Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002007.1 Hibiscus syriacus cultivar Beakdansim tig00004104_pilon, whole genome shotgun sequence
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: 83305
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1726 original size:47 final size:45
Alignment explanation
Indices: 1642--1734 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 45
1632 ATAAATAAAA
**
1642 AAATAAAATAAAATAAAAGTTAGTAGTCCGAGGTTAGTAGTGTTAG
1 AAATAAAATAAAATAAAAGTTAAAAGTCCGA-GTTAGTAGTGTTAG
*
1688 AAATAAAAATAAAATAAAAGTTAAAAGCTAGCGA-TTAGTAGTGTTAG
1 AAAT-AAAATAAAATAAAAGTTAAAAG-T-CCGAGTTAGTAGTGTTAG
1735 CATTTTAACC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
46 4 0.10
47 33 0.80
48 1 0.02
49 3 0.07
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.27
Consensus pattern (45 bp):
AAATAAAATAAAATAAAAGTTAAAAGTCCGAGTTAGTAGTGTTAG
Found at i:13528 original size:21 final size:21
Alignment explanation
Indices: 13504--13543 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13494 TTTGCTTCCA
*
13504 TTATCGTTATAATTGCATTCG
1 TTATCGTTATAATTACATTCG
* *
13525 TTATTGTTGTAATTACATT
1 TTATCGTTATAATTACATT
13544 AAAAGTAACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.53
Consensus pattern (21 bp):
TTATCGTTATAATTACATTCG
Found at i:14625 original size:17 final size:18
Alignment explanation
Indices: 14603--14644 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
14593 AACATATTTT
14603 AATATTATAAAAATA-AA
1 AATATTATAAAAATATAA
*
14620 AATATT-T-AAAATATTA
1 AATATTATAAAAATATAA
14636 AATATTATA
1 AATATTATA
14645 TATATAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
15 6 0.29
16 8 0.38
17 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATATTATAAAAATATAA
Found at i:15518 original size:21 final size:21
Alignment explanation
Indices: 15494--15560 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
15484 GCAATTTCGC
*
15494 GTTGCATTTCGCGTTGCGGTA
1 GTTGCATTTCGCGTTGCGATA
* **
15515 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
15535 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
15556 GTTGC
1 GTTGC
15561 GTTGCGCTTT
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.15, C:0.19, G:0.28, T:0.37
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:15543 original size:41 final size:35
Alignment explanation
Indices: 15525--15666 Score: 171
Period size: 34 Copynumber: 3.9 Consensus size: 35
15515 GTTGAAAATC
15525 GCGTTGCGATTTTCCATTTCGCGTTGCGATAG-TT
1 GCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTT
* * *
15559 GCGTTGCGCTTTTCTATTTCGCGTTGTGATAG-TT
1 GCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTT
*
15593 GCGTTGCGCTTTTCCATTTCGCGTTGCGATAGTTGAAAAT
1 GCGTTGCGATTTTCCATTTCGCGTTGCGATAGTT-----T
*
15633 CGCGTTGCGATTTTCCATTTCGCGGTGCGATAGT
1 -GCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
15667 CTACAGTTGT
Statistics
Matches: 94, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
34 61 0.65
35 1 0.01
40 1 0.01
41 31 0.33
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (35 bp):
GCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTT
Found at i:15572 original size:34 final size:34
Alignment explanation
Indices: 15525--15627 Score: 179
Period size: 34 Copynumber: 3.0 Consensus size: 34
15515 GTTGAAAATC
*
15525 GCGTTGCGATTTTCCATTTCGCGTTGCGATAGTT
1 GCGTTGCGCTTTTCCATTTCGCGTTGCGATAGTT
* *
15559 GCGTTGCGCTTTTCTATTTCGCGTTGTGATAGTT
1 GCGTTGCGCTTTTCCATTTCGCGTTGCGATAGTT
15593 GCGTTGCGCTTTTCCATTTCGCGTTGCGATAGTT
1 GCGTTGCGCTTTTCCATTTCGCGTTGCGATAGTT
15627 G
1 G
15628 AAAATCGCGT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.10, C:0.20, G:0.27, T:0.43
Consensus pattern (34 bp):
GCGTTGCGCTTTTCCATTTCGCGTTGCGATAGTT
Found at i:15682 original size:42 final size:41
Alignment explanation
Indices: 15589--15691 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 41
15579 GCGTTGTGAT
* *
15589 AGTTGCGTTGCGCTTTTCCATTTCGCGTTGCGATAGTTGAA
1 AGTTGCGTTGCGATTTTCCATTTCGCGGTGCGATAGTTGAA
* * *
15630 AATCGCGTTGCGATTTTCCATTTCGCGGTGCGATAGTCT-AC
1 AGTTGCGTTGCGATTTTCCATTTCGCGGTGCGATAGT-TGAA
15671 AGTTGTCGTTGCGATTTTCCA
1 AGTTG-CGTTGCGATTTTCCA
15692 AATTCGTTGC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 37 0.70
