Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold239
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: 152578
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3359 original size:13 final size:13
Alignment explanation
Indices: 3341--3367 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3331 ACAGCTTGCT
3341 TTGTATCGATACA
1 TTGTATCGATACA
3354 TTGTATCGATACA
1 TTGTATCGATACA
3367 T
1 T
3368 ATTTATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3462 original size:20 final size:20
Alignment explanation
Indices: 3437--3474 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3427 TATCACTATT
3437 TGTATCGATACATGGTATAA
1 TGTATCGATACATGGTATAA
*
3457 TGTATCGATACATTGTAT
1 TGTATCGATACATGGTAT
3475 CGATACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATGGTATAA
Found at i:3473 original size:13 final size:13
Alignment explanation
Indices: 3457--3515 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
3447 CATGGTATAA
3457 TGTATCGATACAT
1 TGTATCGATACAT
3470 TGTATCGATACA-
1 TGTATCGATACAT
3482 TG-AT-GA-A-A-
1 TGTATCGATACAT
*
3490 TGTATCAATACAT
1 TGTATCGATACAT
3503 TGTATCGATACAT
1 TGTATCGATACAT
3516 GATGAAATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 3 0.08
9 3 0.08
10 3 0.08
11 3 0.08
12 3 0.08
13 24 0.62
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3478 original size:33 final size:33
Alignment explanation
Indices: 3436--3538 Score: 163
Period size: 33 Copynumber: 3.1 Consensus size: 33
3426 CTATCACTAT
*
3436 TTGTATCGATACATGGT-ATAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
*
3469 TTGTATCGATACATGATGAAATGTATCAATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
*
3502 TTGTATCGATACATGATGAAATCTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
3535 TTGT
1 TTGT
3539 TTGTAACAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
33 64 0.98
34 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:3493 original size:20 final size:20
Alignment explanation
Indices: 3470--3535 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
3460 ATCGATACAT
3470 TGTATCGATACATGATGAAA
1 TGTATCGATACATGATGAAA
*
3490 TGTATCAATAC---AT----
1 TGTATCGATACATGATGAAA
3503 TGTATCGATACATGATGAAA
1 TGTATCGATACATGATGAAA
*
3523 TCTATCGATACAT
1 TGTATCGATACAT
3536 TGTTTGTAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 14
0.68 0.06 0.26
Matches are distributed among these distances:
13 10 0.28
16 2 0.06
17 2 0.06
20 22 0.61
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATGATGAAA
Found at i:8296 original size:328 final size:329
Alignment explanation
Indices: 7698--8319 Score: 1219
Period size: 328 Copynumber: 1.9 Consensus size: 329
7688 AGTGGGCCTT
*
7698 TTTTTTTTCTTTCCTGGCCCTAATTTTTTTGGATGGAAAACTCTTTAATTATAATTTTCTCGGCC
1 TTTTTTTTCTTTCCTGGCCCTAATTTTTTTGGATGGAAAACTCTTTAATTATAATTTTCTCGACC
7763 TTTACAGTCATTTTAATCATCTCTCTAGAAATTACAAGATCAACAAAATTCTTGTTGCATTTTCT
66 TTTACAGTCATTTTAATCATCTCTCTAGAAATTACAAGATCAACAAAATTCTTGTTGCATTTTCT
7828 ACTAACTTTTCATGATAGGAGGATAAAGGGTATTCACGAATAGCATTAAGGTTTCTTTCTTAATC
131 ACTAACTTTTCATGATAGGAGGATAAAGGGTATTCACGAATAGCATTAAGGTTTCTTTCTTAATC
7893 AAAAGAGGTCGGACCTGAGAGGCCATTTTTCTCTATTTTTGTGTATATTCCTTAAAAGATTTCAT
196 AAAAGAGGTCGGACCTGAGAGGCCATTTTTCTCTATTTTTGTGTATATTCCTTAAAAGATTTCAT
*
7958 GGACTTCTTTTCCATGCTCTGAAGGGTTAGTTTACAGTCATTTTAAAAGAGGTCGGACCTGAGAG
261 GGACTTCTTTTCCATGCTCTAAAGGGTTAGTTTACAGTCATTTTAAAAGAGGTCGGACCTGAGAG
8023 GCCA
326 GCCA
8027 TTTTTTTTCTTTCCTGGCCCTAA-TTTTTTGGATGGAAAACTCTTTAATTATAATTTTCTCGACC
1 TTTTTTTTCTTTCCTGGCCCTAATTTTTTTGGATGGAAAACTCTTTAATTATAATTTTCTCGACC
8091 TTTACAGTCATTTTAATCATCTCTCTAGAAATTACAAGATCAACAAAATTCTTGTTGCATTTTCT
66 TTTACAGTCATTTTAATCATCTCTCTAGAAATTACAAGATCAACAAAATTCTTGTTGCATTTTCT
8156 ACTAACTTTTCATGATAGGAGGATAAAGGGTATTCACGAATAGCATTAAGGTTTCTTTCTTAATC
131 ACTAACTTTTCATGATAGGAGGATAAAGGGTATTCACGAATAGCATTAAGGTTTCTTTCTTAATC
8221 AAAAGAGGTCGGACCTGAGAGGCCATTTTTCTCTATTTTTGTGTATATTCCTTAAAAGATTTCAT
196 AAAAGAGGTCGGACCTGAGAGGCCATTTTTCTCTATTTTTGTGTATATTCCTTAAAAGATTTCAT
8286 GGACTTCTTTTCCATGCTCTAAAGGGTTAGTTTA
261 GGACTTCTTTTCCATGCTCTAAAGGGTTAGTTTA
8320 TCAGGCAACC
Statistics
Matches: 291, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
328 268 0.92
329 23 0.08
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (329 bp):
TTTTTTTTCTTTCCTGGCCCTAATTTTTTTGGATGGAAAACTCTTTAATTATAATTTTCTCGACC
TTTACAGTCATTTTAATCATCTCTCTAGAAATTACAAGATCAACAAAATTCTTGTTGCATTTTCT
ACTAACTTTTCATGATAGGAGGATAAAGGGTATTCACGAATAGCATTAAGGTTTCTTTCTTAATC
AAAAGAGGTCGGACCTGAGAGGCCATTTTTCTCTATTTTTGTGTATATTCCTTAAAAGATTTCAT
GGACTTCTTTTCCATGCTCTAAAGGGTTAGTTTACAGTCATTTTAAAAGAGGTCGGACCTGAGAG
GCCA
Found at i:9359 original size:12 final size:12
Alignment explanation
Indices: 9342--9366 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9332 CGATACATAA
9342 AGTTGTATCGAT
1 AGTTGTATCGAT
9354 AGTTGTATCGAT
1 AGTTGTATCGAT
9366 A
1 A
9367 CATAGTTGTA
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:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (12 bp):
AGTTGTATCGAT
Found at i:9434 original size:13 final size:13
Alignment explanation
Indices: 9416--9440 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9406 ATTACCCAAA
9416 TGTATCGATACAT
1 TGTATCGATACAT
9429 TGTATCGATACA
1 TGTATCGATACA
9441 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:9507 original size:52 final size:52
Alignment explanation
Indices: 9451--9577 Score: 218
Period size: 52 Copynumber: 2.4 Consensus size: 52
9441 CTGATCTTTG
9451 TATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAATA
1 TATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAATA
* * *
9503 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAATA
*
9555 TATTGATACATGCAGGCAAATTT
1 TATCGATACATGCAGGCAAATTT
9578 TCATATTTCG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (52 bp):
TATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAATA
Found at i:14653 original size:19 final size:19
Alignment explanation
Indices: 14608--14680 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
14598 CTACCAGTTT
* *
14608 CATGTATCAATACAATTGAG
1 CATGTATCGATACAA-TGAA
*
14628 TATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
14647 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
14668 -ATGTATCGATACA
1 CATGTATCGATACA
14681 TCTGGATGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 18 0.39
20 27 0.59
21 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:15383 original size:17 final size:17
Alignment explanation
Indices: 15361--15394 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
15351 TTCTCCCCCT
15361 TTGTCAAATGCCAATGC
1 TTGTCAAATGCCAATGC
15378 TTGTCAAATGCCAATGC
1 TTGTCAAATGCCAATGC
15395 CAAATTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (17 bp):
