Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002828.1 Hibiscus syriacus cultivar Beakdansim tig00005817_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: 59359
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Found at i:514 original size:3 final size:3
Alignment explanation
Indices: 501--548 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
491 TCTACAAAAA
* * * *
501 TAT TA- TAT TAT TAT TAT TAT CAT TAT TAT CAT TAA TAT TAT TAG TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
548 T
1 T
549 TTTTACATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:794 original size:21 final size:22
Alignment explanation
Indices: 768--810 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
758 CCCGTGAGCT
*
768 GCCGCCG-TTGCTTCCCAAGCC
1 GCCGCCGAGTGCTTCCCAAGCC
*
789 GCCGCCGAGTGCTTCCCGAGCC
1 GCCGCCGAGTGCTTCCCAAGCC
811 AATCAGAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.09, C:0.47, G:0.28, T:0.16
Consensus pattern (22 bp):
GCCGCCGAGTGCTTCCCAAGCC
Found at i:1990 original size:29 final size:29
Alignment explanation
Indices: 1957--2033 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 29
1947 CATATTACTG
*
1957 TTTAGTCCCTTATGTTTCTGTTTTGATAT
1 TTTAGTCCCTTATGTTTATGTTTTGATAT
* * * *
1986 TTTAGTCCTTTAAATGTCTATTTTTTGTTAT
1 TTTAGTCCCTT--ATGTTTATGTTTTGATAT
*
2017 TTTAGTCCCTTAAGTTT
1 TTTAGTCCCTTATGTTT
2034 TTATTTTTAC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
29 14 0.37
31 24 0.63
ACGTcount: A:0.17, C:0.13, G:0.12, T:0.58
Consensus pattern (29 bp):
TTTAGTCCCTTATGTTTATGTTTTGATAT
Found at i:2028 original size:60 final size:59
Alignment explanation
Indices: 1957--2181 Score: 170
Period size: 60 Copynumber: 3.8 Consensus size: 59
1947 CATATTACTG
* * *
1957 TTTAGTCCCTTATGTTTCTGTTTTGATATTTTAGTCCTTTAAATGTCTATTTTTTGTTAT
1 TTTAGTCCCTTAAGTTTCTGTTTTGATATTTTAATCCTTTAAATGTCTATTTTTT-ATAT
* * * * * * * *
2017 TTTAGTCCCTTAAGTTTTTATTTTTACTA-TTTAACCCTTTAAGTTTCAATATTTTATAT
1 TTTAGTCCCTTAAGTTTCTGTTTTGA-TATTTTAATCCTTTAAATGTCTATTTTTTATAT
* * * *
2076 TTTAGTCCTTTAACTTTCTATTTTTTATATTTTAATCCTTTAAAT-T-TATGTTTTTACTAT
1 TTTAGTCCCTTAAGTTTCT-GTTTTGATATTTTAATCCTTTAAATGTCTAT-TTTTTA-TAT
* * ** * *
2136 TTTAG-CCTCTCAAGATTCTGTTAAGCATATTTTAGTCCCTTAAATG
1 TTTAGTCC-CTTAAGTTTCTGTTTTG-ATATTTTAATCCTTTAAATG
2182 ATTAGTTTTG
Statistics
Matches: 128, Mismatches: 29, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
58 2 0.02
59 31 0.24
60 93 0.73
61 2 0.02
ACGTcount: A:0.23, C:0.14, G:0.08, T:0.56
Consensus pattern (59 bp):
TTTAGTCCCTTAAGTTTCTGTTTTGATATTTTAATCCTTTAAATGTCTATTTTTTATAT
Found at i:2048 original size:30 final size:29
Alignment explanation
Indices: 1957--2140 Score: 138
Period size: 30 Copynumber: 6.2 Consensus size: 29
1947 CATATTACTG
* * *
1957 TTTAGTCCCTTATGTTTCTGTTTTGATAT
1 TTTAGTCCCTTAAGTTTCTATTTTTATAT
* * * *
1986 TTTAGTCCTTTAAATGTCTATTTTTTGTTAT
1 TTTAGTCCCTTAAGTTTCTA-TTTTT-ATAT
*
2017 TTTAGTCCCTTAAGTTTTTATTTTTACTA-
1 TTTAGTCCCTTAAGTTTCTATTTTTA-TAT
* *
2046 TTTA-ACCCTTTAAGTTTCAATATTTTATAT
1 TTTAGTCCC-TTAAGTTTCTAT-TTTTATAT
* *
2076 TTTAGTCCTTTAACTTTCTATTTTTTATAT
1 TTTAGTCCCTTAAGTTTCTA-TTTTTATAT
* * * * *
2106 TTTAATCCTTTAAATTTATGTTTTTACTAT
1 TTTAGTCCCTTAAGTTTCTATTTTTA-TAT
2136 TTTAG
1 TTTAG
2141 CCTCTCAAGA
Statistics
Matches: 122, Mismatches: 24, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
28 3 0.02
29 37 0.30
30 60 0.49
31 22 0.18
ACGTcount: A:0.22, C:0.12, G:0.07, T:0.59
Consensus pattern (29 bp):
TTTAGTCCCTTAAGTTTCTATTTTTATAT
Found at i:5916 original size:14 final size:14
Alignment explanation
Indices: 5899--5936 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
5889 GAGAAAATCA
