Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000320.1 Hibiscus syriacus cultivar Beakdansim tig00000602_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: 65209
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:1010 original size:24 final size:22
Alignment explanation
Indices: 983--1032 Score: 82
Period size: 24 Copynumber: 2.2 Consensus size: 22
973 AAGTTATTAA
983 ATTATAATTTAAATAATTGTTTAT
1 ATTATAATTTAAAT-ATTGTTT-T
1007 ATTATAATTTAAATATTGTTTT
1 ATTATAATTTAAATATTGTTTT
1029 ATTA
1 ATTA
1033 AAATAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 5 0.19
23 7 0.27
24 14 0.54
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (22 bp):
ATTATAATTTAAATATTGTTTT
Found at i:3730 original size:37 final size:36
Alignment explanation
Indices: 3655--3730 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
3645 TTTTTATATT
* * *
3655 TTTAATTTTTTTTAAAAATTATATAAATATTATGAA
1 TTTAATTTTTTTAAAAAAATATATAAATATTATCAA
*
3691 TTTAA-TTTTTTAAAGAAAATATATAAATATTTTACAA
1 TTTAATTTTTTTAAA-AAAATATATAAATATTAT-CAA
3728 TTT
1 TTT
3731 GTAATATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 8 0.24
36 21 0.62
37 5 0.15
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (36 bp):
TTTAATTTTTTTAAAAAAATATATAAATATTATCAA
Found at i:7367 original size:25 final size:25
Alignment explanation
Indices: 7339--7409 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
7329 AGAAAAAAAT
*
7339 TATTTTTTAAATAATAATTTGAATA
1 TATTTTTTAAATAATAAATTGAATA
*
7364 TATTTTTTAAATAATAAATTGAA-G
1 TATTTTTTAAATAATAAATTGAATA
* *
7388 T-TTTTTAAAATAAAAAATTGAA
1 TATTTTTTAAATAATAAATTGAA
7410 ATTTTATATG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.45
24 1 0.02
25 22 0.52
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (25 bp):
TATTTTTTAAATAATAAATTGAATA
Found at i:7398 original size:23 final size:22
Alignment explanation
Indices: 7340--7414 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 22
7330 GAAAAAAATT
*
7340 ATTTTTTAAATAATAATTTGAATA
1 ATTTTTTAAATAATAAATTG-A-A
7364 TATTTTTTAAATAATAAATTGAA
1 -ATTTTTTAAATAATAAATTGAA
* *
7387 GTTTTTTAAAATAAAAAATTGAA
1 ATTTTTT-AAATAATAAATTGAA
7410 ATTTT
1 ATTTT
7415 ATATGTCTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.13
23 19 0.42
24 1 0.02
25 19 0.42
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
ATTTTTTAAATAATAAATTGAA
Found at i:7565 original size:18 final size:18
Alignment explanation
Indices: 7542--7576 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
7532 TTTTAGATCA
7542 TTTAAACACCTAAAATTC
1 TTTAAACACCTAAAATTC
7560 TTTAAACACCTAAAATT
1 TTTAAACACCTAAAATT
7577 AAGTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (18 bp):
TTTAAACACCTAAAATTC
Found at i:9402 original size:59 final size:60
Alignment explanation
Indices: 9309--9423 Score: 205
Period size: 59 Copynumber: 1.9 Consensus size: 60
9299 CTACGAACAA
*
9309 CGATTACCTAAATTTCTCTAAGTAACAAATATTACCTACATCGGTAATTAGGCTTTCACG
1 CGATTACCTAAATTTCTCTAAGTAACAAAGATTACCTACATCGGTAATTAGGCTTTCACG
*
9369 CGATTACCTAAATTTC-CTAAGTAACAACGATTACCTACATCGGTAATTAGGCTTT
1 CGATTACCTAAATTTCTCTAAGTAACAAAGATTACCTACATCGGTAATTAGGCTTT
9424 TTAACTACGC
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
59 37 0.70
60 16 0.30
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (60 bp):
CGATTACCTAAATTTCTCTAAGTAACAAAGATTACCTACATCGGTAATTAGGCTTTCACG