42 16 0.30
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (41 bp):
AGTTGCGTTGCGATTTTCCATTTCGCGGTGCGATAGTTGAA
Found at i:16642 original size:13 final size:13
Alignment explanation
Indices: 16611--16660 Score: 73
Period size: 13 Copynumber: 3.7 Consensus size: 13
16601 ATACTTGAAA
16611 AATAATTTATTACTT
1 AATAATTTATT--TT
16626 AATAATTTATTTT
1 AATAATTTATTTT
16639 AATAATTTATTTT
1 AATAATTTATTTT
*
16652 AATTATTTA
1 AATAATTTA
16661 AAAATAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
13 23 0.68
15 11 0.32
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (13 bp):
AATAATTTATTTT
Found at i:16754 original size:15 final size:15
Alignment explanation
Indices: 16734--16787 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
16724 ATCATTGAAA
16734 AATAATTTATTATTT
1 AATAATTTATTATTT
16749 AATAATTTA-T-TTT
1 AATAATTTATTATTT
* * *
16762 AATTATTTGTTACTT
1 AATAATTTATTATTT
16777 AATAATTTATT
1 AATAATTTATT
16788 TTATATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 10 0.31
14 2 0.06
15 20 0.62
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (15 bp):
AATAATTTATTATTT
Found at i:18122 original size:16 final size:16
Alignment explanation
Indices: 18101--18153 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
18091 CATTTAATAA
*
18101 ATAAACAAACACGAAC
1 ATAAACGAACACGAAC
*
18117 ATAAACGAACATGAAC
1 ATAAACGAACACGAAC
18133 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
18149 ATAAA
1 ATAAA
18154 AGTTGGAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.60, C:0.21, G:0.09, T:0.09
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:19328 original size:14 final size:13
Alignment explanation
Indices: 19252--19340 Score: 88
Period size: 10 Copynumber: 7.3 Consensus size: 13
19242 AATGAACATA
19252 AACGAACATAACAG
1 AACGAACATAAC-G
19266 AACGAACAT-A--
1 AACGAACATAACG
19276 AACGAACATAACAG
1 AACGAACATAAC-G
19290 AACGAACAT-A--
1 AACGAACATAACG
19300 AACGAACATAACG
1 AACGAACATAACG
19313 AACGAACAT-A--
1 AACGAACATAACG
19323 AACGAACATAACCG
1 AACGAACATAA-CG
19337 AACG
1 AACG
19341 TTCACGAACG
Statistics
Matches: 64, Mismatches: 0, Indels: 22
0.74 0.00 0.26
Matches are distributed among these distances:
10 27 0.42
11 3 0.05
12 1 0.02
13 11 0.17
14 22 0.34
ACGTcount: A:0.56, C:0.22, G:0.13, T:0.08
Consensus pattern (13 bp):
AACGAACATAACG
Found at i:19350 original size:24 final size:24
Alignment explanation
Indices: 19232--19340 Score: 177
Period size: 24 Copynumber: 4.6 Consensus size: 24
19222 GATTGAGTTA
*
19232 AACATAA-ATGAATGAACATAAACG
1 AACATAACA-GAACGAACATAAACG
19256 AACATAACAGAACGAACATAAACG
1 AACATAACAGAACGAACATAAACG
19280 AACATAACAGAACGAACATAAACG
1 AACATAACAGAACGAACATAAACG
19304 AACATAAC-GAACGAACATAAACG
1 AACATAACAGAACGAACATAAACG
*
19327 AACATAACCGAACG
1 AACATAACAGAACG
19341 TTCACGAACG
Statistics
Matches: 82, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
23 23 0.28
24 58 0.71
25 1 0.01
ACGTcount: A:0.57, C:0.20, G:0.13, T:0.10
Consensus pattern (24 bp):
AACATAACAGAACGAACATAAACG
Found at i:24843 original size:68 final size:68
Alignment explanation
Indices: 24762--24910 Score: 255
Period size: 68 Copynumber: 2.2 Consensus size: 68
24752 CGCATTTGTA
24762 TGAACGTGGAAAAAAGAAATGATGGTTACATAATTACTATACCATGCATGAAAATGGCCCTCGAA
1 TGAACGTGGAAAAAAGAAATGATGGTTACATAATTACTATACCATGCATGAAAATGGCCCTCGAA
24827 TTG
66 TTG
* * **
24830 TGAACGTGGAAAAAGGAAATGATGGTTACATAATTGCTATACCATGCATGAAGGTGGCCCTCGAA
1 TGAACGTGGAAAAAAGAAATGATGGTTACATAATTACTATACCATGCATGAAAATGGCCCTCGAA
24895 TTG
66 TTG
24898 TGAACGT-GAAAAA
1 TGAACGTGGAAAAA
24911 TCATCACTTG
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
67 6 0.08
68 71 0.92
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.24
Consensus pattern (68 bp):
TGAACGTGGAAAAAAGAAATGATGGTTACATAATTACTATACCATGCATGAAAATGGCCCTCGAA
TTG
Found at i:27630 original size:2 final size:2
Alignment explanation
Indices: 27623--27656 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
27613 GATTCTGATA
27623 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
27657 GGTAAACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35552 original size:15 final size:16
Alignment explanation