*
5899 AAGAAGAAAAAAAT
1 AAGAAGAAAAAAAC
5913 AAGAA-AAAAAAAC
1 AAGAAGAAAAAAAC
5926 AA-AAGAAAAAA
1 AAGAAGAAAAAA
5937 GAGAGGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 2 0.09
13 15 0.68
14 5 0.23
ACGTcount: A:0.84, C:0.03, G:0.11, T:0.03
Consensus pattern (14 bp):
AAGAAGAAAAAAAC
Found at i:5923 original size:15 final size:15
Alignment explanation
Indices: 5898--5936 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
5888 AGAGAAAATC
*
5898 AAAGAAGAAAAAA-A
1 AAAGAAAAAAAAACA
*
5912 TAAGAAAAAAAAACA
1 AAAGAAAAAAAAACA
5927 AAAGAAAAAA
1 AAAGAAAAAA
5937 GAGAGGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (15 bp):
AAAGAAAAAAAAACA
Found at i:5945 original size:12 final size:12
Alignment explanation
Indices: 5930--5955 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5920 AAAAACAAAA
5930 GAAAAAAGAGAG
1 GAAAAAAGAGAG
5942 GAAAAAAGAGAG
1 GAAAAAAGAGAG
5954 GA
1 GA
5956 CAAGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (12 bp):
GAAAAAAGAGAG
Found at i:7023 original size:32 final size:32
Alignment explanation
Indices: 6967--7029 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
6957 AGAAATAATA
6967 AATGATGGGACATCTTTGGAGATTCAACATCG
1 AATGATGGGACATCTTTGGAGATTCAACATCG
* * *
6999 AATGTTGGGGCATCTTTGGGGATTCAACATC
1 AATGATGGGACATCTTTGGAGATTCAACATC
7030 TTGATGTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (32 bp):
AATGATGGGACATCTTTGGAGATTCAACATCG
Found at i:7179 original size:66 final size:66
Alignment explanation
Indices: 7099--7416 Score: 291
Period size: 66 Copynumber: 4.9 Consensus size: 66
7089 TATCAGTATC
* * *
7099 CTTTGATGT-TGTTTCTCTTGAAACAAAATTTTGTTTCTTTTGAGACGGTTTCTTTCGAAGAAAA
1 CTTTGA-GTCTGTTTCTCTTGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGAAAA
7163 AT
65 AT
* * * * * *
7165 CTTTGAGTATGTTTCTCTGGAAATAAAATTTTGTCTCTTTTCATATAGTTTCTTTTGAAGAAAAA
1 CTTTGAGTCTGTTTCTCTTGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAG--AAA
*
7230 AAC
64 AAT
* * *
7233 CTTTGAGTCTCTTTCT-TTGGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAAGGAAA
1 CTTTGAGTCTGTTTCTCTT-GAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGAAAA
7297 AT
65 AT
* * * **
7299 CTTTGAGTCTGTTTCTCCTGAAACAAAA----G--TC-TTTGAGTCTGTTTCTCATGAA-ACAAA
1 CTTTGAGTCTGTTTCTCTTGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGA-AAA
7356 CAT
65 -AT
* ** *
7359 CTTTGAGAT-TGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACATTTTCTTTTGAA
1 CTTTGAG-TCTGTTTCTCTTGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAA
7417 ACATCATCTT
Statistics
Matches: 202, Mismatches: 35, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
59 22 0.11
60 24 0.12
61 1 0.00
62 1 0.00
63 1 0.00
65 4 0.02
66 92 0.46
67 2 0.01
68 55 0.27
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (66 bp):
CTTTGAGTCTGTTTCTCTTGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGAAAAA
T
Found at i:7334 original size:30 final size:29
Alignment explanation
Indices: 7294--7385 Score: 125
Period size: 30 Copynumber: 3.1 Consensus size: 29
7284 CTTTTGAAGG
7294 AAAATCTTTGAGTCTGTTTCTCCTGAAAC
1 AAAATCTTTGAGTCTGTTTCTCCTGAAAC
*
7323 AAAAGTCTTTGAGTCTGTTTCTCATGAAAC
1 AAAA-TCTTTGAGTCTGTTTCTCCTGAAAC
7353 AAACATCTTTGAGAT-TGTTTC-CCTTGAAAC
1 AAA-ATCTTTGAG-TCTGTTTCTCC-TGAAAC
7383 AAA
1 AAA
7386 TTTTGTCTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
29 5 0.09
30 50 0.88
31 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (29 bp):
AAAATCTTTGAGTCTGTTTCTCCTGAAAC
Found at i:7622 original size:91 final size:91
Alignment explanation
Indices: 7449--7684 Score: 273
Period size: 91 Copynumber: 2.6 Consensus size: 91
7439 CCTTAAAACC