TTGTCAAATGCCAATGC
Found at i:17085 original size:31 final size:31
Alignment explanation
Indices: 17044--17117 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
17034 GTGTTTTTGT
* *
17044 TGATG-AATTTGAAGAAAAGTG-AAAGGAAT
1 TGATGAAATTTGAAGAAAAGTGAAAAAGAAA
* **
17073 TGATGCAAATTTGATGAAATTTGAAAAAGAAA
1 TGATG-AAATTTGAAGAAAAGTGAAAAAGAAA
17105 TGATGAAATTTGA
1 TGATGAAATTTGA
17118 GATTGAAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 5 0.14
31 21 0.57
32 11 0.30
ACGTcount: A:0.47, C:0.01, G:0.23, T:0.28
Consensus pattern (31 bp):
TGATGAAATTTGAAGAAAAGTGAAAAAGAAA
Found at i:23486 original size:13 final size:13
Alignment explanation
Indices: 23468--23494 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23458 TACAATAAAC
23468 ATGTATCGATACA
1 ATGTATCGATACA
23481 ATGTATCGATACA
1 ATGTATCGATACA
23494 A
1 A
23495 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:27338 original size:29 final size:29
Alignment explanation
Indices: 27306--27449 Score: 159
Period size: 29 Copynumber: 5.0 Consensus size: 29
27296 GTACTAAGTT
**
27306 CCTAAACTTTTCAAAATTATGCTTTGACC
1 CCTAAACTTTTCAAAATTACACTTTGACC
*
27335 CCTAAAC-TTTCTAAAATTACACTTTGA-T
1 CCTAAACTTTTC-AAAATTACACTTTGACC
*
27363 CCTATAACTTTTCAAAATTGCACTTTGACC
1 CCTA-AACTTTTCAAAATTACACTTTGACC
* * * *
27393 TCTAAAGTTTTCAAAAATGCACTTTG-CC
1 CCTAAACTTTTCAAAATTACACTTTGACC
* *
27421 CTTAAACTTTTCAAAATTACACTTGGACC
1 CCTAAACTTTTCAAAATTACACTTTGACC
27450 TAAAAATGGC
Statistics
Matches: 96, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
28 30 0.31
29 59 0.61
30 7 0.07
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.37
Consensus pattern (29 bp):
CCTAAACTTTTCAAAATTACACTTTGACC
Found at i:28636 original size:5 final size:5
Alignment explanation
Indices: 28626--28653 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28616 GAAACTGTTA
28626 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
28654 TTTTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:35690 original size:2 final size:2
Alignment explanation
Indices: 35685--35716 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
35675 TTATATAATG
*
35685 CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
35717 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:35949 original size:21 final size:21
Alignment explanation
Indices: 35912--36035 Score: 96
Period size: 21 Copynumber: 6.0 Consensus size: 21
35902 TTACAAATGT
*
35912 TATTAAAA-TTATTCCAAAGTTA
1 TATTAAAAGTTA--CCAAAATTA
35934 TATTAAAAGTTACCAAAATTA
1 TATTAAAAGTTACCAAAATTA
* *
35955 TTTTAAAAGTTATCAAAATTA
1 TATTAAAAGTTACCAAAATTA
* * *
35976 TATCAAAAGTTATC-TAA--A
1 TATTAAAAGTTACCAAAATTA
* *
35994 -ACTAAAGGTTACCAAAATTA
1 TATTAAAAGTTACCAAAATTA
* *
36014 TATCAAAAGTTATCTAAAATTA
1 TATTAAAAGTTA-CCAAAATTA
36036 AATGTTACCA
Statistics
Matches: 81, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
17 9 0.11
18 3 0.04
20 3 0.04
21 47 0.58
22 16 0.20
23 3 0.04
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (21 bp):
TATTAAAAGTTACCAAAATTA
Found at i:36019 original size:38 final size:38
Alignment explanation
Indices: 35958--36052 Score: 154
Period size: 38 Copynumber: 2.5 Consensus size: 38
35948 AAAATTATTT
*
35958 TAAAAGTTATCAAAATTATATCAAAAGTTATCTAAAAC
1 TAAAAGTTACCAAAATTATATCAAAAGTTATCTAAAAC
* *
35996 TAAAGGTTACCAAAATTATATCAAAAGTTATCTAAAAT
1 TAAAAGTTACCAAAATTATATCAAAAGTTATCTAAAAC
*
36034 TAAATGTTACCAAAATTAT
1 TAAAAGTTACCAAAATTAT
36053 CAAAATTATA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.33
Consensus pattern (38 bp):
TAAAAGTTACCAAAATTATATCAAAAGTTATCTAAAAC
Found at i:38000 original size:13 final size:13
Alignment explanation
Indices: 37969--38006 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
37959 TTGTATATTT
37969 TATTAA-TTTTAA
1 TATTAATTTTTAA
*
37981 T-TTAATTTTTAC
1 TATTAATTTTTAA
37993 TATTAATTTTTAA
1 TATTAATTTTTAA
38006 T
1 T
38007 TTTTACATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 4 0.18
12 7 0.32
13 11 0.50
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTAATTTTTAA
Found at i:43647 original size:20 final size:20
Alignment explanation
Indices: 43609--43649 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43599 GGGGCCACTC
*
43609 TTTTTTTTATTGATGTTCAT
1 TTTTTTTTATTGATATTCAT
* *
43629 TTTTTTTTTTTGCTATTCAT
1 TTTTTTTTATTGATATTCAT
43649 T
1 T
43650 CTCATTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.73
Consensus pattern (20 bp):
TTTTTTTTATTGATATTCAT
Found at i:51124 original size:16 final size:16
Alignment explanation
Indices: 51105--51182 Score: 63
Period size: 15 Copynumber: 4.9 Consensus size: 16
51095 AAAAAAAACC
51105 AAAAAAAACAAAAAAT
1 AAAAAAAACAAAAAAT
*
51121 -AAAAAAACTAAAAACT
1 AAAAAAAAC-AAAAAAT
*
51137 -AAAAAAACTAAAAA-
1 AAAAAAAACAAAAAAT
** *
51151 AAAACCAAGAAAAAAT
1 AAAAAAAACAAAAAAT
51167 AGCAAAAAAACAAAAA
1 A--AAAAAAACAAAAA
51183 GGGGTCTAGA
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
15 22 0.47
16 15 0.32
18 10 0.21
ACGTcount: A:0.81, C:0.10, G:0.03, T:0.06
Consensus pattern (16 bp):
AAAAAAAACAAAAAAT
Found at i:51133 original size:25 final size:25
Alignment explanation
Indices: 51096--51152 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
51086 TTACACCCCA
51096 AAAAAAACCAAAAA-AAACAAAAAAT
1 AAAAAAACCAAAAACAAA-AAAAAAT
* * *
51121 AAAAAAACTAAAAACTAAAAAAACT
1 AAAAAAACCAAAAACAAAAAAAAAT
51146 AAAAAAA
1 AAAAAAA
51153 AACCAAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 26 0.93
26 2 0.07
ACGTcount: A:0.82, C:0.11, G:0.00, T:0.07
Consensus pattern (25 bp):
AAAAAAACCAAAAACAAAAAAAAAT
Found at i:51182 original size:9 final size:9
Alignment explanation
Indices: 51094--51182 Score: 52
Period size: 11 Copynumber: 8.7 Consensus size: 9
51084 CTTTACACCC
51094 CAAAAAAAA
1 CAAAAAAAA
51103 CCAAAAAAAA
1 -CAAAAAAAA
51113 CAAAAAATAAA
1 C-AAAAA-AAA
*
51124 AAAACTAAAAA
1 CAAA--AAAAA
*
51135 CTAAAAAAA
1 CAAAAAAAA
51144 CTAAAAAAAAA
1 C--AAAAAAAA
51155 CCAAGAAAAAA
1 -CAA-AAAAAA
*
51166 TAGCAAAAAAA
1 CA--AAAAAAA
51177 CAAAAA
1 CAAAAA
51183 GGGGTCTAGA
Statistics
Matches: 63, Mismatches: 6, Indels: 21
0.70 0.07 0.23
Matches are distributed among these distances:
9 11 0.17
10 20 0.32
11 28 0.44
12 4 0.06
ACGTcount: A:0.80, C:0.12, G:0.02, T:0.06
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:53179 original size:14 final size:12
Alignment explanation
Indices: 53157--53193 Score: 56
Period size: 12 Copynumber: 2.9 Consensus size: 12
53147 AGAAGTTTTT
53157 AAAATCCTTAATA
1 AAAATCCTTAA-A
53170 AAATATCCTTAAA
1 AAA-ATCCTTAAA
53183 AAAATCCTTAA
1 AAAATCCTTAA
53194 GCGAGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 7 0.30
14 8 0.35
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAATCCTTAAA
Found at i:53669 original size:34 final size:37
Alignment explanation
Indices: 53611--53709 Score: 98
Period size: 34 Copynumber: 2.8 Consensus size: 37
53601 CCCTAAAAAA
* * *
53611 AGGCTTTGAAAAATCTTTAGTGAAATATCCATAAA-AG
1 AGGCCTTGAAATA-CTTTAATGAAATATCCATAAAGAG
*
53648 AGGCCTT-AAATAC-TTAATGAAATAT-CTTAAAGAG
1 AGGCCTTGAAATACTTTAATGAAATATCCATAAAGAG
* * *
53682 AGGCTTTGAAATTCTTTAATAAAATATC
1 AGGCCTTGAAATACTTTAATGAAATATC
53710 TTCAAGAGAG
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
33 5 0.10
34 19 0.37
35 6 0.12
36 15 0.29
37 6 0.12
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32
Consensus pattern (37 bp):
AGGCCTTGAAATACTTTAATGAAATATCCATAAAGAG
Found at i:53707 original size:36 final size:36
Alignment explanation
Indices: 53611--53721 Score: 120
Period size: 36 Copynumber: 3.1 Consensus size: 36
53601 CCCTAAAAAA
* * *
53611 AGGCTTTGAAAAATCTTTAGTGAAATATCCATAAA-AG
1 AGGCTTTG-AAATTCTTTAATGAAATAT-CTTAAAGAG
* *
53648 AGGCCTT-AAATAC-TTAATGAAATATCTTAAAGAG
1 AGGCTTTGAAATTCTTTAATGAAATATCTTAAAGAG
* *
53682 AGGCTTTGAAATTCTTTAATAAAATATCTTCAAGAG
1 AGGCTTTGAAATTCTTTAATGAAATATCTTAAAGAG
53718 AGGC
1 AGGC
53722 AGTCAGAAGC
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
33 5 0.08
34 19 0.31
35 9 0.15
36 23 0.37
37 6 0.10
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (36 bp):
AGGCTTTGAAATTCTTTAATGAAATATCTTAAAGAG
Found at i:54305 original size:21 final size:21
Alignment explanation
Indices: 54275--54318 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
54265 ATGCATATTT
*
54275 TCAATCAAAAAACCTTCTACC
1 TCAATAAAAAAACCTTCTACC
*
54296 TCAATAAAAAAACCTTCTGCC
1 TCAATAAAAAAACCTTCTACC
54317 TC
1 TC
54319 TATATTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.32, G:0.02, T:0.25
Consensus pattern (21 bp):
TCAATAAAAAAACCTTCTACC
Found at i:55142 original size:20 final size:20
Alignment explanation
Indices: 55117--55163 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
55107 TTTTTGACAA
* *
55117 AATGTATCATTACATAAGTT
1 AATGTATCACTACACAAGTT
*
55137 AATGTATCGCTACACAAGTT
1 AATGTATCACTACACAAGTT
55157 AATGTAT
1 AATGTAT
55164 TGATACATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGTATCACTACACAAGTT
Found at i:55170 original size:20 final size:20
Alignment explanation
Indices: 55117--55170 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
55107 TTTTTGACAA
*
55117 AATGTATC-ATTACATAAGTT
1 AATGTATCGA-TACACAAGTT
*
55137 AATGTATCGCTACACAAGTT
1 AATGTATCGATACACAAGTT
*
55157 AATGTATTGATACA
1 AATGTATCGATACA
55171 TATCCAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACACAAGTT
Found at i:67323 original size:43 final size:43
Alignment explanation
Indices: 67248--67708 Score: 249
Period size: 43 Copynumber: 9.9 Consensus size: 43
67238 ATAAAGATGT
* * * * *
67248 CAATATACTGATTTAAGGCCAACGATAGTGGACTTAAAAGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGTGC
* * *
67291 CAATTTACTGATTCAAGGCCAGCGACATTGGACCTAAAGATGACAAAGGCGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGA-CT-----T-A-AAA-GTGC
** * * *
67343 CAATATGCTGATTCAAGGCCAAAGATATTGGACATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGTGC
* * * *
67386 TAATGTGCTGATTCAAGGCCAGCGACGTTGGGCTT-AAAGATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAAG-TGC
* * *
67429 AAATATGCTGATTCAAGGCCAGCGACGTTGGGCTTAAATATGGTAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGAC-T---TA----AAA-GTGC
* * * *
67481 CAATATACTGATTCAAGGCCAGCAATATTGGACTTAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGTGC
* *
67524 CAATATGCTGATTTAAGGCCAGCGACATTAGACTTAAAGATGACAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGAC-T-----T-A-AAA-GTGC
* * * ** * *
67576 TAATATGCTGATTCAAGGCTAGTGATGTTGGGTTTAAAGATGGTAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATT-GG-----A-CT--TAAAAGTGC
* *
67628 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGTGC
* *
67671 CAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAA
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAA
67709 GATGACAAAG
Statistics
Matches: 326, Mismatches: 56, Indels: 72
0.72 0.12 0.16
Matches are distributed among these distances:
42 3 0.01
43 167 0.51
44 8 0.02
45 2 0.01
46 2 0.01
47 1 0.00
48 2 0.01
49 2 0.01
50 2 0.01
51 9 0.03
52 119 0.37
53 4 0.01
54 1 0.00
55 2 0.01
58 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (43 bp):
CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGTGC
Found at i:67373 original size:52 final size:51
Alignment explanation
Indices: 67287--67761 Score: 357
Period size: 52 Copynumber: 9.8 Consensus size: 51
67277 GGACTTAAAA
* * *
67287 GTGCCAATTTACTGATTCAAGGCCAGCGACATTGGACCTAAAGATGACAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-CAAAG
* ** *
67339 GCGCCAATATGCTGATTCAAGGCCAAAGATATTGGAC------AT--AAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGCAAAG
* * * *
67382 GTGCTAATGTGCTGATTCAAGGCCAGCGACGTTGGGCTTAAAGATGC--A-
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGCAAAG
* * * *
67430 -----AATATGCTGATTCAAGGCCAGCGACGTTGGGCTTAAATATGGTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-GCAAAG
* * *
67477 GTGCCAATATACTGATTCAAGGCCAGCAATATTGGAC-T-----T--AAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGCAAAG
* *
67520 GTGCCAATATGCTGATTTAAGGCCAGCGACATTAGACTTAAAGATGACAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-CAAAG
* * * ** ** *
67572 GTGCTAATATGCTGATTCAAGGCTAGTGATGTTGGGTTTAAAGATGGTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-GCAAAG
*
67624 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T--AAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGCAAAG
* *
67667 GTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-CAAAG
* * * * *
67719 GCGCCAATATGCTAATTCAAGGCCAACGATATTAGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
67762 GTGTCAATGT
Statistics
Matches: 334, Mismatches: 53, Indels: 72
0.73 0.12 0.16
Matches are distributed among these distances:
43 145 0.43
44 3 0.01
46 5 0.01
49 5 0.01
51 2 0.01
52 173 0.52
53 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (51 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGCAAAG
Found at i:67375 original size:95 final size:95
Alignment explanation
Indices: 67199--67806 Score: 410
Period size: 95 Copynumber: 6.4 Consensus size: 95
67189 GTATGATTAG
* * * * * * * * *
67199 TGTACAGATTCAAGGCCTA-CAACACTAGACTTAAAGATGATAAAGATGTCAATATACTGATTTA
1 TGTACTGATTCAAGGCC-AGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGATTCA
*
67263 AGGCCAACGATAGTGGACTTAAAAGTGCCAA
65 AGGCCAACGATATTGGACTTAAAAGTGCCAA
* * *
67294 TTTACTGATTCAAGGCCAGCGACATTGGACCTAAAGATGACAAAGGCGCCAATATGCTGATTCAA
1 TGTACTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGATTCAA
* * * *
67359 GGCCAAAGATATTGGACATAAAGGTGCTAA
66 GGCCAACGATATTGGACTTAAAAGTGCCAA
* * *
67389 TGTGCTGATTCAAGGCCAGCGACGTTGGGCTTAAAGATG-C--A------AATATGCTGATTCAA
1 TGTACTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGATTCAA
* ** *
67445 GGCCAGCGACGTTGGGCTTAAATATGGTAAAGGTGCCAA
66 GGCCAACGATATTGGAC-T---TA----AAA-GTGCCAA
* * * *
67484 TATACTGATTCAAGGCCAGCAATATTGGAC-T-----T---AAAGGTGCCAATATGCTGATTTAA
1 TGTACTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGATTCAA
* * * *
67540 GGCCAGCGACATTAGACTT-AAAGATGACAAA
66 GGCCAACGATATTGGACTTAAAAG-TG-CCAA
* * ** ** **
67571 GGTGCTAATATGCTGATTCAAGGCTAGTGATGTTGGGTTTAAAGATGGTAAAGGTGCCAATATGC
1 --TG----TA--CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGC
* *
67636 TGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAA
58 TGATTCAAGGCCAACGATATTGGACTTAAAAGTGCCAA
* * * *
67674 TGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTAATTCAA
1 TGTACTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGATTCAA
* * *
67739 GGCCAACGATATTAGACTTAAAGGTGTCAA
66 GGCCAACGATATTGGACTTAAAAGTGCCAA
* * * *
67769 TGTACGGATTCAAGGCTAGTGACATTGGGCTTAGAAGA
1 TGTACTGATTCAAGGCCAGCGACATTGGACTTA-AAGA
67807 AGATGCCACC
Statistics
Matches: 404, Mismatches: 70, Indels: 77
0.73 0.13 0.14
Matches are distributed among these distances:
85 1 0.00
86 32 0.08
87 3 0.01
89 3 0.01
90 2 0.00
91 1 0.00
92 1 0.00
93 2 0.00
94 6 0.01
95 296 0.73
96 5 0.01
97 1 0.00
101 3 0.01
103 3 0.01
104 42 0.10
105 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (95 bp):
TGTACTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGATTCAA
GGCCAACGATATTGGACTTAAAAGTGCCAA
Found at i:67761 original size:147 final size:147
Alignment explanation
Indices: 67430--67748 Score: 503
Period size: 147 Copynumber: 2.2 Consensus size: 147
67420 TAAAGATGCA
* *
67430 AATATGCTGATTCAAGGCCAGCGACGTTGGGCTTAAATATGGTAAAGGTGCCAATATACTGATTC
1 AATATGCTGATTCAAGGCCAGCGATGTTGGGCTTAAAGATGGTAAAGGTGCCAATATACTGATTC
*
67495 AAGGCCAGCAATATTGGACTTAAAGGTGCCAATATGCTGATTTAAGGCCAGCGACATTAGACTTA
66 AAGGCCAGCAATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTAGACTTA
* *
67560 AAGATGACAAAGGTGCT
131 AAGATGACAAAGGCGCC
* * * *
67577 AATATGCTGATTCAAGGCTAGTGATGTTGGGTTTAAAGATGGTAAAGGTGCCAATATGCTGATTC
1 AATATGCTGATTCAAGGCCAGCGATGTTGGGCTTAAAGATGGTAAAGGTGCCAATATACTGATTC
* * * *
67642 AAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTA
66 AAGGCCAGCAATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTAGACTTA
67707 AAGATGACAAAGGCGCC
131 AAGATGACAAAGGCGCC
* *
67724 AATATGCTAATTCAAGGCCAACGAT
1 AATATGCTGATTCAAGGCCAGCGAT
67749 ATTAGACTTA
Statistics
Matches: 155, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
147 155 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (147 bp):
AATATGCTGATTCAAGGCCAGCGATGTTGGGCTTAAAGATGGTAAAGGTGCCAATATACTGATTC
AAGGCCAGCAATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTAGACTTA
AAGATGACAAAGGCGCC
Found at i:67854 original size:32 final size:32
Alignment explanation
Indices: 67810--67970 Score: 200
Period size: 32 Copynumber: 5.0 Consensus size: 32
67800 TAGAAGAAGA
67810 TGCCACCAACTTGTGTGGGCTTTTA-AAAGGGT
1 TGCCACCAACTTGTGTGGGC-TTTAGAAAGGGT
* * *
67842 TGCCATCGACTTGTGTGGGCTTTAGAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGT
* *
67874 TGCCACCGACTTATGTGGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGT
* **
67906 TGCCACCAACTTGTGTAGGCTTT-GAAAAAAGT
1 TGCCACCAACTTGTGTGGGCTTTAG-AAAGGGT
* *
67938 TGTCATCAACTTGTGTGGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGT
67970 T
1 T
67971 TCTCCACTGG
Statistics
Matches: 110, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
31 5 0.05
32 104 0.95
33 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.31
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTAGAAAGGGT
Found at i:67894 original size:64 final size:63
Alignment explanation
Indices: 67794--67970 Score: 223
Period size: 64 Copynumber: 2.8 Consensus size: 63
67784 CTAGTGACAT
* * *
67794 TGGGC-TTAGAAGAAGATGCCACCAACTTGTGTGGGCTTTTA-AAAGGGTTGCCATCGACTTGTG
1 TGGGCTTTAGAA-AAGTTGCCACCAACTTGTGTGGGC-TTTAGAAAGGGTTGCCACCAACTTGTG
* *
67857 TGGGCTTTAGAAAAGGTTGCCACCGACTTATGTGGGCTTTAGAAAGGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAAAA-GTTGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAACTTGTG
* * * *
67921 TAGGCTTTGAAAAAAGTTGTCATCAACTTGTGTGGGCTTTAGAAAGGGTT
1 TGGGCTTT-AGAAAAGTTGCCACCAACTTGTGTGGGCTTTAGAAAGGGTT
67971 TCTCCACTGG
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
63 11 0.11
64 83 0.84
65 5 0.05
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (63 bp):
TGGGCTTTAGAAAAGTTGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAACTTGTG
Found at i:68186 original size:28 final size:28
Alignment explanation
Indices: 68147--68213 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
68137 AGCAAGTACT
*
68147 ACTGA-TTGTGGACTTCGAAA-ATATGCC
1 ACTGACTTGTGGACTTC-AAAGAGATGCC
* *
68174 ACTGACTTGTGGATTTCAAAGAGGTGCC
1 ACTGACTTGTGGACTTCAAAGAGATGCC
*
68202 ACTGACTAGTGG
1 ACTGACTTGTGG
68214 GCTTTGAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.24
28 26 0.76
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (28 bp):
ACTGACTTGTGGACTTCAAAGAGATGCC
Found at i:70137 original size:20 final size:21
Alignment explanation
Indices: 70112--70152 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
70102 AAGATGTTGG
70112 ACATA-CTAAAAATGCATGAA
1 ACATACCTAAAAATGCATGAA
*
70132 ACATACCTTAAAATGCATGAA
1 ACATACCTAAAAATGCATGAA
70153 CATGGGCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.22
Consensus pattern (21 bp):
ACATACCTAAAAATGCATGAA
Found at i:85394 original size:15 final size:13
Alignment explanation
Indices: 85354--85407 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
85344 TACTATGCCT
85354 AAAAAAACAAAAA
1 AAAAAAACAAAAA
85367 AAAAACAAC-AAAA
1 AAAAA-AACAAAAA
* *
85380 CACAAAACAAAAA
1 AAAAAAACAAAAA
*
85393 AAAAAGACAAAAA
1 AAAAAAACAAAAA
85406 AA
1 AA
85408 GAGGTGTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
12 3 0.09
13 28 0.82
14 3 0.09
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:86666 original size:41 final size:40
Alignment explanation
Indices: 86614--86757 Score: 143
Period size: 41 Copynumber: 3.6 Consensus size: 40
86604 CTTATTTCCT
* * *
86614 TTTTCCTTTGTCCTCAAGGAGCATGACCCATTTCATCTTC
1 TTTTCCTTTGTCCTCAAAGAGTAAGACCCATTTCATCTTC
* * * * *
86654 TTTTCTCGTTGTCATCAAAGAGTAGGA--CA-TAC-TCTTT
1 TTTTC-CTTTGTCCTCAAAGAGTAAGACCCATTTCATCTTC
*
86691 TTTTCCTTTATCCTCAAAGAGTAAGACCCATTTCATCTTC
1 TTTTCCTTTGTCCTCAAAGAGTAAGACCCATTTCATCTTC
* *
86731 TTTTCCCTTTGTCCTCAATGAGGAAGA
1 TTTT-CCTTTGTCCTCAAAGAGTAAGA
86758 TGTACTCATT
Statistics
Matches: 82, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