Indices: 35532--35564 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35522 TATTCTTCAG
*
35532 TTTCTG-TACATTGCT
1 TTTCTGTTACACTGCT
35547 TTTCTGTTACACTGCT
1 TTTCTGTTACACTGCT
35563 TT
1 TT
35565 ATTCTGGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.12, C:0.21, G:0.12, T:0.55
Consensus pattern (16 bp):
TTTCTGTTACACTGCT
Found at i:36105 original size:17 final size:16
Alignment explanation
Indices: 36037--36105 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 16
36027 TTCGAGTATT
*
36037 CGGGTACCCG-ACATA
1 CGGGTACCCGAACATC
* * *
36052 CGGGTATCCGTAAAATT
1 CGGGTACCCG-AACATC
* *
36069 CGGGTACTCGAA-AAC
1 CGGGTACCCGAACATC
36084 CGGGTACCCGGAACATC
1 CGGGTACCC-GAACATC
36101 CGGGT
1 CGGGT
36106 CGGGACACGG
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
15 18 0.44
16 5 0.12
17 18 0.44
ACGTcount: A:0.26, C:0.28, G:0.29, T:0.17
Consensus pattern (16 bp):
CGGGTACCCGAACATC
Found at i:36454 original size:19 final size:20
Alignment explanation
Indices: 36416--36456 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
36406 AGTATCTACC
*
36416 TAATATTCATACAATGTACA
1 TAATATTCAGACAATGTACA
*
36436 TAATATTCAGAC-GTGTACA
1 TAATATTCAGACAATGTACA
36455 TA
1 TA
36457 CTTGAGCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (20 bp):
TAATATTCAGACAATGTACA
Found at i:39399 original size:19 final size:19
Alignment explanation
Indices: 39363--39399 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39353 TGAAAATGAT
*
39363 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
39382 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
39400 ATGAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:44215 original size:21 final size:21
Alignment explanation
Indices: 44189--44235 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
44179 TAATTTTCAA
44189 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
44210 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
44231 ACATT
1 ACATT
44236 TCAATATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:51965 original size:74 final size:73
Alignment explanation
Indices: 51884--52271 Score: 226
Period size: 71 Copynumber: 5.5 Consensus size: 73
51874 AAATAATTTT
* * *
51884 TTTTATCTCACTTGAGATAATTTTC-CTTAAAACAAGATT-CGTCTCATTTGAGACAGTTTATCT
1 TTTTATCTCGCTTGAGATAATTTTCTCTT-AAA-AA-ATTACGTCTCACTTGAGACAGCTTATCT
*
51947 CGAAACAAAAA
63 CAAAACAAAAA
* * * * * *
51958 TTTTATCTCGCTTGAGATAGTTTTCTCTTGAAAATTTATGTCTCACTTGAGACTGCTTCTCTCAA
1 TTTTATCTCGCTTGAGATAATTTTCTCTTAAAAAATTACGTCTCACTTGAGACAGCTTATCTCAA
52023 AACAAAAA
66 AACAAAAA
* * * ** * * * *
52031 ATTTATCTTGCTTGAGATAATTTACT-TTTGAAAATT-TGTCTCACTCGAGACAGTTTCTCTCAA
1 TTTTATCTCGCTTGAGATAATTTTCTCTTAAAAAATTACGTCTCACTTGAGACAGCTTATCTCAA
* **
52094 AA-TAATT
66 AACAAAAA
* * *** * * ** ** * *
52101 TTTTTTCTCGCTTGAGATAATTTTCTCTT---GAATTTTTTTTTACTCAAGACAATTTGTCTCGA
1 TTTTATCTCGCTTGAGATAATTTTCTCTTAAAAAATTACGTCTCACTTGAGACAGCTTATCTCAA
*
52163 AA-AATAA
66 AACAAAAA
* * * ** ** * * *
52170 -TTTATCTCGCTTGAGATAGTTTTGTCTTGAAATTTTGTGTATCACTTGAAACA-CTTCTCTCAA
1 TTTTATCTCGCTTGAGATAATTTTCTCTTAAAAAATTACGTCTCACTTGAGACAGCTTATCTCAA
52233 AAC-AAAA
66 AACAAAAA
* *
52240 TTTTATCTCACTTAAGAT-ATTTTCTCTTAAAA
1 TTTTATCTCGCTTGAGATAATTTTCTCTTAAAA
52272 TAAATTTCAT
Statistics
Matches: 244, Mismatches: 61, Indels: 22
0.75 0.19 0.07
Matches are distributed among these distances:
68 29 0.12
69 23 0.09
70 47 0.19
71 55 0.23
72 9 0.04
73 53 0.22
74 25 0.10
75 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (73 bp):
TTTTATCTCGCTTGAGATAATTTTCTCTTAAAAAATTACGTCTCACTTGAGACAGCTTATCTCAA
AACAAAAA
Found at i:52044 original size:73 final size:72
Alignment explanation
Indices: 51884--52272 Score: 332
Period size: 73 Copynumber: 5.5 Consensus size: 72
51874 AAATAATTTT
* * * * * *
51884 TTTTATCTCACTTGAGATAATTTTC-CTTAAAACAAGATTCGTCTCATTTGAGACAGTTTATCTC
1 TTTTATCTCGCTTGAGATAATTTTCTCTT-GAA-AA-TTTTGTCTCACTTGAGACAGTTTCTCTC
*
51948 GAAACAAAAA
63 AAAACAAAAA
* * *
51958 TTTTATCTCGCTTGAGATAGTTTTCTCTTGAAAATTTATGTCTCACTTGAGACTGCTTCTCTCAA
1 TTTTATCTCGCTTGAGATAATTTTCTCTTGAAAATTT-TGTCTCACTTGAGACAGTTTCTCTCAA
52023 AACAAAAA
65 AACAAAAA
* * * * *
52031 ATTTATCTTGCTTGAGATAATTTACTTTTGAAAA-TTTGTCTCACTCGAGACAGTTTCTCTCAAA