Found at i:10970 original size:2 final size:2
Alignment explanation
Indices: 10963--10991 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10953 CGTTTGAGTT
10963 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10992 ATTAGTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11262 original size:18 final size:18
Alignment explanation
Indices: 11235--11271 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
11225 TTATGTTGAG
*
11235 TATATTTATAAATAATAT
1 TATATATATAAATAATAT
11253 TATATATATAAATAATAT
1 TATATATATAAATAATAT
11271 T
1 T
11272 TATTAAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATATATATAAATAATAT
Found at i:12070 original size:24 final size:24
Alignment explanation
Indices: 12038--12093 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
12028 CGTTGGATTA
*
12038 TATATTCGTTCATTTATGTTTATT
1 TATATTCGTTCATTTATGTTAATT
12062 TATATTCGTTCATTTATGTTAATT
1 TATATTCGTTCATTTATGTTAATT
*
12086 TATGTTCG
1 TATATTCG
12094 AACAGAGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.21, C:0.09, G:0.11, T:0.59
Consensus pattern (24 bp):
TATATTCGTTCATTTATGTTAATT
Found at i:12393 original size:20 final size:20
Alignment explanation
Indices: 12360--12399 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12350 GTTTATAATT
* *
12360 CGTTCGTTTGTGTTCGTTTA
1 CGTTCATTTATGTTCGTTTA
*
12380 CGTTCATTTATGTTTGTTTA
1 CGTTCATTTATGTTCGTTTA
12400 TCATTTAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.57
Consensus pattern (20 bp):
CGTTCATTTATGTTCGTTTA
Found at i:21000 original size:42 final size:43
Alignment explanation
Indices: 20947--21097 Score: 171
Period size: 43 Copynumber: 3.5 Consensus size: 43
20937 ATTTGGGCCT
* * * *
20947 TCTATTTTTTCATCTTTATAATTAGGTTCTTAAT-TTTTTAAA
1 TCTAATTTTTCATCTTTATAATTAGGGTCATAATATTATTAAA
* * * * *
20989 TTTTATTTTTCACCTTTATAATTGGGGTCATAATATTATTCAA
1 TCTAATTTTTCATCTTTATAATTAGGGTCATAATATTATTAAA
* * *
21032 TCTAATTTTTTATCTTTATAATTGGGGTCATAATATTATTCAA
1 TCTAATTTTTCATCTTTATAATTAGGGTCATAATATTATTAAA
21075 TCTAACTTTTT-ATCTTTATAATT
1 TCTAA-TTTTTCATCTTTATAATT
21098 GAAGTCTCTA
Statistics
Matches: 94, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
42 27 0.29
43 62 0.66
44 5 0.05
ACGTcount: A:0.28, C:0.11, G:0.07, T:0.55
Consensus pattern (43 bp):
TCTAATTTTTCATCTTTATAATTAGGGTCATAATATTATTAAA
Found at i:21098 original size:43 final size:43
Alignment explanation
Indices: 21002--21098 Score: 185
Period size: 43 Copynumber: 2.3 Consensus size: 43
20992 TATTTTTCAC
*
21002 CTTTATAATTGGGGTCATAATATTATTCAATCTAATTTTTTAT
1 CTTTATAATTGGGGTCATAATATTATTCAATCTAACTTTTTAT
21045 CTTTATAATTGGGGTCATAATATTATTCAATCTAACTTTTTAT
1 CTTTATAATTGGGGTCATAATATTATTCAATCTAACTTTTTAT
21088 CTTTATAATTG
1 CTTTATAATTG
21099 AAGTCTCTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (43 bp):
CTTTATAATTGGGGTCATAATATTATTCAATCTAACTTTTTAT
Found at i:21152 original size:43 final size:42
Alignment explanation
Indices: 20993--21414 Score: 161
Period size: 43 Copynumber: 9.8 Consensus size: 42
20983 TTTAAATTTT
* * * * **
20993 ATTTTTCACCTTTATAATTGGGGTCATAATATTATTC-AATCTA
1 ATTTTT-ACCTTTATAATTGAGGCCCTAAT-TTTTTCTAATCCC
* * * * * **
21036 ATTTTTTATCTTTATAATTGGGGTCATAATATTATTC-AATCTA
1 A-TTTTTACCTTTATAATTGAGGCCCTAAT-TTTTTCTAATCCC
* * *
21079 ACTTTTTATCTTTATAATTGAAGTCTCTAATTTTTTCTAATCCC
1 A-TTTTTACCTTTATAATTG-AGGCCCTAATTTTTTCTAATCCC
* * *
