACTTCA-GGAGGATAAGACT
148683 AGATATGATC
Statistics
Matches: 66, Mismatches: 2, Indels: 13
0.81 0.02 0.16
Matches are distributed among these distances:
44 30 0.45
45 32 0.48
46 4 0.06
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (46 bp):
GCTCCACTGCAACTTCAGGAGGATAAGACTTCGCCACCTTCAGTCT
Found at i:148749 original size:84 final size:83
Alignment explanation
Indices: 148471--148761 Score: 266
Period size: 89 Copynumber: 3.4 Consensus size: 83
148461 ACTTGCTTTC
* * *
148471 TTAAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAAC-CGATGTGATCTACTATACAGCAACTT
1 TTAA-TCTGCTCCACTGCAACTTCAGGGAGATAAG-ACTCGAT-TGATCTGCTCT-CTGCAACTT
*
148535 TAGAGAGATAGGATTATTGGCT
62 TAGGGAGATAGGATTATTGGCT
* * * * *
148557 TTAATCCGCTCCACTACAACTTCAGGGAGATAAGATTCGCCACCTTCAGTCTGCCTCACTGCAAC
1 TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTCG--A--TTGA-TCTG-CTCTCTGCAAC
* * * *
148622 TTCA-GGAGGATAAGACTTGCTT-AC-
60 TTTAGGGA-GATAGGA-TT-ATTGGCT
* * *
148646 TTAGTCTGCTCCACTGCAACTTCATGGAGATAAGACTAGATATGATCTGCTCTCTGCAACTTTAG
1 TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGAT-TGATCTGCTCTCTGCAACTTTAG
148711 GGAGATAGGATTATTGGCT
65 GGAGATAGGATTATTGGCT
* *
148730 TTCATCTGCTCTACTGCAACTTCAGGGAGATA
1 TTAATCTGCTCCACTGCAACTTCAGGGAGATA
148762 GGATTATTGG
Statistics
Matches: 162, Mismatches: 29, Indels: 30
0.73 0.13 0.14
Matches are distributed among these distances:
82 2 0.01
83 3 0.02
84 48 0.30
85 38 0.23
86 6 0.04
87 2 0.01
88 4 0.02
89 52 0.32
90 5 0.03
91 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (83 bp):
TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTGATCTGCTCTCTGCAACTTTAGG
GAGATAGGATTATTGGCT
Found at i:148751 original size:44 final size:44
Alignment explanation
Indices: 148528--148810 Score: 213
Period size: 44 Copynumber: 6.5 Consensus size: 44
148518 CTACTATACA
* * * *
148528 GCAACTTTAGAGAGATAGGATTATTGGCTTTAATCCGCTCCACT
1 GCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCTACT
* * ***** * *
148572 ACAACTTCAGGGAGATAAGATTCGCCACCTTCAGTCTGC-CTCACT
1 GCAACTTCAGGGAGATAGGATT-ATTGGCTTTAATCTGCTCT-ACT
* * * * *
148617 GCAACTTCA-GGAGGATAAGACTTGCTT-AC-TTAGTCTGCTCCACT
1 GCAACTTCAGGGA-GATAGGA-TT-ATTGGCTTTAATCTGCTCTACT
* * * * * *
148661 GCAACTTCATGGAGATAAGACTA---GATATGATCTGCTCT-CT
1 GCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCTACT
* *
148701 GCAACTTTAGGGAGATAGGATTATTGGCTTTCATCTGCTCTACT
1 GCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCTACT
*
148745 GCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACT
1 GCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCTACT
*
148789 GCAACTTCAGGGAGATAAGATT
1 GCAACTTCAGGGAGATAGGATT
148811 CGCCATCTTC
Statistics
Matches: 188, Mismatches: 40, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
40 21 0.11
41 8 0.04
43 13 0.07
44 113 0.60
45 31 0.16
46 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (44 bp):
GCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCTACT
Found at i:148972 original size:50 final size:50
Alignment explanation
Indices: 148833--149082 Score: 164
Period size: 50 Copynumber: 5.0 Consensus size: 50
148823 TATTTTTAAT
* *
148833 TGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCAC
1 TGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTTTTTCAC
* ** **** ** * * *
148883 TACACCGCCAAGGAAGTAAGATTCACCGGTGCG--GTTTTAATCTTTTTCAC
1 TGCAATGTTGGGGAAACAAGATTCGCC-GT-CGTAGCTTCAATCTTTTTCAC
* * * * *
148933 TGTAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTTAATCTATTACAC
1 TGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTTTTTCAC
* *** ** * * ** * *
148983 TACACA-GCCAGGGAAGTAAGATTCGCTGTTGCGGCTTCAATCTTTTTAAT
1 TGCA-ATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTTTTTCAC
*
149033 TGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTTCAC
1 TGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTTTTTCAC
149083 CACACCGCCA
Statistics
Matches: 137, Mismatches: 57, Indels: 12
0.67 0.28 0.06
Matches are distributed among these distances:
48 2 0.01
49 3 0.02
50 127 0.93
51 3 0.02
52 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (50 bp):
TGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTTTTTCAC
Found at i:149158 original size:100 final size:100
Alignment explanation
Indices: 148825--149139 Score: 434
Period size: 100 Copynumber: 3.1 Consensus size: 100
148815 ATCTTCAGTA
* * *
148825 TTTTTAATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCG
1 TTTTTCATTGTAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTACACTACACCG
* * * * *
148890 CCAAGGAAGTAAGATTCACCGGTGCGGTTTTAATC
66 CCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAATC
* * * * *
148925 TTTTTCACTGTAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTTAATCTATTACACTACACAG
1 TTTTTCATTGTAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTACACTACACCG
*
148990 CCAGGGAAGTAAGATTCGCTGTTGCGGCTTCAATC