* * *
7449 ATTATCCCTAAAGATAGCCTACCGTCCTCATCAAGTAGGAACCGTGTCACCACTAGATAACCAGC
1 ATTATCCCTAAAGATAGCCTATCGTCCTCATCACGTAGGAACCGTGTCACCACTAGATAACCAGA
* *
7514 CTTCCTAATCACGTAGGAACCATGTT
66 CTTCATAATCACATAGGAACCATGTT
* * *
7540 ATTATCCCTAAAGATAGCCTGATC-TCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAATCA-
1 ATTATCCCTAAAGATAGCCT-ATCGTCCTCATCACGTAGGAACCGTGTCACCACTAGATAACCAG
* * *
7603 ACTATCATTATCTCATAGGAACCGTGTT
65 ACT-TCATAATCACATAGGAACCATGTT
* * *
7631 ATCT-TCCCTAATA-ATGGTCTATCGTCCTCATCGCGTAGGAACCGTGTCATCCAC
1 AT-TATCCCTAA-AGATAGCCTATCGTCCTCATCACGTAGGAACCGTGTCA-CCAC
7685 CTACTAGACC
Statistics
Matches: 123, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
90 5 0.04
91 111 0.90
92 7 0.06
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (91 bp):
ATTATCCCTAAAGATAGCCTATCGTCCTCATCACGTAGGAACCGTGTCACCACTAGATAACCAGA
CTTCATAATCACATAGGAACCATGTT
Found at i:8072 original size:3 final size:3
Alignment explanation
Indices: 8054--8115 Score: 83
Period size: 3 Copynumber: 21.3 Consensus size: 3
8044 TATACACAAA
*
8054 TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
8100 TAA TAT TAT TAG TAT T
1 TAT TAT TAT TAT TAT T
8116 TTGTGCAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
2 4 0.08
3 47 0.92
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:10061 original size:20 final size:21
Alignment explanation
Indices: 10023--10061 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
10013 TAATGGCTTA
*
10023 GTGGATTTAGTTTGGTTTTGG
1 GTGGATTTAGTTTAGTTTTGG
*
10044 GTGGATTT-GTTTATTTTT
1 GTGGATTTAGTTTAGTTTT
10062 TAATGGATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.10, C:0.00, G:0.31, T:0.59
Consensus pattern (21 bp):
GTGGATTTAGTTTAGTTTTGG
Found at i:10487 original size:110 final size:111
Alignment explanation
Indices: 10322--10628 Score: 474
Period size: 111 Copynumber: 2.8 Consensus size: 111
10312 TGTTCCATTG
* * * *
10322 CACTCATGGAATATCAAATCTTGAAAGAGAGGGATATGTTCCGCTTTTTCTAAGGGAATATCATA
1 CACTCAGGGAATATCAAATCTTGGAAGAGAGGGATATGTTCCGCTTCTTCTAAGGGAATATCAGA
* *
10387 TATGGGAAAGTTGATCCATTGAAT-TGGGTAGACTTATTCCGCTGT
66 TCTGGGAAAGTTGATCCATTGAATCAGGGTAGACTTATTCCGCTGT
**
10432 CACTCAGGGAATATCAAATCTTGGAAGAGAGGGATATGTTTTGCTTCTTCTAAGGGAATATCAGA
1 CACTCAGGGAATATCAAATCTTGGAAGAGAGGGATATGTTCCGCTTCTTCTAAGGGAATATCAGA
* *
10497 TCTTGGAAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGT
66 TCTGGGAAAGTTGATCCATTGAATCAGGGTAGACTTATTCCGCTGT
* * *
10543 CACTCAGGGAATATCAAATCTTAGAAGAGAGGGATTTGTTCCGCTTCTT-TGAAAGGAATATCAG
1 CACTCAGGGAATATCAAATCTTGGAAGAGAGGGATATGTTCCGCTTCTTCT-AAGGGAATATCAG
10607 ATCTGGGAAAGTTGATCCATTG
65 ATCTGGGAAAGTTGATCCATTG
10629 GGATCGAACC
Statistics
Matches: 179, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
110 82 0.46
111 97 0.54
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (111 bp):
CACTCAGGGAATATCAAATCTTGGAAGAGAGGGATATGTTCCGCTTCTTCTAAGGGAATATCAGA
TCTGGGAAAGTTGATCCATTGAATCAGGGTAGACTTATTCCGCTGT
Found at i:15348 original size:4 final size:4
Alignment explanation
Indices: 15315--15363 Score: 55
Period size: 4 Copynumber: 11.5 Consensus size: 4
15305 TCCCAAATCA
15315 AAAT ATAAT GAAAT -AAT AATAT ATAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT A-AAT -AAAT AAAT AA-AT A-AAT AAAT AAAT AAAT AAAT AAAT
15362 AA
1 AA
15364 TGAAAGGGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
3 3 0.08
4 23 0.57
5 12 0.30
6 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:15360 original size:16 final size:17
Alignment explanation
Indices: 15315--15363 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
15305 TCCCAAATCA
15315 AAATATAATGAAAT-AAT
1 AAATATAAT-AAATAAAT