1 TTTTATCTCGCTTGAGATAATTTTCTCTTGAAAATTTTGTCTCACTTGAGACAGTTTCTCTCAAA
* **
52095 A-TAATT
66 ACAAAAA
* * * * ** * * *
52101 TTTTTTCTCGCTTGAGATAATTTTCTCTTG--AATTTTTTTTTACTCAAGACAATTTGTCTCGAA
1 TTTTATCTCGCTTGAGATAATTTTCTCTTGAAAATTTTGTCTCACTTGAGACAGTTTCTCTCAAA
*
52164 A-AATAA
66 ACAAAAA
* * * * * *
52170 -TTTATCTCGCTTGAGATAGTTTTGTCTTGAAATTTTGTGTATCACTTGAAACA-CTTCTCTCAA
1 TTTTATCTCGCTTGAGATAATTTTCTCTTGAAAATTT-TGTCTCACTTGAGACAGTTTCTCTCAA
52233 AAC-AAAA
65 AACAAAAA
* *
52240 TTTTATCTCACTTAAGAT-ATTTTCTCTT-AAAAT
1 TTTTATCTCGCTTGAGATAATTTTCTCTTGAAAAT
52273 AAATTTCATC
Statistics
Matches: 251, Mismatches: 56, Indels: 21
0.77 0.17 0.06
Matches are distributed among these distances:
68 28 0.11
69 29 0.12
70 51 0.20
71 51 0.20
72 4 0.02
73 60 0.24
74 25 0.10
75 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (72 bp):
TTTTATCTCGCTTGAGATAATTTTCTCTTGAAAATTTTGTCTCACTTGAGACAGTTTCTCTCAAA
ACAAAAA
Found at i:52187 original size:68 final size:68
Alignment explanation
Indices: 51959--52205 Score: 224
Period size: 68 Copynumber: 3.5 Consensus size: 68
51949 AAACAAAAAT
* ** ***
51959 TTTATCTCGCTTGAGATAGTTTTCTCTTGAAAATTTATGTCTCACTTGAGACTGCTTCTCTCAAA
1 TTTATCTCGCTTGAGATAATTTTCTCTTG-AAATTT-T-TCTCACTCAAGACAATTTCTCTC-AA
*
52024 ACAAAAAA
62 A-AAATAA
* * * * * *
52032 TTTATCTTGCTTGAGATAATTTACTTTTGAAAATTTGTCTCACTCGAGACAGTTTCTCTCAAAAT
1 TTTATCTCGCTTGAGATAATTTTCTCTTG-AAATTTTTCTCACTCAAGACAATTTCTCTCAAAA-
**
52097 AATTT
64 AATAA
* * * * * *
52102 TTTTTCTCGCTTGAGATAATTTTCTCTTGAATTTTTTTTTACTCAAGACAATTTGTCTCGAAAAA
1 TTTATCTCGCTTGAGATAATTTTCTCTTGAAATTTTTCTCACTCAAGACAATTTCTCTCAAAAAA
52167 TAA
66 TAA
* *
52170 TTTATCTCGCTTGAGATAGTTTTGTCTTGAAATTTT
1 TTTATCTCGCTTGAGATAATTTTCTCTTGAAATTTT
52206 GTGTATCACT
Statistics
Matches: 144, Mismatches: 29, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
68 35 0.24
69 27 0.19
70 30 0.21
71 20 0.14
73 32 0.22
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.45
Consensus pattern (68 bp):
TTTATCTCGCTTGAGATAATTTTCTCTTGAAATTTTTCTCACTCAAGACAATTTCTCTCAAAAAA
TAA
Found at i:52258 original size:71 final size:71
Alignment explanation
Indices: 51944--52272 Score: 269
Period size: 70 Copynumber: 4.7 Consensus size: 71
51934 AGACAGTTTA
* * * *
51944 TCTCGAAACAAAAATTTTATCTCGCTTGAGATAGTTTTCTCTTGAAAATTTATGTCTCACTTGAG
1 TCTCAAAAC-AAAATTTTATCTCGCTTGAGATAATTTTCTCTTG-AAATTTTTGTCTCACTTGAA
**
52009 ACTGCTTC
64 ACAACTTC
* * * * * * *
52017 TCTCAAAACAAAAAATTTATCTTGCTTGAGATAATTTACTTTTGAAA-ATTTGTCTCACTCGAGA
1 TCTCAAAAC-AAAATTTTATCTCGCTTGAGATAATTTTCTCTTGAAATTTTTGTCTCACTTGAAA
**
52081 CAGTTTC
65 CAACTTC
* ** * * * *
52088 TCTCAAAATAATTTTTTTTCTCGCTTGAGATAATTTTCTCTTG-AATTTTT-TTTTAC-TCAAGA
1 TCTCAAAACAAAATTTTATCTCGCTTGAGATAATTTTCTCTTGAAATTTTTGTCTCACTTGAA-A
* *
52150 CAATTTG
65 CAACTTC
* * * *
52157 TCTCGAAAA-ATAA-TTTATCTCGCTTGAGATAGTTTTGTCTTGAAATTTTGTGTATCACTTGAA
1 TCTC-AAAACAAAATTTTATCTCGCTTGAGATAATTTTCTCTTGAAATTTT-TGTCTCACTTGAA
52220 AC-ACTTC
64 ACAACTTC
* * *
52227 TCTCAAAACAAAATTTTATCTCACTTAAGAT-ATTTTCTCTTAAAAT
1 TCTCAAAACAAAATTTTATCTCGCTTGAGATAATTTTCTCTTGAAAT
52273 AAATTTCATC
Statistics
Matches: 203, Mismatches: 44, Indels: 21
0.76 0.16 0.08
Matches are distributed among these distances:
68 27 0.13
69 27 0.13
70 57 0.28
71 48 0.24
72 6 0.03
73 38 0.19
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (71 bp):
TCTCAAAACAAAATTTTATCTCGCTTGAGATAATTTTCTCTTGAAATTTTTGTCTCACTTGAAAC
AACTTC
Found at i:55044 original size:3 final size:3
Alignment explanation
Indices: 55036--55146 Score: 186
Period size: 3 Copynumber: 36.7 Consensus size: 3
55026 TTAATATATC
* *
55036 TAA TAA TAA TAG TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
55084 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
55133 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
55147 TGGATAAAAA
Statistics
Matches: 101, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
3 98 0.97
4 3 0.03
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:55710 original size:113 final size:113
Alignment explanation
Indices: 55465--55885 Score: 718
Period size: 113 Copynumber: 3.7 Consensus size: 113
55455 AGAATTATGC
* * * * *
55465 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * * *
55530 TATGAAC-TTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAAGT
66 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
*
55577 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
55642 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
66 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
55690 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
55755 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
66 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
55803 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
55868 TATGAACTTTCTCTGGAA
66 TATGAACTTTCTCTGGAA
55886 GAAATGATCC
Statistics
Matches: 294, Mismatches: 14, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
112 66 0.22
113 228 0.78
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
Found at i:57002 original size:85 final size:84
Alignment explanation
Indices: 56642--57193 Score: 952
Period size: 85 Copynumber: 6.6 Consensus size: 84
56632 CCTACTGAAT
* *
56642 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTT-TAAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCAT-TTTCTAAATTC
56705 AATGATT-GTTCTGTCCAAC
65 AATGATTGGTTCTGTCCAAC
* * *
56724 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA-CAAATTCATCTTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATTTTCTAAATTCA
*
56788 ATGATT-GTTTTGTCCAAC
66 ATGATTGGTTCTGTCCAAC
* *
56806 CAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATTTTCTAAATTCA
56871 ATGATTGGTTCTGTCCAAC
66 ATGATTGGTTCTGTCCAAC
56890 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCTATTTTCTAAATTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTC-ATTTTCTAAATTC
56955 AATGATTGGTTCTGTCCAAC
65 AATGATTGGTTCTGTCCAAC
*
56975 CAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCTATTTTCTAAATTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTC-ATTTTCTAAATTC
57040 AATGATTGGTTCTGTCCAAC
65 AATGATTGGTTCTGTCCAAC
*
57060 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATTTTCTAAATTCA
57125 ATGATTGGTTCTGTCCAAC
66 ATGATTGGTTCTGTCCAAC
57144 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT
57194 ATATTTGTTC
Statistics
Matches: 453, Mismatches: 12, Indels: 8
0.96 0.03 0.02
Matches are distributed among these distances:
81 2 0.00
82 114 0.25
83 28 0.06
84 143 0.32
85 166 0.37
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (84 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATTTTCTAAATTCA
ATGATTGGTTCTGTCCAAC
Found at i:57023 original size:169 final size:168
Alignment explanation
Indices: 56642--57193 Score: 968
Period size: 169 Copynumber: 3.3 Consensus size: 168
56632 CCTACTGAAT
* * *
56642 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTTTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
56706 ATGATT-GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA-CA
66 ATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCA
* * *
56769 AATTCATCTTCTAAACTCAATGATT-GTTTTGTCCAAC
131 CATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAAC
*
56806 CAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
56871 ATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCA
66 ATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCA
*
56936 CATTCTATTTTCTAAATTCAATGATTGGTTCTGTCCAAC
131 CATTC-ATCTTCTAAATTCAATGATTGGTTCTGTCCAAC
* *
56975 CAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCTATTTTCTAAATTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTC-ATCTTCTAAATTC
57040 AATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGC
65 AATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGC
57105 ACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAAC
130 ACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAAC
57144 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT
57194 ATATTTGTTC
Statistics
Matches: 369, Mismatches: 13, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
164 38 0.10
165 28 0.08
166 55 0.15
167 6 0.02
168 18 0.05
169 141 0.38
170 83 0.22
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (168 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
ATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCA
CATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAAC
Found at i:57106 original size:254 final size:249
Alignment explanation
Indices: 56642--57199 Score: 967
Period size: 254 Copynumber: 2.2 Consensus size: 249
56632 CCTACTGAAT
*
56642 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTC-ATCTTTTAAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCTAT-TTTTAAACTC
56705 AATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAA
65 AATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAA
*
56770 ATTCATCTTCTAAACTCAATGATTGTTTTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
130 ATTCATCTTCTAAACTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
56835 AAAGATGCTATTGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAAC
195 AAAGATGCTATTGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAAC
*
56890 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCTATTTTCTAAATTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCTATTTT-TAAACTC
*
56955 AATGATTGGTTCTGTCCAACCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGC
65 AATGATT-GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA-C
* * *
57020 ACATTCTATTTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
128 AAATTC-ATCTTCTAAACTCAATGATT-GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
*
57085 TCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAAC
191 TCCAAAAGATGCTATTGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAAC
*
57144 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATATTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCTATTT
57200 GTTCCAGTTA
Statistics
Matches: 294, Mismatches: 9, Indels: 8
0.95 0.03 0.03
Matches are distributed among these distances:
248 39 0.13
249 13 0.04
250 15 0.05
251 54 0.18
252 6 0.02
253 18 0.06
254 149 0.51
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (249 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCTATTTTTAAACTCA
ATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
TTCATCTTCTAAACTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAA
AAGATGCTATTGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAAC
Found at i:58355 original size:10 final size:10
Alignment explanation
Indices: 58342--58419 Score: 106
Period size: 10 Copynumber: 7.7 Consensus size: 10
58332 TTGACCCACC
58342 TTTTTTTCTTT
1 TTTTTTTC-TT
58353 TTTTTTTCTT
1 TTTTTTTCTT
58363 TTTTTTTCTT
1 TTTTTTTCTT
*
58373 TTTTCTTCTT
1 TTTTTTTCTT
58383 TTTTTTTC--
1 TTTTTTTCTT
58391 TTTTTTTCTT
1 TTTTTTTCTT
58401 TTTTTTTCTCCT
1 TTTTTTTCT--T
58413 TTTTTTT
1 TTTTTTT
58420 TAAGCATAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
8 8 0.13
10 37 0.61
11 8 0.13
12 8 0.13
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:58385 original size:31 final size:32
Alignment explanation
Indices: 58342--58420 Score: 119
Period size: 30 Copynumber: 2.6 Consensus size: 32
58332 TTGACCCACC
58342 TTTTT-TTCTTTTTTTTTTCTTTTTTT-TTCT
1 TTTTTCTTCTTTTTTTTTTCTTTTTTTCTTCT
*
58372 TTTTTCTTC-TTTTTTTTTCTTTTTTTCTTTT
1 TTTTTCTTCTTTTTTTTTTCTTTTTTTCTTCT
*
58403 TTTTTCTCCTTTTTTTTT
1 TTTTTCTTCTTTTTTTTT
58421 AAGCATAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
30 22 0.50
31 14 0.32
32 8 0.18
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (32 bp):
TTTTTCTTCTTTTTTTTTTCTTTTTTTCTTCT
Found at i:58420 original size:1 final size:1
Alignment explanation
Indices: 58342--58407 Score: 69
Period size: 1 Copynumber: 66.0 Consensus size: 1
58332 TTGACCCACC
* * * * * * *
58342 TTTTTTTCTTTTTTTTTTCTTTTTTTTTCTTTTTTCTTCTTTTTTTTTCTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
58407 T
1 T
58408 CTCCTTTTTT
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:71127 original size:3 final size:3
Alignment explanation
Indices: 71119--71207 Score: 142
Period size: 3 Copynumber: 29.7 Consensus size: 3
71109 TTAATATATC
* *
71119 TAA TAA TAA TAG TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
71167 TAA TAA TAG TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
71208 TGGATAAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:74929 original size:36 final size:36
Alignment explanation
Indices: 74882--74953 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
74872 AATGTTTAAA
74882 TTAGGTATTTCCACTAGCATTGAAAAAATGCTCAAG