66 CCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAATC
* * * *
149025 TTTTTAATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTTCACCACACCG
1 TTTTTCATTGTAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTACACTACACCG
* *
149090 CCAGGGGAGTAAGATTCGCCGTTGCAGCTTCAAT-
66 CCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAATC
149124 TTTTTCCATTGTAATG
1 TTTTT-CATTGTAATG
149140 CCAAAGAGAT
Statistics
Matches: 186, Mismatches: 28, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
99 5 0.03
100 181 0.97
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (100 bp):
TTTTTCATTGTAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTACACTACACCG
CCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAATC
Found at i:149434 original size:88 final size:88
Alignment explanation
Indices: 149330--149491 Score: 288
Period size: 88 Copynumber: 1.8 Consensus size: 88
149320 ACGAGTGTCA
* * *
149330 TCGATCTGCTTCACTGCCAGCACAGGAAGATAAGATCTGTTATTTTCAACCTACTCCACTGCTGC
1 TCGATCTACTTCACTGCCAACACAGGAAGATAAGATCTGCTATTTTCAACCTACTCCACTGCTGC
149395 TCAGGGAGACAAAGCTGGTATCT
66 TCAGGGAGACAAAGCTGGTATCT
*
149418 TCGATCTACTTCACTGCCAATACAGGAAGATAAGATCTGCTATTTTCAACCTACTCCACTGCTGC
1 TCGATCTACTTCACTGCCAACACAGGAAGATAAGATCTGCTATTTTCAACCTACTCCACTGCTGC
149483 TCAGGGAGA
66 TCAGGGAGA
149492 TAAGGCTGAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 70 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (88 bp):
TCGATCTACTTCACTGCCAACACAGGAAGATAAGATCTGCTATTTTCAACCTACTCCACTGCTGC
TCAGGGAGACAAAGCTGGTATCT
Found at i:162934 original size:24 final size:26
Alignment explanation
Indices: 162870--162934 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 26
162860 ACATTCTTTT
*
162870 AAAATATAAATGAAAACATAAATCAATA
1 AAAATATAAA-G-AAACATAAATCAACA
*
162898 AACAA-ATGAAGAAA-ATAAA-CAACA
1 AA-AATATAAAGAAACATAAATCAACA
162922 AAAATATAAAGAA
1 AAAATATAAAGAA
162935 TAAAAGGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
23 2 0.06
24 13 0.41
25 5 0.16
26 3 0.09
27 1 0.03
28 6 0.19
29 2 0.06
ACGTcount: A:0.71, C:0.08, G:0.06, T:0.15
Consensus pattern (26 bp):
AAAATATAAAGAAACATAAATCAACA
Found at i:163266 original size:11 final size:12
Alignment explanation
Indices: 163245--163273 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
163235 TAAATTATTT
163245 TAAAAACATAAA
1 TAAAAACATAAA
163257 TAAAAA-ATAAA
1 TAAAAACATAAA
163268 TAAAAA
1 TAAAAA
163274 TTATAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.17
Consensus pattern (12 bp):
TAAAAACATAAA
Found at i:164464 original size:15 final size:15
Alignment explanation
Indices: 164444--164483 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
164434 TAACTATTGT
164444 TTTGGGCCTGGTTAG
1 TTTGGGCCTGGTTAG
*
164459 TTTGGGCCTCTGTTTAG
1 TTTGGG-C-CTGGTTAG
164476 TTTGGGCC
1 TTTGGGCC
164484 ACATAGGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.32
16 2 0.09
17 13 0.59
ACGTcount: A:0.05, C:0.17, G:0.35, T:0.42
Consensus pattern (15 bp):
TTTGGGCCTGGTTAG
Found at i:164730 original size:17 final size:17
Alignment explanation
Indices: 164708--164741 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
164698 TAATATAATC
164708 ATATTTA-CTTATACTCA
1 ATATTTAGCTTAT-CTCA
164725 ATATTTAGCTTATCTCA
1 ATATTTAGCTTATCTCA
164742 CAACCGAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.32, C:0.18, G:0.03, T:0.47
Consensus pattern (17 bp):
ATATTTAGCTTATCTCA
Found at i:166038 original size:43 final size:43
Alignment explanation
Indices: 165959--166075 Score: 119
Period size: 43 Copynumber: 2.7 Consensus size: 43
165949 TTCGTACAAC
* * *
165959 GCCAACGTCCCAGAC-GTGGTCTTACATGTAATCACAAATCGAT
1 GCCAACGTCCCAGACAG-GGTCTTACACGAAAACACAAATCGAT
** * * *
166002 GCCATTGTCCCGGACAGGGTCTTACACGAAAACACAAGTTGAT
1 GCCAACGTCCCAGACAGGGTCTTACACGAAAACACAAATCGAT
* * *
166045 GCCAACGTCCTAGATATGGTCTTACACGAAA
1 GCCAACGTCCCAGACAGGGTCTTACACGAAA
166076 TCACTTATCA
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
43 58 0.98
44 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (43 bp):
GCCAACGTCCCAGACAGGGTCTTACACGAAAACACAAATCGAT
Found at i:167706 original size:22 final size:24
Alignment explanation
Indices: 167663--167706 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
167653 TGATAATATG
167663 TTTTGATATAACAAATTAAAGTGT
1 TTTTGATATAACAAATTAAAGTGT
*
167687 TTTTGA-ATAA-AAGTTAAAGT
1 TTTTGATATAACAAATTAAAGT
167707 TGAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTGT
Found at i:167831 original size:20 final size:20
Alignment explanation
Indices: 167806--167847 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
167796 CCAACTTTAA
*
167806 AATCAAGTTAAAATGATTTT
1 AATCAAGTAAAAATGATTTT
*
167826 AATCAAGTAAAAATTATTTT
1 AATCAAGTAAAAATGATTTT
167846 AA
1 AA
167848 CTAGTCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (20 bp):
AATCAAGTAAAAATGATTTT
