Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005798.1 Hibiscus syriacus cultivar Beakdansim tig00013593_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: 105980
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:4140 original size:21 final size:21
Alignment explanation
Indices: 4114--4173 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
4104 ACTTAATGAT
4114 GATATTGACATATTATCATAA
1 GATATTGACATATTATCATAA
*
4135 GATATTGGCATATTATCATAA
1 GATATTGACATATTATCATAA
* *
4156 -ATAATAACATATTATCAT
1 GATATTGACATATTATCAT
4174 TAAAAAGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
20 15 0.43
21 20 0.57
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.38
Consensus pattern (21 bp):
GATATTGACATATTATCATAA
Found at i:5312 original size:21 final size:21
Alignment explanation
Indices: 5266--5315 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
5256 TGATTACGGT
*
5266 CGTCGCGGATGCTATTGCGAC
1 CGTCGCGGACGCTATTGCGAC
*
5287 TGTCGCGGACGCTATTG-GAGC
1 CGTCGCGGACGCTATTGCGA-C
5308 CGTCGCGG
1 CGTCGCGG
5316 GTAACTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.12, C:0.28, G:0.38, T:0.22
Consensus pattern (21 bp):
CGTCGCGGACGCTATTGCGAC
Found at i:7174 original size:2 final size:2
Alignment explanation
Indices: 7167--7207 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
7157 TAACTTCTAT
7167 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7208 GTTTATTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12177 original size:15 final size:16
Alignment explanation
Indices: 12157--12187 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12147 AACTGTTCTC
12157 CTTCGGG-CTGCTCTG
1 CTTCGGGTCTGCTCTG
12172 CTTCGGGTCTGCTCTG
1 CTTCGGGTCTGCTCTG
12188 ACTTAGCCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.00, C:0.32, G:0.32, T:0.35
Consensus pattern (16 bp):
CTTCGGGTCTGCTCTG
Found at i:12544 original size:51 final size:51
Alignment explanation
Indices: 12358--12619 Score: 301
Period size: 51 Copynumber: 5.0 Consensus size: 51
12348 TACTTGAAAA
* * * *
12358 ATCTTCAA-ATAACGGGTCTGCTCCCTTTTCTTTCAAGGAGTATAAGACTCG
1 ATCTTCAACA-AACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCG
* * * * *
12409 AACAATCATTGGCAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAACA
1 ATC-TTCA---ACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACT----CG
12468 ATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCG
1 ATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCG
12519 ATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCG
1 ATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCG
* * * * * *
12570 ATCTTCAATAAAGGTGTCCGCTCCCTATTCCTTCAGAGAGTATATGACTC
1 ATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTC
12620 AAACAATCTT
Statistics
Matches: 183, Mismatches: 19, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
51 98 0.54
52 3 0.02
55 75 0.41
56 1 0.01
58 3 0.02
59 3 0.02
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (51 bp):
ATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCG
Found at i:12958 original size:55 final size:55
Alignment explanation
Indices: 12357--12971 Score: 712
Period size: 55 Copynumber: 11.3 Consensus size: 55
12347 ATACTTGAAA
* * * *
12357 AATCTTCA-AATAACGGGTCTGCTCCCTTTTCTTTCA-AGGAGTATA-AGACTCGAAC
1 AATCTTCATAA-AACGGGTCCGCTCTCTATTCCTTCAGA-GAGTATAGA-ACTCGAAC
*** * * * * * *
12412 AATCATT-GGCAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCAAAC
1 AATC-TTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* * * * *
12467 AATCTTCA-ACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATA-AGACTCG---
1 AATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* * * * *
12519 -ATCTTCA-ACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATA-AGACTCG---
1 AATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* *
12570 -ATCTTCA-ATAAA-GGTGTCCGCTCCCTATTCCTTCAGAGAGTATATG-ACTCAAAC
1 AATCTTCATA-AAACGG-GTCCGCTCTCTATTCCTTCAGAGAGTATA-GAACTCGAAC
* ** *
12624 AATCTTCAAAAAATAGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCAAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
*
12679 AATCTTCATAAAACGAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
12734 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
12789 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
12844 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
12899 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
12954 AATCTTCATAAAACGGGT
1 AATCTTCATAAAACGGGT
12972 TTGCTTCACT
Statistics
Matches: 520, Mismatches: 25, Indels: 30
