Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000806.1 Hibiscus syriacus cultivar Beakdansim tig00001564_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: 56071
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:1148 original size:23 final size:23
Alignment explanation
Indices: 1118--1163 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1108 AATAATTTTC
*
1118 TCTTTGTGATACGTTTATCTCTG
1 TCTTTGTGACACGTTTATCTCTG
* *
1141 TCTTTGTGGCACGTTTGTCTCTG
1 TCTTTGTGACACGTTTATCTCTG
1164 CATAGTTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.09, C:0.20, G:0.22, T:0.50
Consensus pattern (23 bp):
TCTTTGTGACACGTTTATCTCTG
Found at i:1347 original size:3 final size:3
Alignment explanation
Indices: 1339--1401 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
1329 GGACTACAAA
1339 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1387 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
1402 ACAAAATCAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:7606 original size:2 final size:2
Alignment explanation
Indices: 7599--7637 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
7589 TTTAATACGC
7599 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7638 ATTTGTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16000 original size:20 final size:21
Alignment explanation
Indices: 15963--16005 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
15953 GATCAACATT
*
15963 TTGCATCTGCATTTGCA-TCA
1 TTGCATCTGCATTGGCATTCA
15983 TTGCATTCTGCA-TGGCATTCA
1 TTGCA-TCTGCATTGGCATTCA
16004 TT
1 TT
16006 CAAACATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (21 bp):
TTGCATCTGCATTGGCATTCA
Found at i:17196 original size:12 final size:12
Alignment explanation
Indices: 17166--17265 Score: 55
Period size: 12 Copynumber: 8.0 Consensus size: 12
17156 ATATCAAATC
17166 AAAACAAAGAGAA
1 AAAACAAAGA-AA
17179 ACAAACAAAGAAA
1 A-AAACAAAGAAA
**
17192 AAAACAAAGGGCA
1 AAAACAAA-GAAA
* *
17205 AAGA-AAAG-GA
1 AAAACAAAGAAA
17215 AAAACAAAGGGAAA
1 AAAACAAA--GAAA
17229 AAAAGCAAA-AGAA
1 AAAA-CAAAGA-AA
*
17242 AAAACAAATAAA
1 AAAACAAAGAAA
17254 AAAGAC-AAGAAA
1 AAA-ACAAAGAAA
17266 CACATGCAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 21
0.71 0.07 0.21
Matches are distributed among these distances:
10 4 0.06
11 4 0.06
12 25 0.36
13 19 0.27
14 14 0.20
15 4 0.06
ACGTcount: A:0.74, C:0.09, G:0.16, T:0.01
Consensus pattern (12 bp):
AAAACAAAGAAA
Found at i:17206 original size:23 final size:23
Alignment explanation
Indices: 17180--17238 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
17170 CAAAGAGAAA
*
17180 CAAACAAAGAAAAAAACAAAGGG
1 CAAAAAAAGAAAAAAACAAAGGG
*
17203 CAAAGAAAAG-GAAAAACAAAGGG
1 CAAA-AAAAGAAAAAAACAAAGGG
*
17226 -AAAAAAAGCAAAA
1 CAAAAAAAGAAAAA
17239 GAAAAAACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 5 0.16
22 6 0.19
23 16 0.52
24 4 0.13
ACGTcount: A:0.71, C:0.10, G:0.19, T:0.00
Consensus pattern (23 bp):
CAAAAAAAGAAAAAAACAAAGGG
Found at i:17256 original size:27 final size:26
Alignment explanation
Indices: 17204--17265 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
17194 AACAAAGGGC