36 17 0.21
37 9 0.11
38 4 0.05
39 4 0.05
40 13 0.16
41 35 0.43
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (40 bp):
TTTTCCTTTGTCCTCAAAGAGTAAGACCCATTTCATCTTC
Found at i:86743 original size:77 final size:75
Alignment explanation
Indices: 86612--86792 Score: 218
Period size: 77 Copynumber: 2.4 Consensus size: 75
86602 TCCTTATTTC
* * * * *
86612 CTTTTTCCTTTGTCCTCAAGGAGCATGACCCATTTCATCTTCTTTTCTCGTTGTCATCAAAGAGT
1 CTTTTTCCTTTGTCCTCAAAGAGTAAGACCCATTTCATCTTCTTTTCCCGTTGTCATCAAAGAGG
*
86677 AGGACATACT
66 AAGACATACT
* * * *
86687 CTTTTTTTCCTTTATCCTCAAAGAGTAAGACCCATTTCATCTTCTTTTCCCTTTGTCCTCAATGA
1 C--TTTTTCCTTTGTCCTCAAAGAGTAAGACCCATTTCATCTTCTTTTCCCGTTGTCATCAAAGA
**
86752 GGAAGATGTACT
64 GGAAGACATACT
* *
86764 CATTTTCCTTTGTCCTCAAAAAGTAAGAC
1 CTTTTTCCTTTGTCCTCAAAGAGTAAGAC
86793 GTCTACTCTT
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
75 26 0.29
77 63 0.71
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (75 bp):
CTTTTTCCTTTGTCCTCAAAGAGTAAGACCCATTTCATCTTCTTTTCCCGTTGTCATCAAAGAGG
AAGACATACT
Found at i:86892 original size:43 final size:41
Alignment explanation
Indices: 86798--86910 Score: 97
Period size: 43 Copynumber: 2.7 Consensus size: 41
86788 AAGACGTCTA
* *
86798 CTCTTTTTC-CCTTTATCCTCAAGGAACGAGACACATTCTT
1 CTCTTTTTCTCCTTTATCCTCAAGGAGCAAGACACATTCTT
* * **
86838 TTTTTCCTTTCTCCTTTATCCTCAAGGAGCAAGACTTATTTCATT
1 CTCTT--TTTCTCCTTTATCCTCAAGGAGCAAGACACA-TTC-TT
*
86883 CTCTTTTTCT--TTTCATCCTCAAAGAGCA
1 CTCTTTTTCTCCTTT-ATCCTCAAGGAGCA
86911 TGACGTACTC
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
40 3 0.05
41 3 0.05
42 17 0.29
43 27 0.47
44 3 0.05
45 5 0.09
ACGTcount: A:0.21, C:0.27, G:0.09, T:0.42
Consensus pattern (41 bp):
CTCTTTTTCTCCTTTATCCTCAAGGAGCAAGACACATTCTT
Found at i:87011 original size:31 final size:31
Alignment explanation
Indices: 86976--87092 Score: 101
Period size: 31 Copynumber: 3.8 Consensus size: 31
86966 CCTCATTTAT
* *
86976 AAGCCCACATGAGTTGGTGGTACCCTAGTCA
1 AAGCCCACATAAGCTGGTGGTACCCTAGTCA
** * * * *
87007 AAGCCCGTACAAGCTGGAGGTACCCAAGTCT
1 AAGCCCACATAAGCTGGTGGTACCCTAGTCA
* * *
87038 AAGCCCGCATAAGTTGGTGGCA-CCTGAGTCA
1 AAGCCCACATAAGCTGGTGGTACCCT-AGTCA
* *
87069 AAGCTCACACAAGCTGGTGGTACC
1 AAGCCCACATAAGCTGGTGGTACC
87093 TAAGTTCGAG
Statistics
Matches: 64, Mismatches: 20, Indels: 3
0.74 0.23 0.03
Matches are distributed among these distances:
30 2 0.03
31 61 0.95
32 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.26, T:0.19
Consensus pattern (31 bp):
AAGCCCACATAAGCTGGTGGTACCCTAGTCA
Found at i:87072 original size:62 final size:62
Alignment explanation
Indices: 86975--87097 Score: 158
Period size: 62 Copynumber: 2.0 Consensus size: 62
86965 TCCTCATTTA
* * **
86975 TAAGCCCACATGAGTTGGTGGTACCCTAGTCAAAGCCCGTACAAGCTGGAGGTACCCAAGTC
1 TAAGCCCACATAAGTTGGTGGCACCCTAGTCAAAGCCCACACAAGCTGGAGGTACCCAAGTC
* * * *
87037 TAAGCCCGCATAAGTTGGTGGCA-CCTGAGTCAAAGCTCACACAAGCTGGTGGTACCTAAGT
1 TAAGCCCACATAAGTTGGTGGCACCCT-AGTCAAAGCCCACACAAGCTGGAGGTACCCAAGT
87098 TCGAGTCAAG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 3 0.06
62 49 0.94
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (62 bp):
TAAGCCCACATAAGTTGGTGGCACCCTAGTCAAAGCCCACACAAGCTGGAGGTACCCAAGTC
Found at i:87274 original size:149 final size:149
Alignment explanation
Indices: 87028--87603 Score: 672
Period size: 149 Copynumber: 3.8 Consensus size: 149
87018 AGCTGGAGGT
* * ** * * *
87028 ACCCAAGTCTAAGCCCGCATAAGTTGGTGGCACCTGAGTCAAAGCTCACACAAGCTGGTGGTACC
1 ACCCAAGTCTAAGCCCACACAAGTTGGCAGCATCTGAGTCAAAGCCCACACAAGCTGGTGGCACC
87093 TAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCTATCTAAGGAGGTCAAGCCTTAGAATGTCAAA
66 TAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCTATCTAAGGAGGTCAAGCCTTAGAATGTCAAA
* *
87158 GCTCGCACAAGCTAGTAGC
131 GCTCACACAAGCTAGTGGC
* * * *
87177 ACCCAAGTCTAAGCCCATACAAGTTGGCAGCATCTAAGTCAAAGCCCATATAAGCTGGTGGCACC
1 ACCCAAGTCTAAGCCCACACAAGTTGGCAGCATCTGAGTCAAAGCCCACACAAGCTGGTGGCACC
* * * *
87242 CAAGTTTGAGTCAAGTCCAAATTAGTTAGCACCTATGTAAGGAGGTCAAGCCTTAGAATGTCAAA
66 TAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCTATCTAAGGAGGTCAAGCCTTAGAATGTCAAA
*
87307 GC-CTACACAAGCTAGCGGC
131 GCTC-ACACAAGCTAGTGGC
* *** * * *
87326 ACTCAAGTCTAAGCTTGCACAAGTTGGCGGCATCTGATTCAAAGCCCACACAAGCTGGTAGCACC
1 ACCCAAGTCTAAGCCCACACAAGTTGGCAGCATCTGAGTCAAAGCCCACACAAGCTGGTGGCACC
* * *
87391 TAAGTTCAAGTCAAGTCAAAATTAGTTGGCAACTATCTAAGGAGGTCAAGCCTTAGAATGTCAAA
66 TAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCTATCTAAGGAGGTCAAGCCTTAGAATGTCAAA
* *
87456 GCTCACATAAGCTGGTGGC
131 GCTCACACAAGCTAGTGGC
* * * * *
87475 ACCTAAGTCTGAGTTAAAGCCTACACAAGCTAGCAGCAGAC-GAGTCAAAGCCCACACAAGCTGG
1 ACCCAAGTC-----T-AAGCCCACACAAGTTGGCAGCA-TCTGAGTCAAAGCCCACACAAGCTGG
* * * * * * *
87539 TGGTACCTAAG-TCTGAGTCAAGTCCACATTAATTGGCATCTGTCTAAAGAGGTCAAACCTTAGA
59 TGGCACCTAAGTTC-GAGTCAAGTCCAAATTAGTTGGCACCTATCTAAGGAGGTCAAGCCTTAGA
87603 A
123 A
87604 AACCAAAACC
Statistics
Matches: 359, Mismatches: 58, Indels: 14
0.83 0.13 0.03
Matches are distributed among these distances:
148 1 0.00
149 262 0.73
150 1 0.00
154 3 0.01
155 91 0.25
156 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (149 bp):
ACCCAAGTCTAAGCCCACACAAGTTGGCAGCATCTGAGTCAAAGCCCACACAAGCTGGTGGCACC
TAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCTATCTAAGGAGGTCAAGCCTTAGAATGTCAAA
GCTCACACAAGCTAGTGGC
Found at i:87505 original size:37 final size:37
Alignment explanation
Indices: 87450--87559 Score: 106
Period size: 37 Copynumber: 3.1 Consensus size: 37
87440 GCCTTAGAAT
* *
87450 GTCAAAGCTCACATAAGCTGGTGGCACCTAAGTCTGA
1 GTCAAAGCCCACACAAGCTGGTGGCACCTAAGTCTGA
* * * * *
87487 GTTAAAGCCTACACAAGC---TAGCAGC--AGAC-GA
1 GTCAAAGCCCACACAAGCTGGTGGCACCTAAGTCTGA
*
87518 GTCAAAGCCCACACAAGCTGGTGGTACCTAAGTCTGA
1 GTCAAAGCCCACACAAGCTGGTGGCACCTAAGTCTGA
87555 GTCAA
1 GTCAA
87560 GTCCACATTA
Statistics
Matches: 54, Mismatches: 13, Indels: 12
0.68 0.16 0.15
Matches are distributed among these distances:
31 18 0.33
32 3 0.06
34 9 0.17
36 3 0.06
37 21 0.39
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (37 bp):
GTCAAAGCCCACACAAGCTGGTGGCACCTAAGTCTGA
Found at i:92898 original size:43 final size:43
Alignment explanation
Indices: 92832--93326 Score: 324
Period size: 43 Copynumber: 10.7 Consensus size: 43
92822 TGTCAATACA
* * * * *
92832 CTGATTTAAGGCCAACGATATTGGACTTAAAGGTGCCAATTTA
1 CTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATATG
*
92875 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATG
1 CTGATTCAAGGCCAGCGACATTGGAC-T-----T---AAAGGTGCCAATATG
** * * * *
92927 CTGATTCAAGGCCAAAGATATTGGACATAAAGGTGCTAATGTG
1 CTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATATG
* * * *