Found at i:169865 original size:22 final size:23
Alignment explanation
Indices: 169835--169879 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
169825 ATTATTAAAG
169835 TAGACTCATAT-TGAATTTATTC
1 TAGACTCATATATGAATTTATTC
* * *
169857 TAGATTCATTTATGGATTTATTC
1 TAGACTCATATATGAATTTATTC
169880 ACTTGTGGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (23 bp):
TAGACTCATATATGAATTTATTC
Found at i:175721 original size:22 final size:23
Alignment explanation
Indices: 175696--175743 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
175686 TTAGTTAACC
175696 TTTATTATTTAA-AAAATTAATA
1 TTTATTATTTAATAAAATTAATA
175718 TTTATTATTTAATAAAATTAATA
1 TTTATTATTTAATAAAATTAATA
175741 TTT
1 TTT
175744 TGGACTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTATTATTTAATAAAATTAATA
Found at i:175742 original size:19 final size:21
Alignment explanation
Indices: 175697--175742 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
175687 TAGTTAACCT
175697 TTATTATTTAAAAAATTAATA
1 TTATTATTTAAAAAATTAATA
175718 TTTATTATTTAATAAAATTAATA
1 -TTATTATTTAA-AAAATTAATA
175741 TT
1 TT
175743 TTGGACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATTATTTAAAAAATTAATA
Found at i:176244 original size:9 final size:9
Alignment explanation
Indices: 176230--176260 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
176220 GTTAAACGAA
176230 TCGAGTTAT
1 TCGAGTTAT
*
176239 TCGAGTTAA
1 TCGAGTTAT
176248 TCGAGTTAT
1 TCGAGTTAT
176257 TCGA
1 TCGA
176261 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:184288 original size:15 final size:15
Alignment explanation
Indices: 184264--184300 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
184254 TGAATTTAGA
184264 TTAA-TTCAAA-ATT
1 TTAATTTCAAATATT
184277 TTGAATTTCAAATATT
1 TT-AATTTCAAATATT
184293 TTAATTTC
1 TTAATTTC
184301 CAAACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.10
14 2 0.10
15 12 0.57
16 5 0.24
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (15 bp):
TTAATTTCAAATATT
Found at i:186371 original size:37 final size:37
Alignment explanation
Indices: 186321--186411 Score: 96
Period size: 37 Copynumber: 2.4 Consensus size: 37
186311 TTCCAAAAAT
* *
186321 AATATTATTTTAATTGT-TTAATATTAAATTAA-ATTA
1 AATATTATCTTAATAGTATT-ATATTAAATTAATATTA
* *
186357 AATACTTATCTTAATAGTATTTTATTAATTTAATATTA
1 AATA-TTATCTTAATAGTATTATATTAAATTAATATTA
186395 AAGTGATTATCTTAATA
1 AA-T-ATTATCTTAATA
186412 TTAAATTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
36 4 0.09
37 21 0.46
38 8 0.17
39 12 0.26
40 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (37 bp):
AATATTATCTTAATAGTATTATATTAAATTAATATTA
Found at i:189031 original size:50 final size:50
Alignment explanation
Indices: 188907--189148 Score: 229
Period size: 50 Copynumber: 4.9 Consensus size: 50
188897 GATAATAACA
* * * * ** * *
188907 TGCCAAAGCCATGTCCCAGAAATGGTTTTACATGAGATGTTTCATGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATAT-CGG
* * * * *
188956 TGCCAATGTCATATCCCAGATATGGTCTTACATGGG-AGTCCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACT-CTCATATCGG
* * ** * *
189006 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATATTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATATCGG
* * * *
189056 TGCCAACGCCGTGTCCCAGACATGGTCTTACATGGGAACTCTCGTCTCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATATCGG
*
189106 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTC
189149 NNNNNNNNNN
Statistics
Matches: 159, Mismatches: 30, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
48 3 0.02
49 35 0.22
50 120 0.75
51 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATATCGG
Found at i:189083 original size:100 final size:100
Alignment explanation
Indices: 188969--189148 Score: 263
Period size: 100 Copynumber: 1.8 Consensus size: 100
188959 CAATGTCATA
* * * * *
188969 TCCCAGATATGGTCTTACATGGG-AGTCCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTC
1 TCCCAGACATGGTCTTACATGGGAACT-CTCATATCGATGCCAACGCCATGTCCCAGACATGGTC
*
189033 TTACGGGGGACCTCTCATATTGGTGCCAACGCCGTG
65 TTACAGGGGACCTCTCATATTGGTGCCAACGCCGTG
* *
189069 TCCCAGACATGGTCTTACATGGGAACTCTCGTCTCGATGCCAACGCCATGTCCCAGACATGGTCT
1 TCCCAGACATGGTCTTACATGGGAACTCTCATATCGATGCCAACGCCATGTCCCAGACATGGTCT
*
189134 TACATGGGACCTCTC
66 TACAGGGGACCTCTC
189149 NNNNNNNNNN
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
100 68 0.97
101 2 0.03
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.26
Consensus pattern (100 bp):
TCCCAGACATGGTCTTACATGGGAACTCTCATATCGATGCCAACGCCATGTCCCAGACATGGTCT
TACAGGGGACCTCTCATATTGGTGCCAACGCCGTG
Found at i:203914 original size:12 final size:12
Alignment explanation
Indices: 203893--203925 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
203883 ATTATTTTAA
203893 TAATATTTAATAT
1 TAATATTTAAT-T
203906 TAA-ATTTAATT
1 TAATATTTAATT
203917 TAATATTTA
1 TAATATTTA
203926 TTAAGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.21