0.90 0.04 0.05
Matches are distributed among these distances:
50 1 0.00
51 92 0.18
54 3 0.01
55 419 0.81
56 5 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (55 bp):
AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
Found at i:13025 original size:37 final size:37
Alignment explanation
Indices: 12971--13053 Score: 132
Period size: 37 Copynumber: 2.2 Consensus size: 37
12961 ATAAAACGGG
*
12971 TTTGCTTCACTATTCTTCCGTGAAGGCTTATAGA-TGA
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTA-AGATTGA
13008 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
*
13045 TTTGTTTCA
1 TTTGCTTCA
13054 AAGATCCAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 3 0.07
37 40 0.93
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.42
Consensus pattern (37 bp):
TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
Found at i:24036 original size:45 final size:45
Alignment explanation
Indices: 23969--24112 Score: 182
Period size: 45 Copynumber: 3.1 Consensus size: 45
23959 TGTTATCCAC
* ** *
23969 AAAAAGAAATCCTAACCTCATGATATCTAATTCGCATGCTTATTC-
1 AAAAATAAA-CCTAACAGCATGATATCTAGTTCGCATGCTTATTCG
*
24014 AGAAAATAAACCTAACAGCATGATATCTAGTTCGCATGCTTGTTCG
1 A-AAAATAAACCTAACAGCATGATATCTAGTTCGCATGCTTATTCG
* *
24060 AAAAATAAACCTAACCGCATGATATCTAGTTCGCAAGCATTTATTCG
1 AAAAATAAACCTAACAGCATGATATCTAGTTCGCATGC--TTATTCG
24107 AAAAAT
1 AAAAAT
24113 GAAAATAAAT
Statistics
Matches: 87, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
45 67 0.77
46 8 0.09
47 12 0.14
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.28
Consensus pattern (45 bp):
AAAAATAAACCTAACAGCATGATATCTAGTTCGCATGCTTATTCG
Found at i:27005 original size:15 final size:16
Alignment explanation
Indices: 26985--27014 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
26975 AACTGTTCTC
26985 CTTCGGG-CTGCTCTT
1 CTTCGGGTCTGCTCTT
27000 CTTCGGGTCTGCTCT
1 CTTCGGGTCTGCTCT
27015 GACTTAGCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.33, G:0.27, T:0.40
Consensus pattern (16 bp):
CTTCGGGTCTGCTCTT
Found at i:29270 original size:10 final size:11
Alignment explanation
Indices: 29252--29342 Score: 52
Period size: 10 Copynumber: 8.5 Consensus size: 11
29242 TCAAATATAT
29252 TAATATATTTA
1 TAATATATTTA
29263 TAAT-TATTTA
1 TAATATATTTA
*
29273 TTATAT-TTTA
1 TAATATATTTA
*
29283 -AAT-TATTAAAA
1 TAATATATT--TA
29294 TAATATATTTTA
1 TAATATA-TTTA
29306 TAATATACTTT-
1 TAATATA-TTTA
*
29317 TAATA-ATTAAA
1 TAATATATT-TA
*
29328 TAATTTATTT-
1 TAATATATTTA
29338 TAATA
1 TAATA
29343 ATATAAAGAT
Statistics
Matches: 61, Mismatches: 9, Indels: 21
0.67 0.10 0.23
Matches are distributed among these distances:
8 1 0.02
9 6 0.10
10 18 0.30
11 15 0.25
12 17 0.28
13 2 0.03
14 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (11 bp):
TAATATATTTA
Found at i:29327 original size:35 final size:35
Alignment explanation
Indices: 29274--29347 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
29264 AATTATTTAT
*
29274 TATATTTTAAATTATTAAAATAATATATTTT-ATAA
1 TATATTTTAAATAATT-AAATAATATATTTTAATAA
*
29309 TATACTTTT-AATAATTAAATAATTTATTTTAATAA
1 TATA-TTTTAAATAATTAAATAATATATTTTAATAA
29344 TATA
1 TATA
29348 AAGATAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 13 0.37
35 18 0.51
36 4 0.11
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (35 bp):
TATATTTTAAATAATTAAATAATATATTTTAATAA
Found at i:29339 original size:21 final size:23
Alignment explanation
Indices: 29305--29349 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
29295 AATATATTTT
29305 ATAATATACTTTTAATAAT-TAA
1 ATAATATACTTTTAATAATATAA
*
29327 ATAATTTA-TTTTAATAATATAA
1 ATAATATACTTTTAATAATATAA
29349 A
1 A
29350 GATAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAATATACTTTTAATAATATAA
Found at i:29995 original size:14 final size:14
Alignment explanation
Indices: 29978--30008 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
29968 ATTAATTAAA
29978 TTATTAGAATTTAT
1 TTATTAGAATTTAT
29992 TTATTAGAATTTAT
1 TTATTAGAATTTAT
30006 TTA
1 TTA
30009 AATAGTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (14 bp):
TTATTAGAATTTAT
Found at i:34349 original size:2 final size:2
Alignment explanation
Indices: 34342--34375 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
34332 TAATTTATGA
34342 AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34376 CACTACTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38992 original size:183 final size:183
Alignment explanation
Indices: 38684--39033 Score: 619
Period size: 183 Copynumber: 1.9 Consensus size: 183
38674 ATTAAATCCG
