Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006054.1 Hibiscus syriacus cultivar Beakdansim tig00014325_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: 80829
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3248 original size:2 final size:2
Alignment explanation
Indices: 3241--3283 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
3231 ACAATGTATG
3241 AT AT AT AT AT AT A- 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
3282 AT
1 AT
3284 GTTTTGTGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4014 original size:21 final size:21
Alignment explanation
Indices: 3989--4029 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3979 ATATAAATTG
*
3989 TGTATCGATGCATTGCTACAA
1 TGTATCGATGCACTGCTACAA
4010 TGTATCGATGCACTGCTACA
1 TGTATCGATGCACTGCTACA
4030 GTAACTTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (21 bp):
TGTATCGATGCACTGCTACAA
Found at i:6225 original size:24 final size:24
Alignment explanation
Indices: 6180--6225 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
6170 TTTTAAAGAA
*
6180 TTTAATTTTTTTAAATATAATATT
1 TTTAATTTTTTTAAATAAAATATT
*
6204 TTTATTTTTTTTAAGA-AAAATA
1 TTTAATTTTTTTAA-ATAAAATA
6226 AAATTTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTAATTTTTTTAAATAAAATATT
Found at i:10006 original size:31 final size:31
Alignment explanation
Indices: 9960--10019 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
9950 TGTAACGGCC
* *
9960 GGTTACGTCGGGGACCTTATT-CTAAATGGTT
1 GGTTACGTCAGGGACCATATTGC-AAATGGTT
*
9991 GGTTACGTCATGGACCATATTGCAAATGG
1 GGTTACGTCAGGGACCATATTGCAAATGG
10020 ACTAAATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (31 bp):
GGTTACGTCAGGGACCATATTGCAAATGGTT
Found at i:10678 original size:23 final size:23
Alignment explanation
Indices: 10651--10694 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
10641 ATTATTTAAA
10651 TTATT-GGTAATATTTTTAATTTT
1 TTATTAGGTAATA-TTTTAATTTT
*
10674 TTATTAGGTTATATTTTAATT
1 TTATTAGGTAATATTTTAATT
10695 CATATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (23 bp):
TTATTAGGTAATATTTTAATTTT
Found at i:14070 original size:3 final size:3
Alignment explanation
Indices: 14062--14101 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
14052 CTCCTCACTC
*
14062 TCA TCA TCA TCA TCA TCA CCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
14102 AAGGAGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:21066 original size:58 final size:59
Alignment explanation
Indices: 20976--21098 Score: 230
Period size: 58 Copynumber: 2.1 Consensus size: 59
20966 ACAGCCATAA
20976 AAAAGTTATAGTTATTTGCTGTAGGACATTAAGGGAATAATTGTCTAATTTCTCACGG-
1 AAAAGTTATAGTTATTTGCTGTAGGACATTAAGGGAATAATTGTCTAATTTCTCACGGC
*
21034 AAAAGTTATAGTTATTTGCTGTAGGACATTAAGGGAATAATTGTCTAATTTCTCATGGC
1 AAAAGTTATAGTTATTTGCTGTAGGACATTAAGGGAATAATTGTCTAATTTCTCACGGC
21093 AAAAGT
1 AAAAGT
21099 AGCAGAACAA
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 57 0.90
59 6 0.10
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (59 bp):
AAAAGTTATAGTTATTTGCTGTAGGACATTAAGGGAATAATTGTCTAATTTCTCACGGC
Found at i:23091 original size:23 final size:23
Alignment explanation
Indices: 23043--23117 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
23033 GTGTTATATT
* * *
23043 ATATTTTAAA-ATATTAAATAAT
1 ATATTTTAAATATATTTATTAAA
23065 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
* *
23088 ATATTATTAGATTATATATATTAAA
1 ATATT-TTA-AATATATTTATTAAA
23113 TATAT
1 -ATAT
23118 AAATAATATT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
22 10 0.23
23 14 0.32
24 3 0.07
25 13 0.30