* **
17204 AAAGAAAAGGAAAAACAAAGGGAAAA
1 AAAGAAAAGAAAAAACAAAGAAAAAA
*
17230 AAAGCAAAAGAAAAAACAAATAAAAAA
1 AAAG-AAAAGAAAAAACAAAGAAAAAA
17257 GACAAGAAA
1 -A-AAGAAA
17266 CACATGCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 4 0.14
27 18 0.62
28 4 0.14
29 3 0.10
ACGTcount: A:0.76, C:0.06, G:0.16, T:0.02
Consensus pattern (26 bp):
AAAGAAAAGAAAAAACAAAGAAAAAA
Found at i:18605 original size:68 final size:65
Alignment explanation
Indices: 18501--18674 Score: 206
Period size: 68 Copynumber: 2.6 Consensus size: 65
18491 TTTTTCTTAA
* * *
18501 AAACAAATTTTTTCTCCCTTGAGACAGTTCCTCTTGAAACACAAAATCTTTGAGTCTGTTTCTCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTCCTCTTGAAACAC-AAATCTTTGAGTC-ATTTCACT
18566 TG
64 TG
* ** *
18568 AAACAAAGTTTTGTCTCCCTTGATATGGTTTCC-CTTGAAACACATATCTTTGAGTCATTTCACT
1 AAACAAA-TTTTGTCTCCCTTGAGACAG-TTCCTCTTGAAACACAAATCTTTGAGTCATTTCACT
18632 TG
64 TG
* * * *
18634 AAACGAATTTTGTCTCTCTTGAGACATTTTCTCTTGAAACA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTCCTCTTGAAACA
18675 AATTTTGTCT
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
64 3 0.03
65 24 0.27
66 14 0.16
67 19 0.21
68 26 0.29
69 4 0.04
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTCCTCTTGAAACACAAATCTTTGAGTCATTTCACTTG
Found at i:18688 original size:21 final size:20
Alignment explanation
Indices: 18630--18691 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
18620 AGTCATTTCA
18630 CTTGAAACGAATTTTGTCTCT
1 CTTGAAAC-AATTTTGTCTCT
*
18651 CTTGAGAC-A--TT-T-TCT
1 CTTGAAACAATTTTGTCTCT
18666 CTTGAAACAAATTTTGTCTCT
1 CTTGAAAC-AATTTTGTCTCT
18687 CTTGA
1 CTTGA
18692 GAGAGTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
15 10 0.30
16 1 0.03
17 3 0.09
19 3 0.09
20 1 0.03
21 15 0.45
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (20 bp):
CTTGAAACAATTTTGTCTCT
Found at i:18738 original size:66 final size:66
Alignment explanation
Indices: 18661--18841 Score: 292
Period size: 66 Copynumber: 2.7 Consensus size: 66
18651 CTTGAGACAT
*
18661 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAGAGTTTCTCTTGAAACACCCATCTTTGAGATT
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAGAGTTTCTCTTGAAACACCCATCTTTGAGATT
18726 G
66 G
** * *
18727 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCCATCTTTGAGTTT
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAGAGTTTCTCTTGAAACACCCATCTTTGAGATT
18792 G
66 G
*
18793 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATG-GTTTCCCTTGAAAC
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA-GAGTTTCTCTTGAAAC
18842 CAATATCCCT
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
66 105 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (66 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAGAGTTTCTCTTGAAACACCCATCTTTGAGATT
G
Found at i:18749 original size:102 final size:102
Alignment explanation
Indices: 18558--18776 Score: 316
Period size: 102 Copynumber: 2.1 Consensus size: 102
18548 CTTTGAGTCT
* *
18558 GTTTCTCTTGAAACAAAGTTTTGTCTCCCTTGATATGGTTTCCCTTGAAACACATATCTTTGAGT
1 GTTTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGATGGTTTCCCTTGAAACACACATCTTTGAGT