92970 CTGATTCAAGGCCAGCGACGTTGGGCTTAAAGATGCAAATATG
1 CTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATATG
* *
93013 CTGATTCAAGGCCAGCGACGTTGGGCTTAAAGGTGCCAATATG
1 CTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATATG
* * *
93056 CTGATTTAAGGCCAGCAACATTAGACTTAAAGATGACAAAGGTGCCAATATG
1 CTGATTCAAGGCCAGCGACATTGGAC-T-----T---AAAGGTGCCAATATG
* * ** *
93108 CTGATTCAAGGCTAGTGATGTTGGGTTTAAAGATGGTAAAGGTGCCAATATG
1 CTGATTCAAGGCCAGCGACATT-GG-----A-CT--TAAAGGTGCCAATATG
* *
93160 CTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTG
1 CTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATATG
* *
93203 CTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAAGACGCCAATATG
1 CTGATTCAAGGCCAGCGACATTGGACTT-AA-A-G-----G-TGCCAATATG
* * * * * *
93255 CTAATTCAAGGCCAACGATATTAGACTTAAAGGTGTCAATGTG
1 CTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATATG
* *
93298 CTGATTCAAGGCCAGTGACATTGGGCTTA
1 CTGATTCAAGGCCAGCGACATTGGACTTA
93327 GAAGAAGATG
Statistics
Matches: 357, Mismatches: 61, Indels: 68
0.73 0.13 0.14
Matches are distributed among these distances:
43 202 0.57
44 5 0.01
45 2 0.01
46 3 0.01
49 3 0.01
50 1 0.00
51 5 0.01
52 131 0.37
53 1 0.00
55 2 0.01
58 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (43 bp):
CTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATATG
Found at i:92931 original size:95 final size:94
Alignment explanation
Indices: 92832--93191 Score: 367
Period size: 95 Copynumber: 3.8 Consensus size: 94
92822 TGTCAATACA
* * *
92832 CTGATTTAAGGCCAACGATATTGGACTTAAAGGTGCCAATTTACTGATTCAAGGCCAGCGACATT
1 CTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATT
92897 GGACTTAAAGATGACAAAGGCGCCAATATG
66 GGACTTAAAGATGACAAAGG-GCCAATATG
* * * * *
92927 CTGATTCAAGGCCAAAGATATTGGACATAAAGGTGCTAATGTGCTGATTCAAGGCCAGCGACGTT
1 CTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATT
*
92992 GGGCTTAAAGATG-C--A-----AATATG
66 GGACTTAAAGATGACAAAGGGCCAATATG
* ** * * *
93013 CTGATTCAAGGCCAGCGACGTTGGGCTTAAAGGTGCCAATATGCTGATTTAAGGCCAGCAACATT
1 CTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATT
*
93078 AGACTTAAAGATGACAAAGGTGCCAATATG
66 GGACTTAAAGATGACAAAGG-GCCAATATG
* ** * *
93108 CTGATTCAAGGCTAGTGATGTTGGGTTTAAAGATGGTAAAGGTGCCAATATGCTGATTCAAGGCC
1 CTGATTCAAGGCCAACGATATT-GG-----A-CT--TAAAGGTGCCAATATGCTGATTCAAGGCC
*
93173 AGCGATATTGGACTTAAAG
57 AGCGACATTGGACTTAAAG
93192 GTGCCAATGT
Statistics
Matches: 217, Mismatches: 30, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
86 71 0.33
87 1 0.00
89 1 0.00
92 1 0.00
94 1 0.00
95 95 0.44
96 2 0.01
102 1 0.00
104 44 0.20
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (94 bp):
CTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATT
GGACTTAAAGATGACAAAGGGCCAATATG
Found at i:92938 original size:52 final size:51
Alignment explanation
Indices: 92860--93286 Score: 315
Period size: 52 Copynumber: 8.9 Consensus size: 51
92850 TATTGGACTT
* *
92860 AAAGGTGCCAATTTACTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-C
* ** *
92912 AAAGGCGCCAATATGCTGATTCAAGGCCAAAGATATTGGAC------AT--
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGC
* * * *
92955 AAAGGTGCTAATGTGCTGATTCAAGGCCAGCGACGTTGGGCTTAAAGATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGC
* *
93006 --A------AATATGCTGATTCAAGGCCAGCGACGTTGGGC-T-----T--
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGC
* * *
93041 AAAGGTGCCAATATGCTGATTTAAGGCCAGCAACATTAGACTTAAAGATGAC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-C
* * ** ** *
93093 AAAGGTGCCAATATGCTGATTCAAGGCTAGTGATGTTGGGTTTAAAGATGGT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-GC
*
93145 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T--
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGC
* *
93188 AAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGAC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-C
** * * * *
93240 AAAGACGCCAATATGCTAATTCAAGGCCAACGATATTAGACTTAAAG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
93287 GTGTCAATGT
Statistics
Matches: 294, Mismatches: 46, Indels: 70
0.72 0.11 0.17
Matches are distributed among these distances:
37 2 0.01
42 1 0.00
43 129 0.44
44 2 0.01
46 3 0.01
49 5 0.02
51 1 0.00
52 150 0.51
53 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (51 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGC
Found at i:93193 original size:95 final size:95
Alignment explanation
Indices: 93093--93331 Score: 334
Period size: 95 Copynumber: 2.5 Consensus size: 95
93083 TAAAGATGAC
* * ** ** ** **
93093 AAAGGTGCCAATATGCTGATTCAAGGCTAGTGATGTTGGGTTTAAAGATGGTAAAGGTGCCAATA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAAGACGCCAATA
* * *
93158 TGCTGATTCAAGGCCAGCGATATTGGACTT
66 TGCTAATTCAAGGCCAACGATATTAGACTT
93188 AAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAAGACGCCAATA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAAGACGCCAATA
93253 TGCTAATTCAAGGCCAACGATATTAGACTT
66 TGCTAATTCAAGGCCAACGATATTAGACTT
* *
93283 AAAGGTGTCAATGTGCTGATTCAAGGCCAGTGACATTGGGCTTAGAAGA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTA-AAGA
93332 AGATGCCACC
Statistics
Matches: 128, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
95 124 0.97
96 4 0.03
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (95 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAAGACGCCAATA
TGCTAATTCAAGGCCAACGATATTAGACTT
Found at i:93264 original size:147 final size:147
Alignment explanation
Indices: 92997--93266 Score: 423
Period size: 147 Copynumber: 1.8 Consensus size: 147
92987 ACGTTGGGCT
* *
92997 TAAAGATGCAAATATGCTGATTCAAGGCCAGCGACGTTGGGCTTAAAGGTGCCAATATGCTGATT
1 TAAAGATGCAAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATATGCTGATT
* ** *
93062 TAAGGCCAGCAACATTAGACTTAAAGATGACAAAGGTGCCAATATGCTGATTCAAGGCTAGTGAT
66 CAAGGCCAGCAACATTAGACTTAAAGATGACAAAGACGCCAATATGCTAATTCAAGGCTAGTGAT
93127 GTTGGGTTTAAAGATGG
131 GTTGGGTTTAAAGATGG
* * * *
93144 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATT
1 TAAAGATGCAAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATATGCTGATT
** *
93209 CAAGGCCAGTGACATTGGACTTAAAGATGACAAAGACGCCAATATGCTAATTCAAGGC
66 CAAGGCCAGCAACATTAGACTTAAAGATGACAAAGACGCCAATATGCTAATTCAAGGC
93267 CAACGATATT
Statistics
Matches: 110, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
147 110 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (147 bp):
TAAAGATGCAAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATATGCTGATT
CAAGGCCAGCAACATTAGACTTAAAGATGACAAAGACGCCAATATGCTAATTCAAGGCTAGTGAT
GTTGGGTTTAAAGATGG
Found at i:93379 original size:32 final size:32
Alignment explanation
Indices: 93335--93495 Score: 191
Period size: 32 Copynumber: 5.0 Consensus size: 32
93325 TAGAAGAAGA