26 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:23128 original size:27 final size:27
Alignment explanation
Indices: 23098--23180 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
23088 ATATTATTAG
23098 ATTATATATATTAAATATA-TAAATAAT
1 ATTAT-TATATTAAATATAGTAAATAAT
* *
23125 ATTATTCATTATT-AATA-ATTTAATAAT
1 ATTATT-A-TATTAAATATAGTAAATAAT
*
23152 ATTATTTATATGAAAT-TAGTAAATAAT
1 ATTA-TTATATTAAATATAGTAAATAAT
23179 AT
1 AT
23181 AAATTTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
26 5 0.11
27 35 0.76
28 6 0.13
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (27 bp):
ATTATTATATTAAATATAGTAAATAAT
Found at i:23175 original size:54 final size:54
Alignment explanation
Indices: 23098--23211 Score: 144
Period size: 54 Copynumber: 2.1 Consensus size: 54
23088 ATATTATTAG
* * *
23098 ATTATATATATTAAATATATAAATAATAT-TATTCATTATTAATAATTTAATA-AT
1 ATTATTTATATGAAATATATAAATAATATAAATT--TTATTAATAATTTAATATAT
*
23152 ATTATTTATATGAAAT-TAGTAAATAATATAAATTTTATTAATAATTTATTATAT
1 ATTATTTATATGAAATATA-TAAATAATATAAATTTTATTAATAATTTAATATAT
23206 ATTATT
1 ATTATT
23212 AAAATAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
53 18 0.34
54 32 0.60
55 3 0.06
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (54 bp):
ATTATTTATATGAAATATATAAATAATATAAATTTTATTAATAATTTAATATAT
Found at i:25754 original size:5 final size:5
Alignment explanation
Indices: 25744--25769 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
25734 ACCCAAAGCT
25744 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
25770 GCTTATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:30377 original size:35 final size:34
Alignment explanation
Indices: 30292--30378 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 34
30282 AATATAATTT
*
30292 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
*
30326 TAAATGATAA-ACAAATTACAATAATTGATATTAAATGG
1 TAAAT-ACAACA-AAATTACAATAA--G-TATTAAATGG
30364 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
30379 ACCAAAATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
34 6 0.13
35 22 0.49
36 2 0.04
37 4 0.09
38 11 0.24
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:30419 original size:34 final size:34
Alignment explanation
Indices: 30373--30447 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 34
30363 GTAATAAACA
* *
30373 AAATTAACCAAAATACATTAACAA-AAAGTCCAA-C
1 AAATTAACCAAAAAAAATTAA-AATAAA-TCCAATC
30407 AAATGTAA-CAAAAAAAATTAAAATAAATCCAATC
1 AAAT-TAACCAAAAAAAATTAAAATAAATCCAATC
30441 AAATTAA
1 AAATTAA
30448 TGAAATAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
33 10 0.28
34 23 0.64
35 3 0.08
ACGTcount: A:0.63, C:0.15, G:0.03, T:0.20
Consensus pattern (34 bp):
AAATTAACCAAAAAAAATTAAAATAAATCCAATC
Found at i:30980 original size:33 final size:33
Alignment explanation
Indices: 30922--30984 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
30912 TCCTCCAGGA
**
30922 GGGGTCATAAAACTCTATGACGGTGGCGGCGGC
1 GGGGTCATAAAACTAGATGACGGTGGCGGCGGC
* *
30955 GGGGTCATAAAACTAGGTGATGGTGGCGGC
1 GGGGTCATAAAACTAGATGACGGTGGCGGC
30985 AGTAGCATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.22, C:0.17, G:0.41, T:0.19
Consensus pattern (33 bp):
GGGGTCATAAAACTAGATGACGGTGGCGGCGGC
Found at i:32755 original size:17 final size:19
Alignment explanation
Indices: 32735--32776 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
32725 ATTAATTAAA
32735 TAAAATA-TTAAA-AAATT
1 TAAAATACTTAAATAAATT
32752 T-AAATACTTAAATAAATT
1 TAAAATACTTAAATAAATT
*
32770 AAAAATA
1 TAAAATA
32777 AAATATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 6 0.29
18 5 0.24
19 5 0.24
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATACTTAAATAAATT
Found at i:32764 original size:24 final size:23
Alignment explanation
Indices: 32737--32797 Score: 56
Period size: 24 Copynumber: 2.6 Consensus size: 23
32727 TAATTAAATA
*
32737 AAATATTAAAAAATTTAAATACTT
1 AAATATTAAAAAATTAAAATA-TT
32761 AAATAAATT-AAAAA-TAAAATATT
1 AAAT--ATTAAAAAATTAAAATATT
32784 AAATA-TAATAAAAT
1 AAATATTAA-AAAAT
32798 ATACCTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
20 1 0.03
21 2 0.06
22 4 0.13
23 6 0.19
24 10 0.32
25 5 0.16
26 3 0.10
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATATTAAAAAATTAAAATATT
Found at i:36204 original size:15 final size:15
Alignment explanation
Indices: 36184--36221 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
36174 AGGTAGGGGT
36184 GAATAAACTCGTCTC
1 GAATAAACTCGTCTC
36199 GAATAAACTCGTCTC
1 GAATAAACTCGTCTC
*
36214 GAAAAAAC
1 GAATAAAC
36222 CGTACTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.42, C:0.24, G:0.13, T:0.21
Consensus pattern (15 bp):
GAATAAACTCGTCTC
Found at i:39679 original size:51 final size:51
Alignment explanation
Indices: 39455--39976 Score: 487
Period size: 51 Copynumber: 9.8 Consensus size: 51
39445 ACGAGTCTGT
* *
39455 TCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATA-AAA-TGTGTCTGC
1 TCCCTATTCCTTCAGAG-AGTATAGGACT----CAATCTTCA-ACAAACT-TGTCCGC
* * * * **
39510 TCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAACAGGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGAC-T---CAATCTTCAA-CAAACTTGTCCGC
* * * * * *
39566 TCTCTACTCCTTCAGAGAGTATAGAACTCAGAAAATCTTCAATAAACATGCCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACAAACTTGTCCGC
* * * * *
39621 TCTCTATTCTTTCAGAGAGTATAGGACTCAATCTTTAACAAACGTGTTCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
* ** *
39672 TCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATC-TCATA-AAACGGGTCCAC
1 TCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCA-ACAAACTTGTCCGC
* * *
39726 TCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAACTTGTCCGC
* *
39781 TCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACGAACTTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
* *
39832 TCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
*
39883 TCCCTATTCCTTCAGAGAATATAGGACTCAATCTTCAACAAACTTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
* *
39934 TCCCTATTCTTTCAGAGAGTATAGGACTCAGTCTTCAACAAAC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAAC
39977 GAATTTGCTT
Statistics
Matches: 407, Mismatches: 44, Indels: 36
0.84 0.09 0.07
Matches are distributed among these distances:
51 202 0.50
52 1 0.00
54 48 0.12
55 114 0.28
56 42 0.10
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (51 bp):
TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
Found at i:39739 original size:160 final size:158
Alignment explanation
Indices: 39487--39977 Score: 595
Period size: 160 Copynumber: 3.1 Consensus size: 158
39477 AAGACTCGAA
* * *
39487 CAATCTTCATA-AAATGTGTCTGCTCTCTATTCATTCAGAGAGTATA-AGACTTGAACAATCTTC
1 CAATCTTCA-ACAAACGTGTCCGCTCCCTATTCATTCAGAGAGTATAGA-AC-TG-ACAATCTTC
* * *
39550 AATAAAACAGGTCCGCTCTCTACTCCTTCAGAGAGTATAGAACTCAGAAAATCTTCAATAAACAT
62 -ATAAAACAGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTC-GAAAATCTTCAACAAACTT
* *
39615 GCCCGCTCTCTATTCTTTCAGAGAGTATAGGACT
125 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACT
* * *
39649 CAATCTTTAACAAACGTGTTCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATC-TCAT
1 CAATCTTCAACAAACGTGTCCGCTCCCTATTCATTCAGAGAGTATAGAACT-GA-CAATCTTCAT
* * *
39713 AAAACGGGTCCACTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTC
64 AAAACAGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAA-AATCTTCAACAAACTTGTC
* *
39778 CGCTCCCTATTCCTTCAGAGAGTATAAGACT
128 CGCTCCCTATTCTTTCAGAGAGTATAGGACT
* * *
39809 CAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT--CAATCTTCA-AC
1 CAATCTTCAACAAACGTGTCCGCTCCCTATTCATTCAGAGAGTATAGAACTGACAATCTTCATA-
* ** * * *
39871 GAACTTGTCCGCTCCCTATTCCTTCAGAGAATATAGGACTC---AATCTTCAACAAACTTGTCCG
65 AAACAGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAATCTTCAACAAACTTGTCCG
39933 CTCCCTATTCTTTCAGAGAGTATAGGACT
130 CTCCCTATTCTTTCAGAGAGTATAGGACT
*
39962 CAGTCTTCAACAAACG
1 CAATCTTCAACAAACG
39978 AATTTGCTTC
Statistics
Matches: 287, Mismatches: 35, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
153 60 0.21
156 6 0.02
157 37 0.13
159 3 0.01
160 129 0.45
161 5 0.02
162 46 0.16
163 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (158 bp):
CAATCTTCAACAAACGTGTCCGCTCCCTATTCATTCAGAGAGTATAGAACTGACAATCTTCATAA
AACAGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAATCTTCAACAAACTTGTCCGC
TCCCTATTCTTTCAGAGAGTATAGGACT
Found at i:41315 original size:16 final size:16
Alignment explanation
Indices: 41290--41395 Score: 64
Period size: 16 Copynumber: 6.7 Consensus size: 16
41280 TGAACCCTCC
41290 TTTT-ATTTTTCTCTT
1 TTTTCATTTTTCTCTT
41305 TTTTCATTTTTCTC-T
1 TTTTCATTTTTCTCTT
*
41320 TTTT-GTTTTTCTC--
1 TTTTCATTTTTCTCTT
*
41333 -TTTCATTTTTCTTCCAT
1 TTTTCATTTTTC-T-CTT
*
41350 TTTCCATTTTTTTCTCTT
1 TTTTCA--TTTTTCTCTT
*
41368 TTTTCCTCTTTT-TCTT
1 TTTTCAT-TTTTCTCTT
*
41384 CTTCTCATTTTT
1 -TTTTCATTTTT
41396 ATTATTATTT
Statistics
Matches: 72, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
12 3 0.04
13 6 0.08
14 9 0.12
15 10 0.14
16 18 0.25
17 9 0.12
18 10 0.14
19 1 0.01
20 6 0.08
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.73
Consensus pattern (16 bp):
TTTTCATTTTTCTCTT
Found at i:41341 original size:13 final size:14
Alignment explanation
Indices: 41289--41344 Score: 62
Period size: 14 Copynumber: 4.0 Consensus size: 14
41279 TTGAACCCTC
41289 CTTTT-ATTTTTCT
1 CTTTTCATTTTTCT
41302 CTTTTTTCATTTTTCT
1 C--TTTTCATTTTTCT
**
41318 CTTTTTGTTTTTCT
1 CTTTTCATTTTTCT
41332 C-TTTCATTTTTCT
1 CTTTTCATTTTTCT
41345 TCCATTTTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 11 0.31
14 12 0.33
15 4 0.11
16 9 0.25
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (14 bp):
CTTTTCATTTTTCT
Found at i:41369 original size:10 final size:10
Alignment explanation
Indices: 41356--41436 Score: 51
Period size: 10 Copynumber: 7.6 Consensus size: 10
41346 CCATTTTCCA
41356 TTTTTTTCTC
1 TTTTTTTCTC
*
41366 TTTTTTCCTC
1 TTTTTTTCTC
41376 TTTTTCTTCTTC
1 TTTTT-TTC-TC
*
41388 TCATTTTTAT-TA
1 T--TTTTT-TCTC
41400 TTATTTTT-TC
1 TT-TTTTTCTC
41410 ATTTTTTT-TC
1 -TTTTTTTCTC
41420 ATTTTTTTCTC
1 -TTTTTTTCTC
41431 TTTTTT
1 TTTTTT
41437 CTTCTTCAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
10 38 0.64
11 10 0.17
12 5 0.08
13 1 0.02
14 5 0.08
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:41434 original size:16 final size:16
Alignment explanation
Indices: 41289--41369 Score: 59
Period size: 14 Copynumber: 5.3 Consensus size: 16
41279 TTGAACCCTC
*
41289 CTTTT-ATTTTTCTCT
1 CTTTTCATTTTTTTCT
*
41304 TTTTTCA--TTTTTCT
1 CTTTTCATTTTTTTCT
*
41318 CTTTT--TGTTTTTCT
1 CTTTTCATTTTTTTCT
41332 C-TTTCATTTTTCTTC-
1 CTTTTCATTTTT-TTCT
41347 CATTTTCCATTTTTTTCT
1 C-TTTT-CATTTTTTTCT
41365 CTTTT
1 CTTTT
41370 TTCCTCTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
13 3 0.06
14 18 0.35
15 9 0.17
16 4 0.08
17 10 0.19
18 8 0.15
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.73
Consensus pattern (16 bp):
CTTTTCATTTTTTTCT