38684 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * *
38749 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTACTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGATGTTTGCTCCACTACTT
*
38814 TTATCAGGTCAAAGACTTTGTGATGAGACGAACCCTTTAGTGATTTGTCCCTC
131 TTATCAGGCCAAAGACTTTGTGATGAGACGAACCCTTTAGTGATTTGTCCCTC
38867 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
38932 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGATGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGATGTTTGCTCCACTACTT
* *
38997 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTT
131 TTATCAGGCCAAAGACTTTGTGATGAGACGAACCCTT
39034 CAGTTAAACC
Statistics
Matches: 158, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 158 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGATGTTTGCTCCACTACTT
TTATCAGGCCAAAGACTTTGTGATGAGACGAACCCTTTAGTGATTTGTCCCTC
Found at i:40452 original size:104 final size:102
Alignment explanation
Indices: 40292--40598 Score: 431
Period size: 104 Copynumber: 3.0 Consensus size: 102
40282 TTTAAAGAAG
* * *
40292 ATTTTATCT-TGCTTAAGATAGTTTCCCTCGAAACAGAAAATTTTTTCTCCCTTGAGACAATTTC
1 ATTTTATCTCT-CTTGAGATAGTTTCCCTTGAAAC--AAAATTTTGTCTCCCTTGAGACAATTTC
40356 TCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT-A
63 TCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* * *
40395 ATTTTTTTTTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGCCTCCCTTGAGACATTTTC
1 A---TTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTC
40460 TCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
63 TCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* * *
40500 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGATAGTTTCTAT
1 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCT
* *
40564 TGAGACATAAACTTTGAAAACAGTTTCCCTTGAAA
66 TGAAACATAAACATTGAAAACA-TTTCCCTTGAAA
40599 CAAAATCTTT
Statistics
Matches: 185, Mismatches: 13, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
101 46 0.25
102 44 0.24
103 1 0.01
104 63 0.34
105 2 0.01
106 28 0.15
107 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (102 bp):
ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
Found at i:40532 original size:36 final size:36
Alignment explanation
Indices: 40485--40560 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
40475 ATTGAAAACA
** *
40485 TTTCCCTTGAAATGAATTTTATCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTATCTCCCTTGAGATAG
*
40521 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTATCTCCCTTGAGATAG
40557 TTTC
1 TTTC
40561 TATTGAGACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTATCTCCCTTGAGATAG
Found at i:40729 original size:90 final size:90
Alignment explanation
Indices: 40589--40773 Score: 261
Period size: 90 Copynumber: 2.1 Consensus size: 90
40579 GAAAACAGTT
* *
40589 TCCCTTGAAAC---AAAATCTTTGAATATGTTTTACATTAAACTAATTTCGTCTCCCTTGAGACA
1 TCCCTTGAAACAAAAAAATCTTTGAATATGTTTTACATTAAACAAATTCCGTCTCCCTTGAGACA
40651 ATTTCTTTTAGAACAAAGTTTTGTC
66 ATTTCTTTTAGAACAAAGTTTTGTC
* * *
40676 TCTCTTGAAACAAAAAAATCTTTGAATATGTTTT-CCTTAAAACAAATTCCGTCTCCCTTGAGAT
1 TCCCTTGAAACAAAAAAATCTTTGAATATGTTTTACATT-AAACAAATTCCGTCTCCCTTGAGAC
* * *
40740 AGTTTCTTTTGGAACTAAGTTTTGTC
65 AATTTCTTTTAGAACAAAGTTTTGTC
40766 TCCCTTGA
1 TCCCTTGA
40774 GACAGTTTCT
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
87 10 0.12
89 3 0.04
90 72 0.85
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (90 bp):
TCCCTTGAAACAAAAAAATCTTTGAATATGTTTTACATTAAACAAATTCCGTCTCCCTTGAGACA
ATTTCTTTTAGAACAAAGTTTTGTC
Found at i:40781 original size:37 final size:37
Alignment explanation
Indices: 40715--40820 Score: 160
Period size: 37 Copynumber: 2.9 Consensus size: 37
40705 GTTTTCCTTA
** *
40715 AAACAAATTCCGTCTCCCTTGAGATAGTTTCTTTTGG
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGG
*
40752 -AACTAAGTTTTGTCTCCCTTGAGACAGTTTCTTTTGG
1 AAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTTTTGG
40789 AAACAAATTTTGTCTCCCTTGAGACAGTTTCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCT
40821 CTCGAAGCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
36 3 0.05
37 56 0.90
38 3 0.05
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.40
Consensus pattern (37 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGG
Found at i:41179 original size:105 final size:105
Alignment explanation
Indices: 40887--41206 Score: 437
Period size: 107 Copynumber: 3.0 Consensus size: 105
40877 TAGTTCGAAG
* * *
40887 CGAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAGT
1 CGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA-T
*