18623 CATTTCACTTGAAACGAATTTTGTCTCTCTTGAGACA
66 CATTTCACTTGAAACGAATTTTGTCTCTCTTGAGACA
* * * *
18660 TTTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGA-GAGTTTCTCTTGAAACACCCATCTTTGAG
1 GTTTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGATG-GTTTCCCTTGAAACACACATCTTTGAG
** * *
18723 ATTGTTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACA
65 -TCATTTCACTTGAAACGAATTTTGTCTCTCTTGAGACA
18762 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
18777 CCCATCTTTG
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
100 1 0.01
101 39 0.38
102 64 0.62
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (102 bp):
GTTTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGATGGTTTCCCTTGAAACACACATCTTTGAGT
CATTTCACTTGAAACGAATTTTGTCTCTCTTGAGACA
Found at i:18766 original size:36 final size:36
Alignment explanation
Indices: 18617--18775 Score: 154
Period size: 36 Copynumber: 4.6 Consensus size: 36
18607 ACACATATCT
* *
18617 TTGAGTCA-TTTCACTTGAAACGAATTTTGTCTCTC
1 TTGAGACAGTTTCTCTTGAAACGAATTTTGTCTCTC
* *
18652 TTGAGACATTTTCTCTTGAAACAAATTTTGTCTCTC
1 TTGAGACAGTTTCTCTTGAAACGAATTTTGTCTCTC
* **
18688 TTGAGAGAGTTTCTCTTGAAAC--A----CCCATCT-
1 TTGAGACAGTTTCTCTTGAAACGAATTTTGTC-TCTC
** * *
18718 TTGAGATTGTTTCCCTTGAAATGAATTTTGTCTCTC
1 TTGAGACAGTTTCTCTTGAAACGAATTTTGTCTCTC
18754 TTGAGACAGTTTCTCTTGAAAC
1 TTGAGACAGTTTCTCTTGAAAC
18776 ACCCATCTTT
Statistics
Matches: 98, Mismatches: 17, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
30 19 0.19
31 3 0.03
32 1 0.01
34 1 0.01
35 10 0.10
36 64 0.65
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (36 bp):
TTGAGACAGTTTCTCTTGAAACGAATTTTGTCTCTC
Found at i:23425 original size:21 final size:22
Alignment explanation
Indices: 23399--23452 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
23389 CGGTTCAACC
23399 TAAATGTTTTTAGT-TTTTTAT
1 TAAATGTTTTTAGTATTTTTAT
*
23420 TAAATGTTTTTTGTATTTTTAT
1 TAAATGTTTTTAGTATTTTTAT
*
23442 TTAAT-TTTTTA
1 TAAATGTTTTTA
23453 AATAATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TAAATGTTTTTAGTATTTTTAT
Found at i:25030 original size:2 final size:2
Alignment explanation
Indices: 25023--25050 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25013 TAGAACCAAG
25023 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
25051 TATGTCACGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26475 original size:3 final size:3
Alignment explanation
Indices: 26454--26493 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
26444 CCTACAAAAT
* *
26454 ATA ATT ATA ATA TTA ATA ATA A-A ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
26494 TAGTTAGAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:26480 original size:17 final size:17
Alignment explanation
Indices: 26460--26492 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
26450 AAATATAATT
*
26460 ATAATATTAATAATAAA
1 ATAATAATAATAATAAA
26477 ATAATAATAATAATAA
1 ATAATAATAATAATAA
26493 TTAGTTAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAATAATAATAATAAA
Found at i:27106 original size:30 final size:30
Alignment explanation