Found at i:41438 original size:9 final size:9
Alignment explanation
Indices: 41303--41437 Score: 54
Period size: 9 Copynumber: 14.8 Consensus size: 9
41293 TATTTTTCTC
41303 TTTTTTCAT
1 TTTTTTCAT
*
41312 TTTTCTC-T
1 TTTTTTCAT
41320 TTTTGTT--T
1 TTTT-TTCAT
41328 TTCTCTTTCAT
1 TT-T-TTTCAT
41339 TTTTCTTCCA-
1 TTTT-TT-CAT
*
41349 -TTTTCCAT
1 TTTTTTCAT
41357 TTTTTTC-T
1 TTTTTTCAT
*
41365 CTTTTTTCCT
1 -TTTTTTCAT
*
41375 CTTTTTC-T
1 TTTTTTCAT
* *
41383 TCTTCTCAT
1 TTTTTTCAT
41392 TTTTATT-ATT
1 TTTT-TTCA-T
41402 ATTTTTTCATT
1 -TTTTTTCA-T
41413 TTTTTTCAT
1 TTTTTTCAT
41422 TTTTTTC-T
1 TTTTTTCAT
41430 CTTTTTTC
1 -TTTTTTC
41438 TTCTTCAAGC
Statistics
Matches: 99, Mismatches: 10, Indels: 34
0.69 0.07 0.24
Matches are distributed among these distances:
7 2 0.02
8 16 0.16
9 52 0.53
10 17 0.17
11 12 0.12
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.73
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:56107 original size:16 final size:16
Alignment explanation
Indices: 56069--56110 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
56059 TAATTTCGGT
56069 GAAGGA-AAAAAAGAA
1 GAAGGAGAAAAAAGAA
*
56084 AAATGGAGAAAAAAGAA
1 GAA-GGAGAAAAAAGAA
56101 GAAGGAGAAA
1 GAAGGAGAAA
56111 GTGAGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 10 0.43
17 11 0.48
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (16 bp):
GAAGGAGAAAAAAGAA
Found at i:61079 original size:40 final size:40
Alignment explanation
Indices: 61035--61114 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
61025 ATGGCACAAG
* *
61035 TGTGTAGGTGTAAGGTGGGAAGCCTTCCTCTT-ACTTACCT
1 TGTGTAGGTGTAAGCTGGGAAGCCTCCCT-TTCACTTACCT
*
61075 TGTGTGGGTGTAAGCTGGGAAGCCTCCCTTTCACTTACCT
1 TGTGTAGGTGTAAGCTGGGAAGCCTCCCTTTCACTTACCT
61115 AGGTATCCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 2 0.06
40 34 0.94
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.34
Consensus pattern (40 bp):
TGTGTAGGTGTAAGCTGGGAAGCCTCCCTTTCACTTACCT
Found at i:63454 original size:48 final size:48
Alignment explanation
Indices: 63383--63482 Score: 155
Period size: 48 Copynumber: 2.1 Consensus size: 48
63373 CATTATTAGA
* * *
63383 GTCACTACGAGCAGGACTATGGGGTTGACTGTGGGGCTGAGTAGTTGG
1 GTCACTACGAGCAGGACTATGGGGCTGACTGTGGGGATGAGCAGTTGG
* *
63431 GTCACTATGAGCAGGACTATGGGGCTGACTGTGTGGATGAGCAGTTGG
1 GTCACTACGAGCAGGACTATGGGGCTGACTGTGGGGATGAGCAGTTGG
63479 GTCA
1 GTCA
63483 ATACTGTTGT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.20, C:0.15, G:0.40, T:0.25
Consensus pattern (48 bp):
GTCACTACGAGCAGGACTATGGGGCTGACTGTGGGGATGAGCAGTTGG
Found at i:77153 original size:39 final size:39
Alignment explanation
Indices: 77109--77186 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
77099 TCCGACATTC
77109 ACTTGTGTTTTGAATACATTCGTAGGTTCCGAATGTAGT
1 ACTTGTGTTTTGAATACATTCGTAGGTTCCGAATGTAGT
77148 ACTTGTGTTTTGAATACATTCGTAGGTTCCGAATGTAGT
1 ACTTGTGTTTTGAATACATTCGTAGGTTCCGAATGTAGT
77187 GGGATGTATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.41
Consensus pattern (39 bp):
ACTTGTGTTTTGAATACATTCGTAGGTTCCGAATGTAGT
Found at i:80033 original size:7 final size:7
Alignment explanation
Indices: 80021--80079 Score: 68
Period size: 7 Copynumber: 8.4 Consensus size: 7
80011 TATTTAGTAC
80021 ATATATA
1 ATATATA
80028 ATATATA
1 ATATATA
80035 ATATATA
1 ATATATA
80042 ATATATA
1 ATATATA
*
80049 ATAAATTA
1 ATATA-TA
80057 ATA-A-A
1 ATATATA
*
80062 ATAAATA
1 ATATATA
80069 ATAATATA
1 AT-ATATA
80077 ATA
1 ATA
80080 CTTATATTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
5 4 0.09
6 1 0.02
7 30 0.65
8 11 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
ATATATA
Done.