40952 TTTAGAGCCAATTTCAACTTCACAGCGAA-AGATATTGGACT
65 TTCAGAGCCAATTTCAACTTCACAGCGAAGA-ATATTGGACT
* **
40993 CGAGACAACACAAGTTCAAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCCAA
1 CGAGACAACACAAGTTC-AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC-A
*
41058 TTTCAGAGTCAATTTCAACTTCACAGCGAAGAATATTGGACT
64 TTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGGACT
* * * * *
41100 CGAGACAGCACAAGTT-GACTTCACGACGAAGGGACCACTGGTTGTCAATATACAATTTCCCATT
1 CGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCATT
* * *
41164 TCCAGAACCAATTTCAACTTCATAGCGAAGGATATTGGACT
66 T-CAGAGCCAATTTCAACTTCACAGCGAAGAATATTGGACT
41205 CG
1 CG
41207 GAACAATACT
Statistics
Matches: 190, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
104 4 0.02
105 75 0.39
106 16 0.08
107 93 0.49
108 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (105 bp):
CGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCATT
TCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGGACT
Found at i:42883 original size:2 final size:2
Alignment explanation
Indices: 42876--42917 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
42866 TAATTTATGA
42876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42918 CACTACTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47512 original size:9 final size:9
Alignment explanation
Indices: 47498--47524 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
47488 AGAGAAAGCC
47498 AGGAAGGAG
1 AGGAAGGAG
47507 AGGAAGGAG
1 AGGAAGGAG
47516 AGGAAGGAG
1 AGGAAGGAG
47525 CGGTGGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (9 bp):
AGGAAGGAG
Found at i:50526 original size:24 final size:24
Alignment explanation
Indices: 50499--50545 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
50489 TTAATATTAA
50499 AATAAGTCACTAAATTATTTTTTT
1 AATAAGTCACTAAATTATTTTTTT
* ***
50523 AATAATTGTTTAAATTATTTTTT
1 AATAAGTCACTAAATTATTTTTT
50546 GACCCATCCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (24 bp):
AATAAGTCACTAAATTATTTTTTT
Found at i:51926 original size:20 final size:20
Alignment explanation
Indices: 51901--51938 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
51891 TTCCCCTTGA
51901 AGTGCATCGATACATTCTAT
1 AGTGCATCGATACATTCTAT
*
51921 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
51939 TTAACATGTG
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:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAT
Found at i:52942 original size:14 final size:14
Alignment explanation
Indices: 52923--52964 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
52913 CCCTAAATTT
*
52923 ATAAATTCCTAAAC
1 ATAAATTCTTAAAC
52937 ATAAATTCTTAAAC
1 ATAAATTCTTAAAC
52951 ATAAATTCTTAAAC
1 ATAAATTCTTAAAC
52965 CTAATACCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAATTCTTAAAC
Found at i:55865 original size:20 final size:19
Alignment explanation
Indices: 55826--55867 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
55816 TTTCTTCGAT
55826 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
55845 ATTAAAATAATTAATATATA
1 ATTAAAA-AATAAATAAATA
55865 ATT
1 ATT
55868 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:55891 original size:120 final size:116
Alignment explanation
Indices: 55734--55969 Score: 267
Period size: 120 Copynumber: 2.0 Consensus size: 116
55724 AAAAATATAT
* * * * * **
55734 TAATTTATATATATTTATAAGTAAAATATTTATTTATTTAGAAATATCAGAAAAT-GACTTTTAG
1 TAATTAATATATATTTATAAATAAAATATTTACTTATTTAAAAATATCAGAAAATGGACATCCAG
* *
55798 GTGCCTTAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAA
66 GTGCCTTAAGACAGC-CCTTTCTT-AATATTAAAAAATAAATAAAT-ATTAAAA
** *
55852 TAATTAATATATAATTTATAAAATAGGATATTTACTTATTTAAAAATATCATAAAATGGACATCC
1 TAATTAATATAT-ATTTAT-AAATAAAATATTTACTTATTTAAAAATATCAGAAAATGGACATCC
* ** * *
55917 AGTTGTTTTAAGACTGCCCTTTCTTAATATTGAAAAATAAATAAATATTAAAA
64 AGGTGCCTTAAGACAGCCCTTTCTTAATATTAAAAAATAAATAAATATTAAAA
55970 CAGGATTAAA
Statistics
Matches: 98, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
118 18 0.18
119 25 0.26
120 38 0.39
121 17 0.17
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (116 bp):
TAATTAATATATATTTATAAATAAAATATTTACTTATTTAAAAATATCAGAAAATGGACATCCAG
GTGCCTTAAGACAGCCCTTTCTTAATATTAAAAAATAAATAAATATTAAAA
Found at i:57556 original size:3 final size:3
Alignment explanation
Indices: 57538--57596 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
57528 TTGTAATATT
* **
57538 TAA TAAA TAA TAAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TTT TAA
1 TAA T-AA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57585 TAA TAA TAA TAA