15332 AATATATAATAAATAAAT
1 AA-ATATAATAAATAAAT
15350 AAATA-AATAAATAA
1 AAATATAATAAATAA
15364 TGAAAGGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.30
17 9 0.30
18 12 0.40
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
AAATATAATAAATAAAT
Found at i:22205 original size:17 final size:18
Alignment explanation
Indices: 22168--22208 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
22158 CTATTATGTA
*
22168 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
22186 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
22203 TTTACT
1 TTTACT
22209 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:22472 original size:111 final size:111
Alignment explanation
Indices: 22278--22602 Score: 596
Period size: 111 Copynumber: 2.9 Consensus size: 111
22268 ATATATCTCT
* *
22278 ACACTTTGCTGATATGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATATTTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
* *
22343 TGACTTATTTAATGCATGATTATTAGATTAAGAATTAAGTATATCG
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATATCG
22389 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
*
22454 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATATCG
22500 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
*
22565 TGATTTATTTAATGCATGACTATTAGATTAAGAATTAA
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
22603 TTTTTGTAAT
Statistics
Matches: 208, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 208 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (111 bp):
ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATATCG
Found at i:28309 original size:51 final size:51
Alignment explanation
Indices: 28239--28368 Score: 156
Period size: 51 Copynumber: 2.5 Consensus size: 51
28229 CCCGTACGTG
* * *
28239 GCATATAGCGC-GAAGCAGGGGGCGCGCTATACCCCACGT-GTAACCCAGTCA
1 GCATATAGCGCAGTA-CAGGGGGCGCGCTATACCCCACGTGGT-ACCAAATCA
* * *
28290 GCGTATAGCGCAGTACAGGGGGCGCGCTATACTCCACGTGGTGCCAAATCA
1 GCATATAGCGCAGTACAGGGGGCGCGCTATACCCCACGTGGTACCAAATCA
* *
28341 GCATATAGCGCGGTTCAGGGGGCGCGCT
1 GCATATAGCGCAGTACAGGGGGCGCGCT
28369 TTACTGCTAC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
51 64 0.94
52 4 0.06
ACGTcount: A:0.22, C:0.28, G:0.33, T:0.16
Consensus pattern (51 bp):
GCATATAGCGCAGTACAGGGGGCGCGCTATACCCCACGTGGTACCAAATCA
Found at i:33229 original size:2 final size:2
Alignment explanation
Indices: 33222--33321 Score: 200
Period size: 2 Copynumber: 50.0 Consensus size: 2
33212 TTTTCATTTC
33222 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
33264 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
33306 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
33322 TTAAAAAAAA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 98 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39158 original size:18 final size:18
Alignment explanation
Indices: 39137--39171 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39127 GGGGGATCGC
*
39137 AACAAGCCAAGGGACCGT
1 AACAAGCCAAGGCACCGT
39155 AACAAGCCAAGGCACCG
1 AACAAGCCAAGGCACCG
39172 GGAAGGAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.31, G:0.26, T:0.03
Consensus pattern (18 bp):
AACAAGCCAAGGCACCGT
Found at i:54607 original size:19 final size:19
Alignment explanation
Indices: 54583--54654 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
54573 ATTTCCCAAT
*
54583 TCGCAATGCGAATAAGTAA
1 TCGCAACGCGAATAAGTAA
** *
54602 TCGCAACGCGAATTGGGAAA
1 TCGCAACGCGAA-TAAGTAA
*
54622 TTCGCAATGCGAATAAGTAA
1 -TCGCAACGCGAATAAGTAA
54642 TCGCAACGCGAAT
1 TCGCAACGCGAAT
54655 TGGGAAAATC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
19 23 0.55
20 8 0.19
21 11 0.26