Indices: 27072--27180 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 30
27062 TGTGTTGAGG
27072 GAAACAATCTCAAAAGTTTATGTTTCAAGA
1 GAAACAATCTCAAAAGTTTATGTTTCAAGA
*** *
27102 GAAACTGCCTCAAGTGAGATGAAATT-TGTTTCAAGA
1 GAAACAATCTCAA---A-A-G--TTTATGTTTCAAGA
* *
27138 AAAACAATCTCAAAGGTTTATGTTTCAAGA
1 GAAACAATCTCAAAAGTTTATGTTTCAAGA
*
27168 GAAACAGTCTCAA
1 GAAACAATCTCAA
27181 GTGAGAAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
29 2 0.03
30 31 0.53
31 1 0.02
33 2 0.03
34 1 0.02
35 1 0.02
36 19 0.32
37 2 0.03
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (30 bp):
GAAACAATCTCAAAAGTTTATGTTTCAAGA
Found at i:27150 original size:36 final size:35
Alignment explanation
Indices: 27092--27205 Score: 105
Period size: 36 Copynumber: 3.3 Consensus size: 35
27082 CAAAAGTTTA
* *
27092 TGTTTCAAGAGAAACTGCCTCAAGTGAGATGAAATT
1 TGTTTCAAGAGAAACAGTCTCAAGTGAGA-GAAATT
* * *
27128 TGTTTCAAGAAAAACAATCTCAA---AG-G--TTT
1 TGTTTCAAGAGAAACAGTCTCAAGTGAGAGAAATT
*
27157 ATGTTTCAAGAGAAACAGTCTCAAGTGAGAAAAAATT
1 -TGTTTCAAGAGAAACAGTCTCAAGTGAG-AGAAATT
27194 TGTTTCAAGAGA
1 TGTTTCAAGAGA
27206 TATAATCTCA
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
29 2 0.03
30 21 0.34
31 1 0.02
33 4 0.07
36 31 0.51
37 2 0.03
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGAGAAACAGTCTCAAGTGAGAGAAATT
Found at i:27290 original size:67 final size:66
Alignment explanation
Indices: 27028--27358 Score: 448
Period size: 66 Copynumber: 5.0 Consensus size: 66
27018 GGATAATTCA
* * * *
27028 TTTCAAGAGAAATTGTCTCAAGCGAGACAAAATTTGTGTT-GAGGGAAACAATCTCAAAAGTTTA
1 TTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGT-TTCGAGAGAAACAATCTCAAAGGTTTA
27092 TG
65 TG
* ** * *
27094 TTTCAAGAGAAACTGCCTCAAGTGAGATGAAATTTGTTTCAAGAAAAACAATCTCAAAGGTTTAT
1 TTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTCGAGAGAAACAATCTCAAAGGTTTAT
27159 G
66 G
* * * * *
27160 TTTCAAGAGAAACAGTCTCAAGTGAGAAAAAATTTGTTTCAAGAGATATAATCTCAAAGGTTTAT
1 TTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTCGAGAGAAACAATCTCAAAGGTTTAT
*
27225 T
66 G
* *
27226 TTTCAAGAGAAACTGTCTTAAGTGAGACAAAACTTTGTTTCGAGAGAAACAATATCAAAGGTTTA
1 TTTCAAGAGAAACTGTCTCAAGTGAGACAAAA-TTTGTTTCGAGAGAAACAATCTCAAAGGTTTA
27291 TG
65 TG
* **
27293 TTTAAAGAGAAACTGTCTCAAGAAAGACAAATATTTGTTTCGAGAGAAACAATCTCAAAGGTTTA
1 TTTCAAGAGAAACTGTCTCAAGTGAGACAAA-ATTTGTTTCGAGAGAAACAATCTCAAAGGTTTA
27358 T
65 T
27359 CAATTTTTTT
Statistics
Matches: 232, Mismatches: 30, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
65 2 0.01
66 141 0.61
67 88 0.38
68 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (66 bp):
TTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTCGAGAGAAACAATCTCAAAGGTTTAT
G
Found at i:27431 original size:67 final size:67
Alignment explanation
Indices: 27360--27512 Score: 166
Period size: 67 Copynumber: 2.3 Consensus size: 67
27350 AAGGTTTATC
** * * * *
27360 AATTT-TTTTCAAGTGAAACAACTTTCAAAT-TTTGTGTTTTGAGGGAAAATTGTCTCAAGCGAG
1 AATTTGTTTTCAAGAAAAACAA-TCTCAAATGTTCGTGTCTT-AAGGAAAATTGTCTCAAGCGAG
27423 ACAA
64 ACAA
* * * *
27427 AATTTGTTTTTAAGAAAAATAATCTCAAATGTTCGTGTCTTAAGGAAGATTGTCTCAAGTGAGAC
1 AATTTGTTTTCAAGAAAAACAATCTCAAATGTTCGTGTCTTAAGGAAAATTGTCTCAAGCGAGAC