1 TAA TAA TAA TAA
57597 ATTTAAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 42 0.88
4 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:57571 original size:18 final size:18
Alignment explanation
Indices: 57544--57596 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
57534 TATTTAATAA
57544 ATAATAAATAATAATAATT
1 ATAAT-AATAATAATAATT
57563 ATAATAATAATAATAATT
1 ATAATAATAATAATAATT
*
57581 TTAATAATAATAATAA
1 ATAATAATAATAATAA
57597 ATTTAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 28 0.85
19 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATAATAATAATAATT
Found at i:57601 original size:18 final size:18
Alignment explanation
Indices: 57545--57602 Score: 82
Period size: 18 Copynumber: 3.2 Consensus size: 18
57535 ATTTAATAAA
57545 TAATAAATAATAAT-AATT
1 TAAT-AATAATAATAAATT
*
57563 ATAATAATAATAATAATTT
1 -TAATAATAATAATAAATT
57582 TAATAATAATAATAAATT
1 TAATAATAATAATAAATT
57600 TAA
1 TAA
57603 ATTTAAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 29 0.81
19 7 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATAATAATAATAAATT
Found at i:57782 original size:45 final size:45
Alignment explanation
Indices: 57718--58225 Score: 874
Period size: 45 Copynumber: 11.2 Consensus size: 45
57708 GATGGAAATG
* * *
57718 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGC
1 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * *
57763 TTTGAAAACATCAACCACTGAAGGACTTACAGATGACCCGAAGGC
1 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
57808 TTTGAAAACATCAAGCACTGAAGGGCTTACATATGACCCGGAGGT
1 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
57853 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
57898 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGC
1 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
57943 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCC-AGAGGT
1 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGA-AGGT
57988 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-T
58034 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
58079 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGC
1 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
58124 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGGAGGT
1 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
58169 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-T
58215 TTTGAAAACAT
1 TTTGAAAACAT
58226 TAAAAAGCTC
Statistics
Matches: 441, Mismatches: 18, Indels: 7
0.95 0.04 0.02
Matches are distributed among these distances:
44 1 0.00
45 382 0.87
46 58 0.13
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.20
Consensus pattern (45 bp):
TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
Found at i:58324 original size:76 final size:77
Alignment explanation
Indices: 58168--58356 Score: 308
Period size: 76 Copynumber: 2.5 Consensus size: 77
58158 GACCCGGAGG
* * * * * *
58168 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATTAAAAAG
1 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGTCTTTGAAAACATCAAAAAG
58233 CTCCCGAAGGCT
66 CTCCCGAAGGCT
*
58245 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAA-GTCTTTGAAAACATCAAAAAG
1 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGTCTTTGAAAACATCAAAAAG
58309 CTCCCGAAGGCT
66 CTCCCGAAGGCT
58321 TTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 TTTTGGAAACATCATGCACTGTAGGACTTACAGATG
58357 TAGGAAATAG
Statistics
Matches: 105, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
76 67 0.64
77 38 0.36
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (77 bp):
TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGTCTTTGAAAACATCAAAAAG
CTCCCGAAGGCT
Found at i:59242 original size:22 final size:22
Alignment explanation
Indices: 59214--59268 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
59204 CATAAAGCTT
59214 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
59236 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
59258 TCATCTTTGAA
1 TCATCTTTGAA
59269 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:67474 original size:20 final size:19
Alignment explanation
Indices: 67435--67476 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
67425 TTTCTTCGAT
67435 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
67454 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
67474 ATT
1 ATT
67477 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:69169 original size:3 final size:3
Alignment explanation
Indices: 69129--69210 Score: 92
Period size: 3 Copynumber: 26.7 Consensus size: 3