12 12 0.63
13 3 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TAATATTTAATT
Found at i:207492 original size:13 final size:13
Alignment explanation
Indices: 207440--207518 Score: 97
Period size: 13 Copynumber: 6.1 Consensus size: 13
207430 AGTTCTTCAT
207440 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
207453 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
* *
207466 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
207479 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
207492 TGCTTTT-AAGAAG
1 TGCTTTTGAA-AAG
207505 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
207518 T
1 T
207519 TTGGTTTAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
12 1 0.02
13 55 0.95
14 2 0.03
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:207797 original size:15 final size:15
Alignment explanation
Indices: 207777--207808 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
207767 TGGCTTCTCC
207777 TTTTCAGAAGTGCTT
1 TTTTCAGAAGTGCTT
207792 TTTTCAGAAGTGCTT
1 TTTTCAGAAGTGCTT
207807 TT
1 TT
207809 CAAAAGCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (15 bp):
TTTTCAGAAGTGCTT
Found at i:217812 original size:4 final size:4
Alignment explanation
Indices: 217803--217832 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
217793 ATAAAGGCAT
217803 AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
217833 GCCTAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:217923 original size:15 final size:18
Alignment explanation
Indices: 217885--217925 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 18
217875 AGCAAATACT
217885 AATAATAAGAACAGTAAC
1 AATAATAAGAACAGTAAC
*
217903 AGTAATAA-AA-A-TAAC
1 AATAATAAGAACAGTAAC
217918 AATAATAA
1 AATAATAA
217926 TACTAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 11 0.52
16 1 0.05
17 2 0.10
18 7 0.33
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.20
Consensus pattern (18 bp):
AATAATAAGAACAGTAAC
Found at i:217954 original size:19 final size:20
Alignment explanation
Indices: 217930--217975 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
217920 TAATAATACT
* * *
217930 AAAATAAT-TAAAGATAATA
1 AAAATAATAGAAAAATAAAA
217949 AAAATAATAGAAAAATAAAA
1 AAAATAATAGAAAAATAAAA
217969 AAAATAA
1 AAAATAA
217976 AGGGAATGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (20 bp):
AAAATAATAGAAAAATAAAA
Found at i:217957 original size:9 final size:9
Alignment explanation
Indices: 217905--217976 Score: 65
Period size: 9 Copynumber: 7.8 Consensus size: 9
217895 ACAGTAACAG
217905 TAATAAAAA
1 TAATAAAAA
* *
217914 TAACAATAA
1 TAATAAAAA
217923 TAATACTAAAA
1 TAATA--AAAA
*
217934 TAATTAAAGA
1 TAA-TAAAAA
217944 TAATAAAAA
1 TAATAAAAA
*
217953 TAATAGAAA
1 TAATAAAAA
217962 -AATAAAAA
1 TAATAAAAA
*
217970 AAATAAA
1 TAATAAA
217977 GGGAATGGGC
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
8 7 0.14
9 30 0.59
10 6 0.12
11 6 0.12
12 2 0.04
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (9 bp):
TAATAAAAA
Found at i:223812 original size:54 final size:54
Alignment explanation
Indices: 223730--223838 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
223720 ATTTCTTCAC
* *
223730 TTAGTATCTTGATCCGTTGAAATCCCTAAATTATGCTAATATCTCTTTCAAGAG
1 TTAGTATCTTGATCCGTAGAAATCCCTAAATTATGCTAATATATCTTTCAAGAG
223784 TTAGTATCTTGATCCGTAGAAATCCCTAAATTATGCTAATATATCTTTCAAGAG
1 TTAGTATCTTGATCCGTAGAAATCCCTAAATTATGCTAATATATCTTTCAAGAG
223838 T
1 T
223839 AAGAGCAACT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (54 bp):
TTAGTATCTTGATCCGTAGAAATCCCTAAATTATGCTAATATATCTTTCAAGAG
Found at i:225653 original size:19 final size:18
Alignment explanation
Indices: 225631--225680 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
225621 ATTGCAATTG
225631 ATTTTTTATATGATTTTTT
1 ATTTTTTATAT-ATTTTTT
*
225650 ATTTATTTTTATATTTTTT
1 ATTT-TTTATATATTTTTT
*
225669 ATTTTTTTTATA
1 ATTTTTTATATA
225681 ATTGTTGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 8 0.28
19 15 0.52
20 6 0.21
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (18 bp):
ATTTTTTATATATTTTTT
Found at i:228146 original size:25 final size:25
Alignment explanation
Indices: 228118--228202 Score: 62
Period size: 25 Copynumber: 3.2 Consensus size: 25
228108 TGAAATGGTT
228118 ATAAAATCAAATCATAATAAAATTA
1 ATAAAATCAAATCATAATAAAATTA
* * * * ** *
228143 ATAAATTAAAAACATTTTAGTCGAATGGTT
1 ATAAAATCAAATCA---TAATAAAAT--TA
228173 ATAAAATCAAATCATAATAAAATTA
1 ATAAAATCAAATCATAATAAAATTA
228198 ATAAA
1 ATAAA
228203 TTAAAAACTA
Statistics
Matches: 41, Mismatches: 14, Indels: 10
0.63 0.22 0.15
Matches are distributed among these distances:
25 17 0.41
27 6 0.15
28 6 0.15
30 12 0.29
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.31
Consensus pattern (25 bp):
ATAAAATCAAATCATAATAAAATTA
Found at i:228173 original size:55 final size:56
Alignment explanation