21123 TTTTTTACCTTTATAATTGAGGCACCTAA--TTTTGT-AGCCTC
1 ATTTTTACCTTTATAATTGAGGC-CCTAATTTTTTCTAATCC-C
* * ** *
21164 ACTTTTAACTTTATAATTGAGGCTTTTAAGTTTTTTC-AATCTC
1 ATTTTTACCTTTATAATTGAGGC-CCTAA-TTTTTTCTAATCCC
* * * *
21207 ACTTTCTACATTT-TCAATTGAGGCCTCTAAGTTTTTC-AATCTCA
1 A-TTTTTACCTTTAT-AATTGAGGCC-CTAATTTTTTCTAATC-CC
* * *
21251 ATTTCTACATTTATAATTGAGGCCCCTAATTTTTT-TAAACTCAC
1 ATTTTTACCTTTATAATTGAGG-CCCTAATTTTTTCT-AA-TCCC
* * * *
21295 TTTTTTAACTTTATAATTGAGGCCCTTAAGTTTTT-TAATCTC
1 ATTTTTACCTTTATAATTGAGGCCC-TAATTTTTTCTAATCCC
* * * * *
21337 ACTTTCTAAC-TTACTAATTGAGGGTCCT-GTTTTTT-TAATCTCA
1 A-TTTTTACCTTTA-TAATTGA-GGCCCTAATTTTTTCTAATC-CC
*
21380 ATTTCTACCTTTATAATT-AGGGCCTCTAATTTTTT
1 ATTTTTACCTTTATAATTGA-GGCC-CTAATTTTTT
21415 ACAATTTCAT
Statistics
Matches: 300, Mismatches: 53, Indels: 52
0.74 0.13 0.13
Matches are distributed among these distances:
40 3 0.01
41 34 0.11
42 33 0.11
43 152 0.51
44 76 0.25
45 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (42 bp):
ATTTTTACCTTTATAATTGAGGCCCTAATTTTTTCTAATCCC
Found at i:21220 original size:22 final size:22
Alignment explanation
Indices: 21195--21262 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
21185 GCTTTTAAGT
21195 TTTTTCAATCTCACTTTCTACA
1 TTTTTCAATCTCACTTTCTACA
* *
21217 -TTTTCAAT-TGAGGC-CTCTA-A
1 TTTTTCAATCTCA--CTTTCTACA
*
21237 GTTTTTCAATCTCAATTTCTACA
1 -TTTTTCAATCTCACTTTCTACA
21260 TTT
1 TTT
21263 ATAATTGAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 14
0.64 0.09 0.26
Matches are distributed among these distances:
20 3 0.09
21 12 0.35
22 16 0.47
23 3 0.09
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.49
Consensus pattern (22 bp):
TTTTTCAATCTCACTTTCTACA
Found at i:21229 original size:44 final size:44
Alignment explanation
Indices: 21070--21419 Score: 241
Period size: 43 Copynumber: 8.1 Consensus size: 44
21060 CATAATATTA
* * * * *
21070 TTCAATCTAACTTTTTATC-TTTATAATTGAAGTCTCTAA-TTTT
1 TTCAATCTCACTTTCTA-CATTTATAATTGAGGCCCCTAAGTTTT
* * *
21113 TTCTAATC-C-CTTTTTTACCTTTATAATTGAGGCACCTAA-TTTT
1 TTC-AATCTCAC-TTTCTACATTTATAATTGAGGCCCCTAAGTTTT
* ** ***
21156 GT-AGCCTCACTTT-TA-ACTTTATAATTGAGGCTTTTAAGTTTT
1 TTCAATCTCACTTTCTACA-TTTATAATTGAGGCCCCTAAGTTTT
*
21198 TTCAATCTCACTTTCTACATTT-TCAATTGAGGCCTCTAAG-TTT
1 TTCAATCTCACTTTCTACATTTAT-AATTGAGGCCCCTAAGTTTT
*
21241 TTCAATCTCAATTTCTACATTTATAATTGAGGCCCCTAA-TTTT
1 TTCAATCTCACTTTCTACATTTATAATTGAGGCCCCTAAGTTTT
* * * *
21284 TTTAAACTCACTTTTTTA-ACTTTATAATTGAGGCCCTTAAGTTTT
1 TTCAATCTCAC-TTTCTACA-TTTATAATTGAGGCCCCTAAGTTTT
* **
21329 TT-AATCTCACTTTCTA-ACTTACTAATTGAGGGTCCT--GTTTT
1 TTCAATCTCACTTTCTACATTTA-TAATTGAGGCCCCTAAGTTTT
* * * *
21370 TTTAATCTCAATTTCTACCTTTATAATT-AGGGCCTCTAA-TTTT
1 TTCAATCTCACTTTCTACATTTATAATTGA-GGCCCCTAAGTTTT
21413 TTACAAT
1 TT-CAAT
21420 TTCATAAAAT
Statistics
Matches: 247, Mismatches: 37, Indels: 45
0.75 0.11 0.14
Matches are distributed among these distances:
41 29 0.12
42 36 0.15
43 117 0.47
44 58 0.23
45 7 0.03
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (44 bp):
TTCAATCTCACTTTCTACATTTATAATTGAGGCCCCTAAGTTTT
Found at i:21285 original size:87 final size:85
Alignment explanation
Indices: 21089--21419 Score: 263
Period size: 87 Copynumber: 3.9 Consensus size: 85
21079 ACTTTTTATC
* * *
21089 TTTATAATTGAAG-TCTCTAATTTTTTCTAATC-C-CTTTTTTACCTTTATAATTGAGGCAC-CT
1 TTTATAATTGAGGCTC-CTAATTTTTT-TAATCTCAC-TTTCTACATTTATAATTGAGGC-CTCT