*
27492 GA
66 AA
*
27494 AATTTGTTTTTAAGAAAAA
1 AATTTGTTTTCAAGAAAAA
27513 TTGTCTCAAG
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
67 53 0.73
68 20 0.27
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.36
Consensus pattern (67 bp):
AATTTGTTTTCAAGAAAAACAATCTCAAATGTTCGTGTCTTAAGGAAAATTGTCTCAAGCGAGAC
AA
Found at i:27446 original size:37 final size:37
Alignment explanation
Indices: 27405--27548 Score: 135
Period size: 37 Copynumber: 4.1 Consensus size: 37
27395 GTTTTGAGGG
27405 AAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAAGA
1 AAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAAGA
** * * *
27442 AAAATAATCTCAA---ATG------TTCGTGTCTTAAGG
1 AAAATTGTCTCAAGCGA-GACAAAATTTGT-TTTTAAGA
* * *
27472 AAGATTGTCTCAAGTGAGACGAAATTTGTTTTTAAGA
1 AAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAAGA
27509 AAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAAGA
1 AAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAAGA
27546 AAA
1 AAA
27549 CAATCTCAAG
Statistics
Matches: 82, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
29 4 0.05
30 16 0.20
32 1 0.01
33 1 0.01
34 1 0.01
35 1 0.01
37 54 0.66
38 4 0.05
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (37 bp):
AAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAAGA
Found at i:27575 original size:36 final size:36
Alignment explanation
Indices: 27479--27563 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 36
27469 AGGAAGATTG
* * *
27479 TCTCAAGTGAGACGAAATTTGTTTTTAAGAAAA-ATTG
1 TCTCAAGAGAGACAAAATTTGTTTTTAAGAAAACA--A
*
27516 TCTCAAGCGAGACAAAATTTGTTTTTAAGAAAACAA
1 TCTCAAGAGAGACAAAATTTGTTTTTAAGAAAACAA
27552 TCTCAAGAGAGA
1 TCTCAAGAGAGA
27564 TTAATTTTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 11 0.26
37 31 0.72
38 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (36 bp):
TCTCAAGAGAGACAAAATTTGTTTTTAAGAAAACAA
Found at i:37233 original size:19 final size:19
Alignment explanation
Indices: 37211--37259 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
37201 CTTATTTTTG
** *
37211 GTATCGATACTCACTGTGA
1 GTATCGATACTCAAGGTCA
*
37230 GTATCTATACTCAAGGTCA
1 GTATCGATACTCAAGGTCA
37249 GTATCGATACT
1 GTATCGATACT
37260 GCAACCACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (19 bp):
GTATCGATACTCAAGGTCA
Found at i:45076 original size:2 final size:2
Alignment explanation
Indices: 45069--45100 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
45059 TCTCAATTCT
45069 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45101 CCCCACTCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54587 original size:25 final size:27
Alignment explanation
Indices: 54537--54587 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 27
54527 TAGTATTGGA
*
54537 GAAAGCTAGAATGATTGGGATGATTTT
1 GAAAGCTAGAATGATTAGGATGATTTT
54564 GAAA-CTA-AATGAGTTAGGAT-ATTT
1 GAAAGCTAGAATGA-TTAGGATGATTT
54588 ATAGTTGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 9 0.41
26 9 0.41
27 4 0.18
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.33
Consensus pattern (27 bp):
GAAAGCTAGAATGATTAGGATGATTTT
Done.