Indices: 228100--228210 Score: 206
Period size: 55 Copynumber: 2.0 Consensus size: 56
228090 ATAATTAATT
*
228100 ATTTTAGTTGAAATGGTTATAAAATCAAATCATAATAAAATTAATAAATTAAAAAC
1 ATTTTAGTCGAAATGGTTATAAAATCAAATCATAATAAAATTAATAAATTAAAAAC
228156 ATTTTAGTCG-AATGGTTATAAAATCAAATCATAATAAAATTAATAAATTAAAAAC
1 ATTTTAGTCGAAATGGTTATAAAATCAAATCATAATAAAATTAATAAATTAAAAAC
228211 TAATCCCGTA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
55 45 0.83
56 9 0.17
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.33
Consensus pattern (56 bp):
ATTTTAGTCGAAATGGTTATAAAATCAAATCATAATAAAATTAATAAATTAAAAAC
Found at i:228865 original size:45 final size:44
Alignment explanation
Indices: 228812--228902 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 44
228802 TTTGGTTCGC
228812 TGTAATGGAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AATTC-ATGTGTTTGGTTGAA
* *
228857 TGTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAA
228901 TG
1 TG
228903 GGATGGAGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.42
45 24 0.56
ACGTcount: A:0.30, C:0.05, G:0.29, T:0.36
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAA
Found at i:228909 original size:44 final size:45
Alignment explanation
Indices: 228815--228909 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 45
228805 GGTTCGCTGT
*
228815 AATGGAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTGAATGT
1 AATGGAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTGAATGG
* *
228860 AATGGAATAGAGGCGTAATAG-TATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAATGG
*
228904 GATGGA
1 AATGGA
228910 GCTGTAATAG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.34
Consensus pattern (45 bp):
AATGGAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTGAATGG
Found at i:229092 original size:16 final size:15
Alignment explanation
Indices: 229071--229100 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
229061 ATTATATCAA
229071 TTTAATATACTATTTT
1 TTTAATATA-TATTTT
229087 TTTAATATATATTT
1 TTTAATATATATTT
229101 AATTATCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTAATATATATTTT
Found at i:231380 original size:182 final size:180
Alignment explanation
Indices: 230748--231465 Score: 726
Period size: 182 Copynumber: 4.0 Consensus size: 180
230738 TTCCATTACT
* * * * * **
230748 TTTCTCCTTTACTGACACAAACAAATACATAAATAGA-TCACTTTCATCAACTTAACCTGATTTT
1 TTTCTCCTTT-CTGAGACAAATATATACATAAATGGACT-ATTTTCATCAA-TTAACCTGACATT
* * *
230812 TAACACTCCATTAAGCTTAATATTAGCTGCAATTCACTGCTTCTTGATTAATTGTAGTTTGCTTC
63 TAACACTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTTC
* * * * * *
230877 TAAAAAAGAAACTTAACTGACTGAAGCCTGATTATAACATGTAATACTTCAAC
128 TAAGAAAGAAACTAAACTAACCGAAGCCTGATTACAACATGTTATACTTCAAC
*
230930 TTTCTCCTTTTCTGAGACAAATATATACATGAATGGACTATTTTCATCAAATTAACCTGACATTT
1 TTTCTCC-TTTCTGAGACAAATATATACATAAATGGACTATTTTCATC-AATTAACCTGACATTT
* * * * * *
230995 AACCCTCCATTAAGCTTAATA-AAGCTGAAATTCACAGCTTCTTGATTAATAGCAA-TTGGTCAC
64 AACACTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCT-TC
* * * * * *
231058 T-GGAAAAGAAACTAAACTAACCCAAGCCCGGTTACAAC-TTTTGATACTTGAA-
128 TAAG-AAAGAAACTAAACTAACCGAAGCCTGATTACAACATGTT-ATACTTCAAC
*
231110 -TCCT-C-TTCTGAGACAAATATGA-ACATAAATGGACTATTTTCATCAATTTAACCTGACATTT
1 TTTCTCCTTTCTGAGACAAATAT-ATACATAAATGGACTATTTTCATCAA-TTAACCTGACATTT
*
231171 AACCCTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGA-TATATTGCAATTTGCTTC
64 AACACTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTA-ATTGCAATTTGCTTC
* * * *
231235 TAAGAAAGAAACTGAACTGACTGAAGCCTGATTACAACATGTTATACATCAAC
128 TAAGAAAGAAACTAAACTAACCGAAGCCTGATTACAACATGTTATACTTCAAC
* * ** ** *
231288 TTTCTCCTTTCCTAAGACAAATATATACATAAACGGGTTATTTTTGTCAATGTAA-CTCA-ATTT
1 TTTCTCCTTT-CTGAGACAAATATATACATAAATGGACTATTTTCATCAAT-TAACCTGACA-TT
* ** * * * * *
231351 CTAACACTCCATCAAGCTTAATATTAGCTGCAATTTGCATCTTCTTGATGACTTTCAAATTGCTT
63 -TAACACTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTT
* *
231416 CCTAA-AAAGAAACTAAACTAACCGAAGCCTGATTACAACACGTGATACTT
127 -CTAAGAAAGAAACTAAACTAACCGAAGCCTGATTACAACATGTTATACTT
231466 AATCCATAAT
Statistics
Matches: 443, Mismatches: 69, Indels: 48
0.79 0.12 0.09
Matches are distributed among these distances:
175 2 0.00
176 73 0.16
177 66 0.15
178 9 0.02
179 6 0.01
180 8 0.02
181 74 0.17
182 194 0.44
183 11 0.02
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (180 bp):
TTTCTCCTTTCTGAGACAAATATATACATAAATGGACTATTTTCATCAATTAACCTGACATTTAA
CACTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTTCTAA
GAAAGAAACTAAACTAACCGAAGCCTGATTACAACATGTTATACTTCAAC
Found at i:232139 original size:11 final size:11
Alignment explanation
Indices: 232123--232153 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
232113 ACCAAATTGG
232123 CGTAATAGGCC
1 CGTAATAGGCC
*
232134 CGTAATAGACC
1 CGTAATAGGCC
232145 CGTAATAGG
1 CGTAATAGG