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (19 bp):
TCGCAACGCGAATAAGTAA
Found at i:54624 original size:40 final size:40
Alignment explanation
Indices: 54580--54673 Score: 179
Period size: 40 Copynumber: 2.4 Consensus size: 40
54570 GCGATTTCCC
54580 AATTCGCAATGCGAATAAGTAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAATCGCAACGCGAATTGGGA
54620 AATTCGCAATGCGAATAAGTAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAATCGCAACGCGAATTGGGA
*
54660 AAATCGCAATGCGA
1 AATTCGCAATGCGA
54674 TACTGACTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.19
Consensus pattern (40 bp):
AATTCGCAATGCGAATAAGTAATCGCAACGCGAATTGGGA
Found at i:54628 original size:21 final size:20
Alignment explanation
Indices: 54600--54673 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
54590 GCGAATAAGT
54600 AATCGCAACGCGAATTGGGA
1 AATCGCAACGCGAATTGGGA
* ** *
54620 AATTCGCAATGCGAA-TAAGT
1 AA-TCGCAACGCGAATTGGGA
54640 AATCGCAACGCGAATTGGGAA
1 AATCGCAACGCGAATTGGG-A
*
54661 AATCGCAATGCGA
1 AATCGCAACGCGA
54674 TACTGACTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 11 0.26
20 8 0.19
21 23 0.55
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATTGGGA
Found at i:54687 original size:20 final size:20
Alignment explanation
Indices: 54662--54757 Score: 84
Period size: 20 Copynumber: 4.7 Consensus size: 20
54652 AATTGGGAAA
*
54662 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
54682 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
54703 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
54723 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
54743 TTCCGCAACGCGATA
1 AT-CGCAACGCGATA
54758 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
20 35 0.57
21 26 0.43
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:54704 original size:41 final size:41
Alignment explanation
Indices: 54659--54736 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
54649 GCGAATTGGG
* * *
54659 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
54700 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
54737 CTGACTTTCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:54770 original size:21 final size:19
Alignment explanation
Indices: 54662--54777 Score: 61
Period size: 21 Copynumber: 5.7 Consensus size: 19
54652 AATTGGGAAA
* *
54662 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAAT-ACT
* **
54682 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATAAT--ACT
* *
54703 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATA-ATACT
* *
54723 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATAAT-ACT
*
54743 TTCCGCAACGCGATAATACAT
1 AT-CGCAACGCGATAATAC-T
*
54764 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
54778 TTTCAAAGCG
Statistics
Matches: 75, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
19 1 0.01
20 35 0.47
21 37 0.49
22 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (19 bp):
ATCGCAACGCGATAATACT
Found at i:54970 original size:21 final size:22
Alignment explanation
Indices: 54944--54986 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
54934 CACTCTCTCA
54944 CCCATCTCCGACG-AATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
54965 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
54987 TATCTAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.19, C:0.47, G:0.16, T:0.19
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:56631 original size:17 final size:18
Alignment explanation
Indices: 56588--56631 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
56578 TCCACTTCGG
*
56588 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCGACCA
* *