93335 TGCCACCAACTTGTGTGGGCTTTTA-AAAGGGT
1 TGCCACCAACTTGTGTGGGC-TTTAGAAAGGGT
* * *
93367 TGCCATCGACTTGTGTGGGCTTTAGAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGT
* *
93399 TGCCACCGACTTATGTGGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGT
* ***
93431 TGCCACCAACTTGTGTAGGCTTT-GAAAAAAAT
1 TGCCACCAACTTGTGTGGGCTTTAG-AAAGGGT
* *
93463 TGTCATCAACTTGTGTGGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGT
93495 T
1 T
93496 TCGCCACTGG
Statistics
Matches: 108, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
31 5 0.05
32 102 0.94
33 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTAGAAAGGGT
Found at i:93711 original size:28 final size:28
Alignment explanation
Indices: 93670--93738 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
93660 ACAGCAAGTA
*
93670 CCACTGA-TTGTGGACTTCGAAAATATG
1 CCACTGACTTGTGGACTTCGAAAAGATG
* * *
93697 CCACTGACTTGTGGATTTCGAAGAGGTG
1 CCACTGACTTGTGGACTTCGAAAAGATG
*
93725 CCACTGACTAGTGG
1 CCACTGACTTGTGG
93739 GCTTTGAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 7 0.19
28 29 0.81
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (28 bp):
CCACTGACTTGTGGACTTCGAAAAGATG
Found at i:95664 original size:20 final size:21
Alignment explanation
Indices: 95639--95679 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
95629 GAGATGTTGG
95639 ACATA-CTAAAAATGCATGAA
1 ACATACCTAAAAATGCATGAA
*
95659 ACATACCTTAAAATGCATGAA
1 ACATACCTAAAAATGCATGAA
95680 CATGGGCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.22
Consensus pattern (21 bp):
ACATACCTAAAAATGCATGAA
Found at i:110808 original size:10 final size:10
Alignment explanation
Indices: 110793--110839 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 10
110783 TACTATGCCT
110793 AAAAAAAC-A
1 AAAAAAACAA
110802 AAAAAAACAA
1 AAAAAAACAA
110812 CAAAACACAACAA
1 -AAAA-A-AACAA
110825 AAAAAAGACAA
1 AAAAAA-ACAA
110836 AAAA
1 AAAA
110840 GAGGTGTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 8 0.24
10 2 0.06
11 13 0.39
12 5 0.15
13 5 0.15
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:112173 original size:76 final size:75
Alignment explanation
Indices: 112043--112222 Score: 225
Period size: 76 Copynumber: 2.4 Consensus size: 75
112033 TCCTTATTTC
* * * * *
112043 CTTTTTCCTTTGTCCTCAAGGAGCATGACCCATTTCATCTTCTTTTCTCGTTGTCATCAAAGAGT
1 CTTTTTCCTTTGTCCTCAAAGAGTAAGACCCATTTCATCTTCTTTTCCCGTTGTCATCAAAGAGG
*
112108 AGGACATACTT
66 AAGACATAC-T
* * * * *
112119 TTTTTTCCTTTATCCTCAAAGAGTAAGACCCATTTCATCTTCTTTTCCCTTTGTCCTCAATGAGG
1 CTTTTTCCTTTGTCCTCAAAGAGTAAGACCCATTTCATCTTCTTTTCCCGTTGTCATCAAAGAGG
*
112184 AAGACGTACT
66 AAGACATACT
* *
112194 CATTTTCCTTTGTCCTCAAAAAGTAAGAC
1 CTTTTTCCTTTGTCCTCAAAGAGTAAGAC
112223 GTCTACTCTT
Statistics
Matches: 88, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
75 26 0.30
76 62 0.70
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (75 bp):
CTTTTTCCTTTGTCCTCAAAGAGTAAGACCCATTTCATCTTCTTTTCCCGTTGTCATCAAAGAGG
AAGACATACT
Found at i:112176 original size:41 final size:41
Alignment explanation
Indices: 112043--112188 Score: 133
Period size: 41 Copynumber: 3.7 Consensus size: 41
112033 TCCTTATTTC
* * * *
112043 CTTTTTCCTTTGTCCTCAAGGAGCATGACCCATTTCATCTT
1 CTTTTCCCTTTGTCCTCAAAGAGTAAGACCCATTTCATCTT
* * * *
112084 CTTTTCTCGTTGTCATCAAAGAGTAGGA--CA--T-A-CTT
1 CTTTTCCCTTTGTCCTCAAAGAGTAAGACCCATTTCATCTT
* * *
112119 TTTTTTCCTTTATCCTCAAAGAGTAAGACCCATTTCATCTT
1 CTTTTCCCTTTGTCCTCAAAGAGTAAGACCCATTTCATCTT
* *
112160 CTTTTCCCTTTGTCCTCAATGAGGAAGAC
1 CTTTTCCCTTTGTCCTCAAAGAGTAAGAC
112189 GTACTCATTT
Statistics
Matches: 80, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
35 24 0.30
36 1 0.01
37 3 0.04
39 3 0.04
40 1 0.01
41 48 0.60
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (41 bp):
CTTTTCCCTTTGTCCTCAAAGAGTAAGACCCATTTCATCTT
Found at i:112205 original size:34 final size:36
Alignment explanation
Indices: 112161--112249 Score: 110
Period size: 34 Copynumber: 2.5 Consensus size: 36
112151 TTTCATCTTC
**
112161 TTTTCCCTTTGTCCTCAATGAGGAAGACG-TACTCA
1 TTTTCCCTTTGTCCTCAAAAAGGAAGACGCTACTCA
* *
112196 TTTT-CCTTTGTCCTCAAAAAGTAAGACGTCTACTCT
1 TTTTCCCTTTGTCCTCAAAAAGGAAGACG-CTACTCA
*
112232 TTTTCCCTTTATCCTCAA
1 TTTTCCCTTTGTCCTCAA
112250 GGAATGAGAC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
34 21 0.46
35 4 0.09
36 9 0.20
37 12 0.26
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.39
Consensus pattern (36 bp):
TTTTCCCTTTGTCCTCAAAAAGGAAGACGCTACTCA
Found at i:112441 original size:31 final size:31
Alignment explanation
Indices: 112406--112522 Score: 110
Period size: 31 Copynumber: 3.8 Consensus size: 31
112396 CCTCATTTAT
* *
112406 AAGCCCACATAAGTTGGTGGTACCCTAGTCA
1 AAGCCCACACAAGCTGGTGGTACCCTAGTCA
** * * *
112437 AAGCCCGTACAAGCTGGAGGTACCCAAGTCT
1 AAGCCCACACAAGCTGGTGGTACCCTAGTCA
* * * *
112468 AAGCCCGCATAAGTTGGTGGCA-CCTGAGTCA
1 AAGCCCACACAAGCTGGTGGTACCCT-AGTCA
*
112499 AAGCTCACACAAGCTGGTGGTACC
1 AAGCCCACACAAGCTGGTGGTACC
112523 TAAGTTCGAG
Statistics
Matches: 65, Mismatches: 19, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
30 2 0.03
31 62 0.95
32 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.26, T:0.19
Consensus pattern (31 bp):
AAGCCCACACAAGCTGGTGGTACCCTAGTCA
Found at i:112502 original size:62 final size:62
Alignment explanation
Indices: 112405--112527 Score: 167
Period size: 62 Copynumber: 2.0 Consensus size: 62
112395 TCCTCATTTA
* **
112405 TAAGCCCACATAAGTTGGTGGTACCCTAGTCAAAGCCCGTACAAGCTGGAGGTACCCAAGTC
1 TAAGCCCACATAAGTTGGTGGCACCCTAGTCAAAGCCCACACAAGCTGGAGGTACCCAAGTC
* * * *
112467 TAAGCCCGCATAAGTTGGTGGCA-CCTGAGTCAAAGCTCACACAAGCTGGTGGTACCTAAGT
1 TAAGCCCACATAAGTTGGTGGCACCCT-AGTCAAAGCCCACACAAGCTGGAGGTACCCAAGT
112528 TCGAGTCAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
61 3 0.06
62 50 0.94
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.20
Consensus pattern (62 bp):
TAAGCCCACATAAGTTGGTGGCACCCTAGTCAAAGCCCACACAAGCTGGAGGTACCCAAGTC
Found at i:112704 original size:149 final size:149
Alignment explanation
Indices: 112458--112906 Score: 605
Period size: 149 Copynumber: 3.0 Consensus size: 149
112448 AGCTGGAGGT
* * * * *
112458 ACCCAAGTCTAAGCCCGCATAAGTTGGTGGCACCTGAGTCAAAGCTCACACAAGCTGGTGGTACC
1 ACCCAAGTCTAAGCCCGCACAAGTTGGCGGCATCTGAGTCAAAGCCCACACAAGCTGGTGGCACC
112523 TAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCTATCTAAGGAGGTCAAGCCTTAGAATGTCAAA
66 TAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCTATCTAAGGAGGTCAAGCCTTAGAATGTCAAA
* *
112588 GCTCGCACAAGCTAGTAGC
131 GCTCACACAAGCTAGTGGC
** * * * *
112607 ACCCAAGTCTAAGCCCATACAAGTTGGCAGCATCTAAGTCAAAGCCCATATAAGCTGGTGGCACC
1 ACCCAAGTCTAAGCCCGCACAAGTTGGCGGCATCTGAGTCAAAGCCCACACAAGCTGGTGGCACC
* * * *