232154 GTATTACAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (11 bp):
CGTAATAGGCC
Found at i:239618 original size:15 final size:14
Alignment explanation
Indices: 239580--239609 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
239570 TAAAGCTTAG
239580 AGAAAAAAATTGTT
1 AGAAAAAAATTGTT
239594 AGAAAAAAATTGTT
1 AGAAAAAAATTGTT
239608 AG
1 AG
239610 TTCAAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.27
Consensus pattern (14 bp):
AGAAAAAAATTGTT
Found at i:240008 original size:18 final size:19
Alignment explanation
Indices: 239987--240036 Score: 77
Period size: 18 Copynumber: 2.7 Consensus size: 19
239977 AGCAACCGAT
239987 GGAGGAACATGCTCGA-GA
1 GGAGGAACATGCTCGAGGA
*
240005 GGAGGAACATGCT-TAGGA
1 GGAGGAACATGCTCGAGGA
240023 GGAGGAACATGCTC
1 GGAGGAACATGCTC
240037 CGGTGCTGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 1 0.03
18 28 0.97
ACGTcount: A:0.32, C:0.16, G:0.38, T:0.14
Consensus pattern (19 bp):
GGAGGAACATGCTCGAGGA
Found at i:241378 original size:27 final size:27
Alignment explanation
Indices: 241348--241542 Score: 194
Period size: 27 Copynumber: 7.2 Consensus size: 27
241338 TCATCTCCTA
**
241348 GGGGTATAACAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
241375 GGGGTATTTCAATCATTTTATCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
241402 AGGCTATTTCGGTCATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* * **
241429 GGGTTATTTTAGTCATTTTACTTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
241456 GGGGTATTT-TGTTCATTTTACTCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
* * *
241483 GGGGTATTTCGGTCATTCTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
*
241510 GGGGTATTTTAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
241537 GAGGTA
1 GGGGTA
241543 GTTTGGTCAT
Statistics
Matches: 135, Mismatches: 31, Indels: 4
0.79 0.18 0.02
Matches are distributed among these distances:
26 1 0.01
27 133 0.99
28 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:241472 original size:81 final size:81
Alignment explanation
Indices: 241358--241542 Score: 264
Period size: 81 Copynumber: 2.3 Consensus size: 81
241348 GGGGTATAAC
*
241358 AGTCATTTTACCCTATGGGGGTATTTCAATCATTTTA-TCTTATGAGGCTATTTCGGTCATTTTA
1 AGTCATTTTACCCTATGGGGGTATTTCAATCATTTTACTC-TATGAGGCTATTTCGGTCATTCTA
*
241422 CCCTATAGGGTTATTTT
65 CCCTATAGGGGTATTTT
** *** * *
241439 AGTCATTTTACTTTATGGGGGTATTTTGTTCATTTTACTCTATGGGGGTATTTCGGTCATTCTAC
1 AGTCATTTTACCCTATGGGGGTATTTCAATCATTTTACTCTATGAGGCTATTTCGGTCATTCTAC
241504 CCTATAGGGGTATTTT
66 CCTATAGGGGTATTTT
*
241520 AGTCATTTTACCCTATGGAGGTA
1 AGTCATTTTACCCTATGGGGGTA
241543 GTTTGGTCAT
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 89 0.98
82 2 0.02
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (81 bp):
AGTCATTTTACCCTATGGGGGTATTTCAATCATTTTACTCTATGAGGCTATTTCGGTCATTCTAC
CCTATAGGGGTATTTT
Found at i:244597 original size:2 final size:2
Alignment explanation
Indices: 244590--244618 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
244580 GGATTAAGTG
244590 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 A
244619 AAACCAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:249326 original size:456 final size:456
Alignment explanation
Indices: 248473--249384 Score: 1824
Period size: 456 Copynumber: 2.0 Consensus size: 456
248463 ATCTTATAAC
248473 ATCATTTACATTTACTTCCCAAAATGACAAGCATAAGACATCCTAGGTACATGTCGACACAAAAA
1 ATCATTTACATTTACTTCCCAAAATGACAAGCATAAGACATCCTAGGTACATGTCGACACAAAAA
248538 GAAATATACATCACCACGTTTTGAGTCCGGGATCATTGATGGATACTGAATCGGCAATCTAACTT
66 GAAATATACATCACCACGTTTTGAGTCCGGGATCATTGATGGATACTGAATCGGCAATCTAACTT
248603 TAACCTAACCTGCACATGGAAAACAAACCGTACTCTGAGTAAAACTCAGTGGTATTTCTATAATC
131 TAACCTAACCTGCACATGGAAAACAAACCGTACTCTGAGTAAAACTCAGTGGTATTTCTATAATC
248668 TAAATAATTTAAACAAGATATTACAGTTATACATTTGAAATATAAACACTTATTAATATTTAAAT
196 TAAATAATTTAAACAAGATATTACAGTTATACATTTGAAATATAAACACTTATTAATATTTAAAT
248733 ACTATAACAATCATATCATATTCCATTTGTTTCAGAATATCTCAATTCTCATACTTGCTATATAA
261 ACTATAACAATCATATCATATTCCATTTGTTTCAGAATATCTCAATTCTCATACTTGCTATATAA
248798 ATAGCTTTTCACAATTTATTTCACATTTGATCATACATTTGCAATATCCATTCCACATTCAACTC
326 ATAGCTTTTCACAATTTATTTCACATTTGATCATACATTTGCAATATCCATTCCACATTCAACTC
248863 ATGAGTATATAACTCATATAGTCTATGTATTTGCAACATATTTCATAATCTATTTTCAATTCACT
391 ATGAGTATATAACTCATATAGTCTATGTATTTGCAACATATTTCATAATCTATTTTCAATTCACT
248928 A
456 A
248929 ATCATTTACATTTACTTCCCAAAATGACAAGCATAAGACATCCTAGGTACATGTCGACACAAAAA
1 ATCATTTACATTTACTTCCCAAAATGACAAGCATAAGACATCCTAGGTACATGTCGACACAAAAA
248994 GAAATATACATCACCACGTTTTGAGTCCGGGATCATTGATGGATACTGAATCGGCAATCTAACTT
66 GAAATATACATCACCACGTTTTGAGTCCGGGATCATTGATGGATACTGAATCGGCAATCTAACTT
249059 TAACCTAACCTGCACATGGAAAACAAACCGTACTCTGAGTAAAACTCAGTGGTATTTCTATAATC
131 TAACCTAACCTGCACATGGAAAACAAACCGTACTCTGAGTAAAACTCAGTGGTATTTCTATAATC
249124 TAAATAATTTAAACAAGATATTACAGTTATACATTTGAAATATAAACACTTATTAATATTTAAAT