1 TTAGGTATTTCCACTAGCATTGAAAAAATGCTCAAG
* * *
74918 TTAGGTTTTTCCACTAGTATTGGAAAAATGCTCAAG
1 TTAGGTATTTCCACTAGCATTGAAAAAATGCTCAAG
74954 CATTGGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (36 bp):
TTAGGTATTTCCACTAGCATTGAAAAAATGCTCAAG
Found at i:74960 original size:19 final size:19
Alignment explanation
Indices: 74936--74972 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
74926 TTCCACTAGT
74936 ATTGGAAAAATGCTCAAGC
1 ATTGGAAAAATGCTCAAGC
74955 ATTGGAAAAATGCTCAAG
1 ATTGGAAAAATGCTCAAG
74973 TTAGGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (19 bp):
ATTGGAAAAATGCTCAAGC
Found at i:78658 original size:105 final size:105
Alignment explanation
Indices: 78478--78769 Score: 440
Period size: 105 Copynumber: 2.7 Consensus size: 105
78468 AGCTAAGGTT
* * *
78478 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTTTGTTGGATGAGTTCTTCTTATTATGAACT
1 GAACATGTTCTTCTCATTACGAAC--CTTCTCC--TT-TAGGATGAGTTCTTCTTATTATGAACT
* *
78543 CTTCTGGAAATGTTGATTCACTTCCTCCTAGGGTGAATTTGAAAG
61 CTTCTGGAAATGTTGATTCACCTCCTCCTACGGTGAATTTGAAAG
**
78588 GAACATGTTCTTCTCATTACGAACCTTCTCCTTTAGGATGAGTTCTTCCCATTATGAACTCTTCT
1 GAACATGTTCTTCTCATTACGAACCTTCTCCTTTAGGATGAGTTCTTCTTATTATGAACTCTTCT
* * *
78653 AGAAATGTTGATTCACCTCCTTCTACGGTGGATTTGAAAG
66 GGAAATGTTGATTCACCTCCTCCTACGGTGAATTTGAAAG
*
78693 GAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGATGAGTTCTTCTTATTATGAACTCTTCT
1 GAACATGTTCTTCTCATTACGAACCTTCTCCTTTAGGATGAGTTCTTCTTATTATGAACTCTTCT
78758 GGAAATGTTGAT
66 GGAAATGTTGAT
78770 CGGTTTATCC
Statistics
Matches: 168, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
105 137 0.82
106 2 0.01
108 7 0.04
110 22 0.13
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (105 bp):
GAACATGTTCTTCTCATTACGAACCTTCTCCTTTAGGATGAGTTCTTCTTATTATGAACTCTTCT
GGAAATGTTGATTCACCTCCTCCTACGGTGAATTTGAAAG
Found at i:79758 original size:22 final size:22
Alignment explanation
Indices: 79693--79751 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 22
79683 AATTTAAGCT
*
79693 TCATGCTCGAAAGACTTACTGA
1 TCATGCTCGAAAGACTTACTCA
*
79715 T-A-GC-CCAAAGACTTACTCA
1 TCATGCTCGAAAGACTTACTCA
79734 TCATGCTCGAAAGACTTA
1 TCATGCTCGAAAGACTTA
79752 TTTATCAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 14 0.45
20 3 0.10
21 3 0.10
22 11 0.35
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (22 bp):
TCATGCTCGAAAGACTTACTCA
Found at i:79972 original size:53 final size:53
Alignment explanation
Indices: 79795--80043 Score: 243
Period size: 52 Copynumber: 4.6 Consensus size: 53
79785 TTCTTACTTG
* * * *
79795 TCAAGGAACCCCTAAGAATTAGGCTTAGTTTCCTTTTAAAAACTCATTGAAAATCATCA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTT-C-TTT-AAAATTCATTTAAAA--A-CA
* * * *
79854 TCAAGAAACCCCTGAAAATCAGGCTTAGTTTC--TAAAATCTCATTTGAAAATA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTAAAAT-TCATTTAAAAACA
* * *
79906 TCAAGAAATCCCTAAAAATTAGGCTTAATTTCTTTGAAATTCATTTAAAAACA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTAAAATTCATTTAAAAACA
* * * * *
79959 TTAAGAAACCCCT-AAAATTAGGTTTAGTTTCTTTCAAGTTCATTTGAAAACA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTAAAATTCATTTAAAAACA
* * *
80011 TCGAGAAACCCCTGAAAATCAGGCTTAGTTTCT
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCT
80044 AAAAGTCTTC
Statistics
Matches: 160, Mismatches: 26, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
52 74 0.46
53 40 0.25
54 9 0.06
55 9 0.06
58 1 0.01
59 27 0.17
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (53 bp):
TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTAAAATTCATTTAAAAACA
Found at i:80354 original size:36 final size:37
Alignment explanation
Indices: 80262--80369 Score: 123
Period size: 36 Copynumber: 3.0 Consensus size: 37
80252 AGAAAAAAAA
* * * *
80262 TATCTCAAGCGAGACAAAGTCTAT-TTT-AAGGGAAAC
1 TATCTCAAGGGAGACAAAAT-TTTGTTTCAAGAGAAAC
80298 TATCTCAAGGGAGACAAAA-TTTGTTTCAAGAGAAAC
1 TATCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAAC
* * *
80334 TGTCTCATGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TATCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAA
80370 TATATTCAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
34 2 0.03
35 3 0.05
36 42 0.68
37 15 0.24