56606 GAGCTATCACCTC-ACTA
1 GAGCCATCACCTCGACCA
56623 GAGCCATCA
1 GAGCCATCA
56632 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.27, C:0.41, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCGACCA
Found at i:57131 original size:20 final size:19
Alignment explanation
Indices: 57097--57180 Score: 98
Period size: 19 Copynumber: 4.4 Consensus size: 19
57087 TAGTTTACTT
* *
57097 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGACAA
* *
57116 TCGCAACGCAGAAATGGCTA
1 TCGCAACGC-GAAATGACAA
* *
57136 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGACAA
57155 TCGCAACGCGAAATGA-AA
1 TCGCAACGCGAAATGACAA
57173 TCGCAACG
1 TCGCAACG
57181 ACAAAATCGC
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
18 10 0.18
19 30 0.53
20 17 0.30
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGACAA
Found at i:57206 original size:18 final size:17
Alignment explanation
Indices: 57147--57210 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 17
57137 CGCAATGCGA
57147 AATGAAAATCGCAACGCG
1 AATGAAAATCGCAACG-G
57165 AAATG-AAATCGCAAC-G
1 -AATGAAAATCGCAACGG
*
57181 -A-CAAAATCGCAACGTG
1 AATGAAAATCGCAACG-G
57197 AATGAAAATCGCAA
1 AATGAAAATCGCAA
57211 TGCGATTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
14 11 0.29
16 2 0.05
17 1 0.03
18 20 0.53
19 4 0.11
ACGTcount: A:0.48, C:0.20, G:0.19, T:0.12
Consensus pattern (17 bp):
AATGAAAATCGCAACGG
Found at i:57246 original size:14 final size:14
Alignment explanation
Indices: 57227--57283 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
57217 TTGTGTTTCG
57227 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
57241 CGTTGCGATTTCAT-T
1 CGTTGCGATTT--TGT
57256 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
57272 CGTTGCGATTTT
1 CGTTGCGATTTT
57284 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 23 0.61
15 2 0.05
16 2 0.05
17 11 0.29
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:57261 original size:31 final size:33
Alignment explanation
Indices: 57222--57299 Score: 133
Period size: 31 Copynumber: 2.4 Consensus size: 33
57212 GCGATTTGTG
57222 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
57254 -TTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
57286 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
57300 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
31 26 0.60
32 5 0.12
33 12 0.28
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:57298 original size:19 final size:19
Alignment explanation
Indices: 57272--57338 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
57262 GCGATTTTGT
**
57272 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
57291 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
57311 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
57330 CGTTGCGAT
1 CGTTGCGAT
57339 TTAAGTTTCG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:57318 original size:20 final size:19
Alignment explanation
Indices: 57284--57338 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
57274 TTGCGATTTT
*
57284 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
57303 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
57323 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
57339 TTAAGTTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:59201 original size:14 final size:14
Alignment explanation
Indices: 59182--59217 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
59172 ATTGTTTAAT
59182 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
59196 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
59210 TGATTTGT
1 TGATTTGT
59218 TTAATTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Done.