196 TAAATAATTTAAACAAGATATTACAGTTATACATTTGAAATATAAACACTTATTAATATTTAAAT
249189 ACTATAACAATCATATCATATTCCATTTGTTTCAGAATATCTCAATTCTCATACTTGCTATATAA
261 ACTATAACAATCATATCATATTCCATTTGTTTCAGAATATCTCAATTCTCATACTTGCTATATAA
249254 ATAGCTTTTCACAATTTATTTCACATTTGATCATACATTTGCAATATCCATTCCACATTCAACTC
326 ATAGCTTTTCACAATTTATTTCACATTTGATCATACATTTGCAATATCCATTCCACATTCAACTC
249319 ATGAGTATATAACTCATATAGTCTATGTATTTGCAACATATTTCATAATCTATTTTCAATTCACT
391 ATGAGTATATAACTCATATAGTCTATGTATTTGCAACATATTTCATAATCTATTTTCAATTCACT
249384 A
456 A
249385 TTTCACTTCC
Statistics
Matches: 456, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
456 456 1.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.34
Consensus pattern (456 bp):
ATCATTTACATTTACTTCCCAAAATGACAAGCATAAGACATCCTAGGTACATGTCGACACAAAAA
GAAATATACATCACCACGTTTTGAGTCCGGGATCATTGATGGATACTGAATCGGCAATCTAACTT
TAACCTAACCTGCACATGGAAAACAAACCGTACTCTGAGTAAAACTCAGTGGTATTTCTATAATC
TAAATAATTTAAACAAGATATTACAGTTATACATTTGAAATATAAACACTTATTAATATTTAAAT
ACTATAACAATCATATCATATTCCATTTGTTTCAGAATATCTCAATTCTCATACTTGCTATATAA
ATAGCTTTTCACAATTTATTTCACATTTGATCATACATTTGCAATATCCATTCCACATTCAACTC
ATGAGTATATAACTCATATAGTCTATGTATTTGCAACATATTTCATAATCTATTTTCAATTCACT
A
Found at i:249792 original size:11 final size:11
Alignment explanation
Indices: 249776--249800 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
249766 TTCAATTCAA
249776 ATAATCAATAT
1 ATAATCAATAT
249787 ATAATCAATAT
1 ATAATCAATAT
249798 ATA
1 ATA
249801 TATATATACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATCAATAT
Found at i:252254 original size:20 final size:21
Alignment explanation
Indices: 252208--252255 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
252198 TATTTTGAAG
252208 ATGGTATCAATAATTTTATAA
1 ATGGTATCAATAATTTTATAA
*
252229 A-AGTATCAATAATTTTA-AA
1 ATGGTATCAATAATTTTATAA
252248 ATGGTATC
1 ATGGTATC
252256 GATACCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 20 0.83
21 1 0.04
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (21 bp):
ATGGTATCAATAATTTTATAA
Found at i:252498 original size:19 final size:19
Alignment explanation
Indices: 252452--252499 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
252442 GTATATATTT
252452 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
* *
252470 TAAATCTTATTTAGGTATA
1 TAAATTTTATTTAGGTAGA
*
252489 TAAGTTTTATT
1 TAAATTTTATT
252500 CATATTCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.50
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:257117 original size:19 final size:18
Alignment explanation
Indices: 257088--257127 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
257078 GTATATATTT
257088 TAAATTTATTTAGGTAGA
1 TAAATTTATTTAGGTAGA
257106 TAAATCTTATTTAGGTAGA
1 TAAAT-TTATTTAGGTAGA
257125 TAA
1 TAA
257128 GTTTTCTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (18 bp):
TAAATTTATTTAGGTAGA
Found at i:258527 original size:19 final size:20
Alignment explanation
Indices: 258500--258547 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
258490 CTTGGTAAAT
*
258500 ACATGTGTA-ATAATAATAA
1 ACATATGTATATAATAATAA
*
258519 ACATATGTATTTAATAATAA
1 ACATATGTATATAATAATAA
258539 A-ATATGTAT
1 ACATATGTAT
258548 TGCTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (20 bp):
ACATATGTATATAATAATAA
Found at i:258548 original size:19 final size:20
Alignment explanation
Indices: 258510--258548 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
258500 ACATGTGTAA
258510 TAATAATAAACATATGTATT
1 TAATAATAAACATATGTATT
258530 TAATAATAAA-ATATGTATT
1 TAATAATAAACATATGTATT
258549 GCTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TAATAATAAACATATGTATT
Found at i:259383 original size:24 final size:24
Alignment explanation
Indices: 259356--259402 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
259346 ATTGAAATGG
259356 ATTG-ATTTAATATGTGA-TGAATTT
1 ATTGAATTT-ATAT-TGATTGAATTT
259380 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
259403 AGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 14 0.67
25 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:259593 original size:41 final size:39
Alignment explanation
Indices: 259539--259670 Score: 133
Period size: 40 Copynumber: 3.4 Consensus size: 39
259529 CGACTTTGAG
259539 TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAAT
1 TCGATGAGACACTGGGTGTCAA-TTATTACTTCGGATT-AT
* * * * * *
259580 TCAATGAGGCACTGGGTGCCAA-T-TTACTTCAGTTTAG
1 TCGATGAGACACTGGGTGTCAATTATTACTTCGGATTAT
* * *
259617 CCGATGAGACACTGTGTGTCAAATTATTACTTCGAATTAT
1 TCGATGAGACACTGGGTGTC-AATTATTACTTCGGATTAT
*
259657 TCGATGAGGCACTG
1 TCGATGAGACACTG
259671 AGTGCCAAAC
Statistics
Matches: 71, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
37 16 0.23
38 12 0.17
39 2 0.03
40 22 0.31
41 19 0.27
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (39 bp):
TCGATGAGACACTGGGTGTCAATTATTACTTCGGATTAT