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (37 bp):
TATCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAAC
Found at i:80604 original size:66 final size:66
Alignment explanation
Indices: 80498--80673 Score: 273
Period size: 66 Copynumber: 2.7 Consensus size: 66
80488 AAAATTTAAG
* * *
80498 AGAAAAATATCTCAAGCGAGACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTAT-TGTTCC
1 AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATT-TGTGTTCC
80562 GA
65 GA
80564 AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCG
1 AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCG
80629 A
66 A
* * *
80630 AGAAAAATGACTCAAGTGAAACGAAATTTGTTTTAAGAGAAAAA
1 AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTTA-AGAAAAA
80674 TGTCTCAAGT
Statistics
Matches: 102, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
65 1 0.01
66 94 0.92
67 7 0.07
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.29
Consensus pattern (66 bp):
AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCG
A
Found at i:80675 original size:37 final size:37
Alignment explanation
Indices: 80630--80788 Score: 136
Period size: 37 Copynumber: 4.5 Consensus size: 37
80620 TGTGTTCCGA
* *
80630 AGAAAAATGACTCAAGTGAAACGAAATTTGTTTTAAG
1 AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTAAG
* *
80667 AGAAAAATGTCTCAAGTGAGACAAAATTTGTTTTTA-
1 AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTAAG
*** * ** ***
80703 AGAAAAACAACT---TTG-AA-ATTA-TTGTTCCGA-
1 AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTAAG
80733 AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTAAG
1 AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTAAG
*
80770 AGAAAAATGTCTTAAGTGA
1 AGAAAAATGTCTCAAGTGA
80789 GACGACATTT
Statistics
Matches: 91, Mismatches: 24, Indels: 14
0.71 0.19 0.11
Matches are distributed among these distances:
30 15 0.16
31 2 0.02
32 1 0.01
33 4 0.04
34 2 0.02
35 2 0.02
36 15 0.16
37 50 0.55
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (37 bp):
AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTAAG
Found at i:80810 original size:38 final size:37
Alignment explanation
Indices: 80724--80812 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
80714 TTTGAAATTA
*
80724 TTGTTCCGA-AGAAAAATGTCTCAAGTGAAACAAAAT
1 TTGTTTCGAGAGAAAAATGTCTCAAGTGAAACAAAAT
** * * * *
80760 TTGTTTTAAGAGAAAAATGTCTTAAGTGAGACGACATT
1 TTGTTTCGAGAGAAAAATGTCTCAAGTGAAAC-AAAAT
80798 TTGTTTCGAGAGAAA
1 TTGTTTCGAGAGAAA
80813 CAACACCAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
36 6 0.14
37 20 0.48
38 16 0.38
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.30
Consensus pattern (37 bp):
TTGTTTCGAGAGAAAAATGTCTCAAGTGAAACAAAAT
Found at i:80816 original size:103 final size:103
Alignment explanation
Indices: 80564--80791 Score: 404
Period size: 103 Copynumber: 2.2 Consensus size: 103
80554 ATTGTTCCGA
*
80564 AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCG
1 AGAAAAATGTCTCAAGTGAGACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCG
*
80629 AAGAAAAATGACTCAAGTGAAACGAAATTTGTTTTAAG
66 AAGAAAAATGACTCAAGTGAAACAAAATTTGTTTTAAG
80667 AGAAAAATGTCTCAAGTGAGACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTAT-TGTTCC
1 AGAAAAATGTCTCAAGTGAGACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATT-TGTGTTCC
*
80731 GAAGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTAAG
65 GAAGAAAAATGACTCAAGTGAAACAAAATTTGTTTTAAG
*
80770 AGAAAAATGTCTTAAGTGAGAC
1 AGAAAAATGTCTCAAGTGAGAC
80792 GACATTTTGT
Statistics
Matches: 120, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
103 119 0.99
104 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.30
Consensus pattern (103 bp):
AGAAAAATGTCTCAAGTGAGACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCG
AAGAAAAATGACTCAAGTGAAACAAAATTTGTTTTAAG
Found at i:83206 original size:20 final size:20
Alignment explanation
Indices: 83181--83218 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
83171 TTCTCTTTTG
83181 ATTTCC-TCTCATTATTTCCT
1 ATTTCCTTCTCATT-TTTCCT
83201 ATTTCCTTCTCATTTTTC
1 ATTTCCTTCTCATTTTTC
83219 AGCAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.13, C:0.29, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTCCTTCTCATTTTTCCT
Done.