69119 TTGTAATATT
* * * *
69129 TAA TAAA TAA TATT TAA TAT TAA TAT TAA TAT TAA TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
69176 TAA TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
69211 GATTTAAATT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
3 60 0.92
4 5 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:69216 original size:18 final size:17
Alignment explanation
Indices: 69122--69217 Score: 101
Period size: 18 Copynumber: 5.6 Consensus size: 17
69112 TTGGGCTTTG
69122 TAAT-ATTTAAT-A-AA
1 TAATAATTTAATAATAA
*
69136 TAAT-ATTTAATATTAA
1 TAATAATTTAATAATAA
*
69152 TATTAATATTAATAATAA
1 TAATAAT-TTAATAATAA
*
69170 TAATAATAATAATAATAA
1 TAATAAT-TTAATAATAA
69188 TAATAATTTTAATAATAA
1 TAATAA-TTTAATAATAA
69206 TAATAGATTTAA
1 TAATA-ATTTAA
69218 ATTTAAAATG
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
14 11 0.16
16 5 0.07
17 2 0.03
18 50 0.71
19 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (17 bp):
TAATAATTTAATAATAA
Found at i:80690 original size:3 final size:3
Alignment explanation
Indices: 80682--80718 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
80672 GGGTATTAGT
*
80682 TTC TTC TTC TTTC TTC TTC TTT TTC TTC TTC TTC TTC
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC
80719 ACTGAAATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:81453 original size:39 final size:38
Alignment explanation
Indices: 81379--81516 Score: 164
Period size: 39 Copynumber: 3.8 Consensus size: 38
81369 ATCGGTTTCG
* *
81379 AAAATATATAT--TATATA--TTTTGAAAACAGTATTA
1 AAAATATATATGATATATAGTTTTTGAAAACATTTTTA
81413 AAAATATATATGATATATAGTTTTTTGAAAACATTTTTA
1 AAAATATATATGATATATAG-TTTTTGAAAACATTTTTA
* *
81452 AAAATATATATAATATATAGTTTTTGAAAATATTTTTGA
1 AAAATATATATGATATATAGTTTTTGAAAACATTTTT-A
*
81491 AAAATCTA-ATG--ATATAGTTTTTGAAA
1 AAAATATATATGATATATAGTTTTTGAAA
81517 GTATATATCA
Statistics
Matches: 92, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
34 11 0.12
36 21 0.23
38 18 0.20
39 42 0.46
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.43
Consensus pattern (38 bp):
AAAATATATATGATATATAGTTTTTGAAAACATTTTTA
Found at i:81487 original size:38 final size:36
Alignment explanation
Indices: 81379--81636 Score: 160
Period size: 36 Copynumber: 7.4 Consensus size: 36
81369 ATCGGTTTCG
* *
81379 AAAATATATATTATATA--TTTTGAAAACAGTATTA
1 AAAATATATATTATATAGTTTTTGAAAACATTTTTA
81413 AAAATATATATGATATATAGTTTTTTGAAAACATTTTTA
1 AAAATATATAT--TATATAG-TTTTTGAAAACATTTTTA
*
81452 AAAATATATATAATATATAGTTTTTGAAAATATTTTTGA
1 AAAATATATAT--TATATAGTTTTTGAAAACATTTTT-A
* * *
81491 AAAATCTA-ATGATATAGTTTTTG--AA-A---GT-
1 AAAATATATATTATATAGTTTTTGAAAACATTTTTA
*
81519 ---ATATATCA-TATATAGTTTTT-AAAATA-TTTTA
1 AAAATATAT-ATTATATAGTTTTTGAAAACATTTTTA
* *
81550 AAATAAATATATATATATAG-TTTTGAAAATACTTTTT-
1 AAA-ATATATAT-TATATAGTTTTTGAAAACA-TTTTTA
* * * **
81587 AAAATGTATAATATATAGTTTTTTAAATGATTTTTA
1 AAAATATATATTATATAGTTTTTGAAAACATTTTTA
81623 AAAAT-T-TATTATAT
1 AAAATATATATTATAT
81637 TATATTATTA
Statistics
Matches: 181, Mismatches: 18, Indels: 50
0.73 0.07 0.20
Matches are distributed among these distances:
25 4 0.02
26 11 0.06
27 3 0.02
28 1 0.01
30 2 0.01
33 1 0.01
34 21 0.12
35 22 0.12
36 49 0.27
37 3 0.02
38 22 0.12
39 42 0.23
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (36 bp):
AAAATATATATTATATAGTTTTTGAAAACATTTTTA
Found at i:81530 original size:135 final size:131
Alignment explanation
Indices: 81378--81627 Score: 294
Period size: 133 Copynumber: 1.9 Consensus size: 131
81368 AATCGGTTTC
* *
81378 GAAAATATATAT-TATATA-TTTTGAAAACAGTATTAAAA-ATATATATGATATATAGTTTTTTG
1 GAAAATATATATCAATATAGTTTTGAAAACA-TATTAAAATAAATATAT-ATATATAG--TTTTG
81440 AAAACA-TTTTTAAAAATATATATAATATATAGTTTTTGAAAAT-ATTTTTGAAAAATCTAATGA
62 AAAACACTTTTT--AAA-ATATATAATATATAGTTTTT-AAAATGATTTTT-AAAAATCTAATGA
81503 TATAGTTTTT
122 TATAGTTTTT
* * * *
81513 GAAAGTATATATCATATATAGTTTTTAAAATATTTTAAAATAAATATATATATATAGTTTTGAAA
1 GAAAATATATATCA-ATATAGTTTTGAAAACATATTAAAATAAATATATATATATAGTTTTGAAA
* * *
81578 ATACTTTTTAAAATGTATAATATATAGTTTTTTAAATGATTTTTAAAAAT
65 ACACTTTTTAAAATATATAATATATAGTTTTTAAAATGATTTTTAAAAAT
81628 TTATTATATT
Statistics
Matches: 100, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
132 10 0.10
133 25 0.25
134 3 0.03
135 21 0.21
136 5 0.05
137 20 0.20
138 16 0.16
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (131 bp):
GAAAATATATATCAATATAGTTTTGAAAACATATTAAAATAAATATATATATATAGTTTTGAAAA
CACTTTTTAAAATATATAATATATAGTTTTTAAAATGATTTTTAAAAATCTAATGATATAGTTTT
T
Found at i:81568 original size:36 final size:35