112672 CAAGTTTGAGTCAAGTCCAAATTAGTTAGCACCTATGTAAGGAGGTCAAGCCTTAGAATGTCAAA
66 TAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCTATCTAAGGAGGTCAAGCCTTAGAATGTCAAA
* *
112737 GC-CTACACAAACTAGCGGC
131 GCTC-ACACAAGCTAGTGGC
* ** * * *
112756 ACTCAAGTCTAAGCTTGCACAAGTTGGCGGAATCTGATTCAAAGCCCACACAAGCTGGTAGCACC
1 ACCCAAGTCTAAGCCCGCACAAGTTGGCGGCATCTGAGTCAAAGCCCACACAAGCTGGTGGCACC
* * *
112821 TAAGTTCAAGTCAAGTCAAAATTAGTTGGCAAC-ATCTAAGGAGGTCAAGCCTTAGAATGTCAAA
66 TAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCTATCTAAGGAGGTCAAGCCTTAGAATGTCAAA
* *
112885 GCTCACATAAGCTGGTGGC
131 GCTCACACAAGCTAGTGGC
112904 ACC
1 ACC
112907 TAACTTCAAG
Statistics
Matches: 255, Mismatches: 43, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
148 46 0.18
149 209 0.82
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.21
Consensus pattern (149 bp):
ACCCAAGTCTAAGCCCGCACAAGTTGGCGGCATCTGAGTCAAAGCCCACACAAGCTGGTGGCACC
TAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCTATCTAAGGAGGTCAAGCCTTAGAATGTCAAA
GCTCACACAAGCTAGTGGC
Found at i:112939 original size:86 final size:87
Alignment explanation
Indices: 112794--112996 Score: 363
Period size: 86 Copynumber: 2.3 Consensus size: 87
112784 GGAATCTGAT
* * * *
112794 TCAAAGCCCACACAAGCTGGTAGCACCTAAGTTCAAGTCAAGTCAAAATTAGTTGGCAAC-ATCT
1 TCAAAGCTCACATAAGCTGGTGGCACCTAACTTCAAGTCAAGTCAAAATTAGTTGGCAACTATCT
112858 AAGGAGGTCAAGCCTTAGAATG
66 AAGGAGGTCAAGCCTTAGAATG
112880 TCAAAGCTCACATAAGCTGGTGGCACCTAACTTCAAGTCAAGTCAAAATTAGTTGGCAACTATCT
1 TCAAAGCTCACATAAGCTGGTGGCACCTAACTTCAAGTCAAGTCAAAATTAGTTGGCAACTATCT
112945 AAGGAGGTCAAGCCTTAGAATG
66 AAGGAGGTCAAGCCTTAGAATG
112967 TCAAAGCTCACATAAGCTGGTGGCACCTAA
1 TCAAAGCTCACATAAGCTGGTGGCACCTAA
112997 GTCTCAGTTA
Statistics
Matches: 112, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
86 56 0.50
87 56 0.50
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (87 bp):
TCAAAGCTCACATAAGCTGGTGGCACCTAACTTCAAGTCAAGTCAAAATTAGTTGGCAACTATCT
AAGGAGGTCAAGCCTTAGAATG
Found at i:122310 original size:13 final size:13
Alignment explanation
Indices: 122292--122317 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
122282 ATGTAAGTTT
122292 TGTATCGATACAA
1 TGTATCGATACAA
122305 TGTATCGATACAA
1 TGTATCGATACAA
122318 AACCACCCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:122366 original size:20 final size:20
Alignment explanation
Indices: 122341--122382 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
122331 ACTGGCAAGG
122341 AAATGTATCGATACATTACT
1 AAATGTATCGATACATTACT
122361 AAATGTATCGATACATTACT
1 AAATGTATCGATACATTACT
122381 AA
1 AA
122383 TGCTTACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (20 bp):
AAATGTATCGATACATTACT
Found at i:132184 original size:26 final size:25
Alignment explanation
Indices: 132154--132227 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 25
132144 AATAACAATC
*
132154 ATAATATAACATTATAATTAATATTT
1 ATAATATAA-ATTATAATAAATATTT
* *
132180 ATAATAATTAATTGTAATAAATATTT
1 ATAAT-ATAAATTATAATAAATATTT
*
132206 ATTATATTTATAATTATAATAA
1 A-TA-ATATA-AATTATAATAA
132228 TAAATGTGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 20 0.53
27 6 0.16
28 12 0.32
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (25 bp):
ATAATATAAATTATAATAAATATTT
Found at i:132994 original size:16 final size:17
Alignment explanation
Indices: 132950--133003 Score: 67
Period size: 16 Copynumber: 3.2 Consensus size: 17
132940 CCGTTGGATC
132950 TGAAAATCTATTTTATTAT
1 TGAAAAT-TATTTTA-TAT
*
132969 TGAAAA-TATTATATAT
1 TGAAAATTATTTTATAT
132985 T-AAAATTATTTTATAT
1 TGAAAATTATTTTATAT
133001 TGA
1 TGA
133004 TATTTATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 4 0.13
16 14 0.45
17 7 0.23
19 6 0.19
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.50
Consensus pattern (17 bp):
TGAAAATTATTTTATAT
Found at i:133014 original size:32 final size:34
Alignment explanation
Indices: 132952--133015 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 34
132942 GTTGGATCTG
132952 AAAATCTATTTTATTATTGAAAATATTATATATT
1 AAAATCTATTTTATTATTGAAAATATTATATATT
*
132986 AAAAT-TATTTTA-TATTG-ATAT-TTATATATT
1 AAAATCTATTTTATTATTGAAAATATTATATATT
133016 TTCATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 9 0.31
31 3 0.10
32 5 0.17
33 7 0.24
34 5 0.17
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (34 bp):
AAAATCTATTTTATTATTGAAAATATTATATATT
Found at i:134180 original size:23 final size:26
Alignment explanation
Indices: 134129--134184 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 26
134119 TATTAATTAT
134129 TTTTAATTTAATATTATAAAAATATA
1 TTTTAATTTAATATTATAAAAATATA
* *
134155 TTTTAATTT-AT-TTATGAACATA-A
1 TTTTAATTTAATATTATAAAAATATA
134178 TTTTAAT
1 TTTTAAT
134185 ATATATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 8 0.29
24 9 0.32
25 2 0.07
26 9 0.32
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
TTTTAATTTAATATTATAAAAATATA
Found at i:141572 original size:33 final size:33
Alignment explanation
Indices: 141513--141575 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
141503 GTTGTTGGGC
* *
141513 ATAATATATCGATACAATTCTTCATGTATCGAT
1 ATAATATATCAATACAATTCTCCATGTATCGAT
*
141546 ATAATGTATCAATACAATGTC-CCATGTATC
1 ATAATATATCAATACAAT-TCTCCATGTATC
141576 AATACATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 24 0.92
34 2 0.08
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (33 bp):
ATAATATATCAATACAATTCTCCATGTATCGAT
Found at i:141655 original size:19 final size:19
Alignment explanation
Indices: 141610--141665 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
141600 CTACCAGTTT
141610 CATGTATCGATACAATTAAG
1 CATGTATCGATACAA-TAAG
* * *
141630 TATGTATCCATACAATGAG
1 CATGTATCGATACAATAAG
141649 CATGTATCGATACAATA
1 CATGTATCGATACAATA
141666 TATCGATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATAAG
Found at i:146376 original size:12 final size:12
Alignment explanation
Indices: 146354--146387 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
146344 TGGCATAAGT
146354 ATAATATAAAAA
1 ATAATATAAAAA
146366 ATAAT-TAAAAA
1 ATAATATAAAAA
146377 ATAATATAAAA
1 ATAATATAAAA
146388 TACAACAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
ATAATATAAAAA
Found at i:146408 original size:30 final size:31
Alignment explanation
Indices: 146372--146436 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
146362 AAAAATAATT
* *
146372 AAAAAATAATATAAA-AT-ACAACAAAATTTA
1 AAAAAATAATACAAACATGAC-ACAAAATGTA
*
146402 AAAAAATTATACAAACATGACACAAAATGTA
1 AAAAAATAATACAAACATGACACAAAATGTA
146433 AAAA
1 AAAA
146437 CATCTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 13 0.43
31 15 0.50
32 2 0.07
ACGTcount: A:0.68, C:0.09, G:0.03, T:0.20
Consensus pattern (31 bp):
AAAAAATAATACAAACATGACACAAAATGTA
Done.