Found at i:266687 original size:33 final size:33
Alignment explanation
Indices: 266650--266714 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
266640 CAATACAACC
266650 AATGTCTCAATTTCATATATATTATCAACTTGA
1 AATGTCTCAATTTCATATATATTATCAACTTGA
266683 AATGTCTCAATTTCATATATATTATCAACTTG
1 AATGTCTCAATTTCATATATATTATCAACTTG
266715 TATGCATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.43
Consensus pattern (33 bp):
AATGTCTCAATTTCATATATATTATCAACTTGA
Found at i:274245 original size:19 final size:20
Alignment explanation
Indices: 274197--274245 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
274187 ATTCATCATG
274197 TTAA-TATTTTTAACATAAT
1 TTAATTATTTTTAACATAAT
274216 TTAATTA-TTTTATA-AT-AT
1 TTAATTATTTTTA-ACATAAT
274234 TTAATTATTTTT
1 TTAATTATTTTT
274246 GACAAGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.33
19 15 0.56
20 3 0.11
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAATTATTTTTAACATAAT
Found at i:282377 original size:30 final size:31
Alignment explanation
Indices: 282333--282392 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
282323 TTCTTATGTC
282333 AATATTTCGATACCCACATCTTTGAATTTCT
1 AATATTTCGATACCCACATCTTTGAATTTCT
** *
282364 AATATTT-GATACCCTTATCTTTGACTTTC
1 AATATTTCGATACCCACATCTTTGAATTTC
282393 CATAATATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.45
Consensus pattern (31 bp):
AATATTTCGATACCCACATCTTTGAATTTCT
Found at i:298826 original size:27 final size:27
Alignment explanation
Indices: 298790--299308 Score: 592
Period size: 27 Copynumber: 19.2 Consensus size: 27
298780 AGAGGTCAAT
*
298790 AAATGACCAAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
298817 AAATGACCAAAATACTCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
298844 AAATGACCGAAATACCCCCGTAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
298871 AAATGGCCGAAATACCCCCCATAGGGTA
1 AAATGACCGAAATA-CCCCCATAGGGTA
* *
298899 GAATGACC-AAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
298925 AAAT-AGCCAAAATAACCCCATAGGGTA
1 AAATGA-CCGAAATACCCCCATAGGGTA
*
298952 AAATAACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
298979 GAACGCCCGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* **
299006 AAAGGACCGAAATACCCTTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* **
299033 AAATGACTGAAATACTTCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
299060 AAATGACTGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
299087 AAATGACCAAAATAACCCCACAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
299114 GAATGACAGAAATACCCCCATAGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
299141 AAATGACTGAAATACCCCCATAAGATA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
299168 AAATGACTGAAATACCCCCATAAGATA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
299195 AAATGACCGAAATACCCCTATAGTGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
299222 AAATGATCGAAATAACCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
299249 GAATGATCGAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
299276 AAATAATCGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
299303 AAATGA
1 AAATGA
299309 TTGTTATACC
Statistics
Matches: 423, Mismatches: 65, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
25 1 0.00
26 17 0.04
27 386 0.91
28 19 0.04
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.18
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:308099 original size:15 final size:15
Alignment explanation
Indices: 308081--308122 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
308071 TCTTTAGGTT
308081 TTTTTAGGGTTAT-GG
1 TTTTTAGGGTT-TGGG
*
308096 TTTTTAAGGTTTGGG
1 TTTTTAGGGTTTGGG
*
308111 GTTTTAGGGTTT
1 TTTTTAGGGTTT
308123 TTTGGAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 1 0.04
15 22 0.96
ACGTcount: A:0.12, C:0.00, G:0.33, T:0.55
Consensus pattern (15 bp):
TTTTTAGGGTTTGGG
Found at i:308190 original size:17 final size:16
Alignment explanation
Indices: 308147--308216 Score: 61
Period size: 16 Copynumber: 4.2 Consensus size: 16
308137 TTTTTGGTAC
* * *
308147 TTTAGGGTTTATGTTT
1 TTTAGAGTTTAAGGTT
*
308163 TTTAGATTTTAAGGTT
1 TTTAGAGTTTAAGGTT
*
308179 TTTACGAGTTTAGGGCTT
1 TTTA-GAGTTTAAGG-TT
308197 TTATAG-GTTTAAGGTT
1 TT-TAGAGTTTAAGGTT
308213 TTTA
1 TTTA
308217 ACTGTTCTGG
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
15 2 0.05
16 20 0.45
17 15 0.34
18 5 0.11
19 2 0.05
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (16 bp):
TTTAGAGTTTAAGGTT
Found at i:312879 original size:23 final size:23
Alignment explanation
Indices: 312849--312893 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
312839 TTTCTTAGTG
*
312849 TAGTAATTTTCGGGATATTACAA
1 TAGTAATTTTCAGGATATTACAA
312872 TAGTAATTTTCAGGATATTACA
1 TAGTAATTTTCAGGATATTACA
312894 GAGCAATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.40
Consensus pattern (23 bp):
TAGTAATTTTCAGGATATTACAA
Done.