Alignment explanation
Indices: 81508--81625 Score: 132
Period size: 35 Copynumber: 3.3 Consensus size: 35
81498 AATGATATAG
*
81508 TTTTTGAAAGTATATATCATATATAGTTTTTAAAATA
1 TTTTT-AAAATATATAT-ATATATAGTTTTTAAAATA
*
81545 -TTTTAAAATAAATATATATATATAGTTTTGAAAATA
1 TTTTTAAAAT--ATATATATATATAGTTTTTAAAATA
* *
81581 CTTTTTAAAATGTATA-ATATATAGTTTTTTAAATGA
1 -TTTTTAAAATATATATATATATAGTTTTTAAAAT-A
81617 TTTTTAAAA
1 TTTTTAAAA
81626 ATTTATTATA
Statistics
Matches: 71, Mismatches: 5, Indels: 12
0.81 0.06 0.14
Matches are distributed among these distances:
35 29 0.41
36 27 0.38
37 6 0.08
38 9 0.13
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (35 bp):
TTTTTAAAATATATATATATATAGTTTTTAAAATA
Found at i:81568 original size:62 final size:62
Alignment explanation
Indices: 81446--81580 Score: 177
Period size: 62 Copynumber: 2.2 Consensus size: 62
81436 TTTGAAAACA
* ** *
81446 TTTTTAAAAATATATATAATATATAGTTTTTGAAAATATTTTTGAAAAATCTAATGATATAG
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAATATTTTAAAAAAATATAATGATATAG
* *
81508 TTTTTGAAAGTATATATCATATATAGTTTTT-AAAATATTTTAAAATAAATATATAT-ATATAG
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAATATTTTAAAA-AAATATA-ATGATATAG
81570 -TTTTGAAAATA
1 TTTTTGAAAATA
81581 CTTTTTAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
61 22 0.34
62 40 0.62
63 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.46
Consensus pattern (62 bp):
TTTTTGAAAATATATATAATATATAGTTTTTGAAAATATTTTAAAAAAATATAATGATATAG
Found at i:81655 original size:9 final size:9
Alignment explanation
Indices: 81641--81669 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
81631 TTATATTATA
81641 TTATTATTT
1 TTATTATTT
81650 TTATTATTT
1 TTATTATTT
81659 TTATTATTT
1 TTATTATTT
81668 TT
1 TT
81670 TACTTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTATTATTT
Found at i:81677 original size:18 final size:18
Alignment explanation
Indices: 81641--81678 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
81631 TTATATTATA
*
81641 TTATTATTTTTATTATTT
1 TTATTATTTTTACTATTT
81659 TTATTATTTTTTACT-TTT
1 TTATTA-TTTTTACTATTT
81677 TT
1 TT
81679 CAAGGTCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (18 bp):
TTATTATTTTTACTATTT
Found at i:82029 original size:209 final size:206
Alignment explanation
Indices: 81651--82066 Score: 764
Period size: 209 Copynumber: 2.0 Consensus size: 206
81641 TTATTATTTT
81651 TATTATTTTTATTATTTTTTACTTTTTTCAAGGTCTGAATAAGGGTCCACGGGTCGATCCAAAAG
1 TATTATTTTTATTATTTTTTACTTTTTTCAAGGTCTGAATAAGGGTCCACGGGTCGATCCAAAAG
81716 AGGTCCAAACATACGGGCTGATCCAGCCAAAACAAACAGGGTTGTAAAACCCTAGTCATACAAAG
66 AGGTCCAAACATACGGGCTGATCCAGCCAAAACAAACAGGGTTGTAAAACCCTAGTCATACAAAG
81781 CACCAGCGCCACACAAGAGAATACAAGCAGCGCGCGTGGCGGCCACGCG-AACAACCAACGTGAC
131 CACCAGCGCCACACAAGAGAATACAAGCAGCGCGCGTGGCGGCCACGCGCAACAACCAACGTGAC
81845 TGAACCATCCC
196 TGAACCATCCC
81856 TATTATTTTT-TATATTTTTTTACTTTTTTCAAGGTCTGAATAAGGGTCCACGGGTCGATCCAAA
1 TATTATTTTTAT-TA-TTTTTTACTTTTTTCAAGGTCTGAATAAGGGTCCACGGGTCGATCCAAA
81920 AGAGGTCCAAACATACGGGCCTGATCCAGCCCATAAACAAACAGGGTTGTAAAACCCTAGTCATA
64 AGAGGTCCAAACATACGGG-CTGATCCAG-CCA-AAACAAACAGGGTTGTAAAACCCTAGTCATA
81985 CAAAGCACCAGCGCCACACAAGAGAATACAAGCAGCGCGCGTGGCGGCCACGCGCCAACAACCAA
126 CAAAGCACCAGCGCCACACAAGAGAATACAAGCAGCGCGCGTGGCGGCCACGCG-CAACAACCAA
82050 CGTGACTGAACCATCCC
190 CGTGACTGAACCATCCC
82067 GGGTCTTCAG
Statistics
Matches: 204, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
204 1 0.00
205 12 0.06
206 68 0.33
207 9 0.04
208 3 0.01
209 85 0.42
211 26 0.13
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (206 bp):
TATTATTTTTATTATTTTTTACTTTTTTCAAGGTCTGAATAAGGGTCCACGGGTCGATCCAAAAG
AGGTCCAAACATACGGGCTGATCCAGCCAAAACAAACAGGGTTGTAAAACCCTAGTCATACAAAG
CACCAGCGCCACACAAGAGAATACAAGCAGCGCGCGTGGCGGCCACGCGCAACAACCAACGTGAC
TGAACCATCCC
Found at i:83030 original size:25 final size:24
Alignment explanation
Indices: 82978--83031 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
82968 AATTATATCT
** *
82978 ATTTATTTCTATTTTTTTTTAAAC
1 ATTTATTTCTATTTTTACTTAAAA
83002 ATTTATTTCTATTTTTACTTACAAA
1 ATTTATTTCTATTTTTACTTA-AAA
83027 ATTTA
1 ATTTA
83032 ACTTTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTTATTTCTATTTTTACTTAAAA
Found at i:83114 original size:21 final size:21
Alignment explanation
Indices: 83074--83115 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
83064 ATTTTCAATA
*
83074 TTTATTTATCTTAATTTATTT
1 TTTATTTATCTTAATATATTT
* *
83095 TTTATTTATTTTTATATATTT
1 TTTATTTATCTTAATATATTT
83116 CACAATTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTATTTATCTTAATATATTT
Found at i:86737 original size:20 final size:20
Alignment explanation
Indices: 86712--86749 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
86702 TTCCCCTTGA
86712 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
86732 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
86750 TTAACATATG
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:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:93518 original size:27 final size:26
Alignment explanation
Indices: 93480--93556 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 26
93470 TCATTTAAAT
93480 TTATTATTATTATTAAA-T-TTATTA
1 TTATTATTATTATTAAATTATTATTA
93504 TTATTATTATTATTAAA-TATTATTA
1 TTATTATTATTATTAAATTATTATTA
*
93529 TTAGTATATTATTATTAAATAATTATTA
1 TTA-T-TATTATTATTAAATTATTATTA
93557 CAAGCCCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
24 18 0.38
25 9 0.19
26 1 0.02
27 13 0.27
28 7 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTATTATTATTATTAAATTATTATTA
Found at i:93556 original size:3 final size:3
Alignment explanation
Indices: 93480--93545 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
93470 TCATTTAAAT
* *
93480 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTAA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
93526 TTA TTA GTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
93546 AATAATTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
2 3 0.06
3 48 0.89
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:95128 original size:19 final size:19
Alignment explanation
Indices: 95104--95140 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
95094 GATATGTTTA
*
95104 ATTTATATTTTAGATATTT
1 ATTTATATTTTAAATATTT
*
95123 ATTTATTTTTTAAATATT
1 ATTTATATTTTAAATATT
95141 GAAGGAAAGA
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:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTATATTTTAAATATTT
Found at i:97916 original size:7 final size:7
Alignment explanation
Indices: 97881--97921 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
97871 TTTTCATACA
97881 TGCATTT
1 TGCATTT
97888 T-CATTT
1 TGCATTT
97894 TGCATCTT
1 TGCAT-TT
97902 TGCATTT
1 TGCATTT
*
97909 TTCATTT
1 TGCATTT
97916 TGCATT
1 TGCATT
97922 CATACTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:100482 original size:13 final size:13
Alignment explanation
Indices: 100464--100488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
100454 TCCAACAAAG
100464 AAAGAAGAAAAAA
1 AAAGAAGAAAAAA
100477 AAAGAAGAAAAA
1 AAAGAAGAAAAA
100489 GGAAAATTGA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAGAAGAAAAAA
Found at i:103064 original size:114 final size:115
Alignment explanation
Indices: 102860--103177 Score: 480
Period size: 115 Copynumber: 2.8 Consensus size: 115
102850 AGATGAATGT
*
102860 GCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
* *
102924 TCAATCATTGGATTTGAAAGATGAA-TTTGCTCATGGTAGAAATAAGGAG
66 TCAATCATTGGATTTAAAAGATGAATTTTGCTCATAGTAGAAATAAGGAG
102973 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
* *
103038 TTAATCATTGGATTTAAAAGATGAATTTTGTTCATAGTAGAAATAAGGAG
66 TCAATCATTGGATTTAAAAGATGAATTTTGCTCATAGTAGAAATAAGGAG
* * * * *
103088 ACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAAC-CCTAGA
1 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCC-AAA
* * * *
103152 ACCTATCATTGGAATTGAAAGATGAA
65 ATCAATCATTGGATTTAAAAGATGAA
103178 CTGCATGATC
Statistics
Matches: 187, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
113 4 0.02
114 84 0.45
115 99 0.53
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (115 bp):
GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
TCAATCATTGGATTTAAAAGATGAATTTTGCTCATAGTAGAAATAAGGAG
Found at i:105071 original size:14 final size:14
Alignment explanation
Indices: 105052--105081 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
105042 ACCTGTTTTC
105052 TGATGCTGAACCAA
1 TGATGCTGAACCAA
105066 TGATGCTGAACCAA
1 TGATGCTGAACCAA
105080 TG
1 TG
105082 TTGCGATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.23
Consensus pattern (14 bp):
TGATGCTGAACCAA
Found at i:105455 original size:22 final size:22
Alignment explanation
Indices: 105424--105478 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
105414 ATCTACACTC
105424 TTCAAAGATGATAGACTCCT-TT
1 TTCAAAGATGATAGA-TCCTCTT
* *
105446 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATCCTCTT
105468 TTCAAAGATGA
1 TTCAAAGATGA
105479 AAGCTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 3 0.10
22 26 0.90
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGATCCTCTT
Done.