** *
21150 AA-TTTTGT-AGCCTCACTTT-TAA
62 AAGTTTT-TCAATCTCAATTTCTAA
** *
21172 CTTTATAATTGAGGCTTTTAAGTTTTTTCAATCTCACTTTCTACATTT-TCAATTGAGGCCTCTA
1 -TTTATAATTGAGGCTCCTAA-TTTTTTTAATCTCACTTTCTACATTTAT-AATTGAGGCCTCTA
21236 AGTTTTTCAATCTCAATTTCTACA
63 AGTTTTTCAATCTCAATTTCTA-A
* * *
21260 TTTATAATTGAGGCCCCTAATTTTTTTAAACTCACTTTTTTA-ACTTTATAATTGAGGCC-CTTA
1 TTTATAATTGAGGCTCCTAATTTTTTTAATCTCAC-TTTCTACA-TTTATAATTGAGGCCTC-TA
* *
21323 AGTTTTTTAATCTCACTTTCTAA
63 AGTTTTTCAATCTCAATTTCTAA
* * * * *
21346 CTTACTAATTGAGGGTCCT-GTTTTTTTAATCTCAATTTCTACCTTTATAATT-AGGGCCTCTAA
1 TTTA-TAATTGAGGCTCCTAATTTTTTTAATCTCACTTTCTACATTTATAATTGA-GGCCTCTAA
*
21409 TTTTTTACAAT
64 GTTTTT-CAAT
21420 TTCATAAAAT
Statistics
Matches: 201, Mismatches: 27, Indels: 36
0.76 0.10 0.14
Matches are distributed among these distances:
84 22 0.11
85 57 0.28
86 49 0.24
87 71 0.35
88 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.47
Consensus pattern (85 bp):
TTTATAATTGAGGCTCCTAATTTTTTTAATCTCACTTTCTACATTTATAATTGAGGCCTCTAAGT
TTTTCAATCTCAATTTCTAA
Found at i:28464 original size:19 final size:19
Alignment explanation
Indices: 28440--28486 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
28430 ATAAGTAATA
28440 TAACAATTATTGCAAATTT
1 TAACAATTATTGCAAATTT
28459 TAACAATTATTGCAAATTT
1 TAACAATTATTGCAAATTT
28478 TAACAATTA
1 TAACAATTA
28487 ATCAGTTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (19 bp):
TAACAATTATTGCAAATTT
Found at i:34582 original size:23 final size:25
Alignment explanation
Indices: 34550--34598 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
34540 TTATTGATTT
*
34550 TTTTTATCATCTTTT-TCCCTTCTC
1 TTTTTATCATATTTTCTCCCTTCTC
*
34574 TTTTT-TCATATTTTCTCCTTTCTC
1 TTTTTATCATATTTTCTCCCTTCTC
34598 T
1 T
34599 CTCTTATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.08, C:0.27, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTTTATCATATTTTCTCCCTTCTC
Found at i:35452 original size:13 final size:13
Alignment explanation
Indices: 35434--35458 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35424 TTTATCTTTA
35434 AAAAAAATATTTG
1 AAAAAAATATTTG
35447 AAAAAAATATTT
1 AAAAAAATATTT
35459 AATATTAATG
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:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
AAAAAAATATTTG
Found at i:37725 original size:15 final size:15
Alignment explanation
Indices: 37705--37752 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
37695 TTAGCTGGGT
*
37705 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
*
37720 GGGCGGATGCGGGAC
1 GGGCGGATGCGGGGC
37735 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
37750 GGG
1 GGG
37753 TAATGTCTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.08, C:0.17, G:0.67, T:0.08
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:39376 original size:13 final size:13
Alignment explanation
Indices: 39358--39390 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
39348 TAAATGCAAA
39358 AAAATAAAATAAT
1 AAAATAAAATAAT
39371 AAAATAAAATAAT
1 AAAATAAAATAAT
*
39384 CAAATAA
1 AAAATAA
39391 TCAAATAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:39388 original size:21 final size:21
Alignment explanation
Indices: 39355--39398 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
39345 TTATAAATGC
39355 AAAAAAATAAAATAATAAAAT
1 AAAAAAATAAAATAATAAAAT
* * *
39376 AAAATAATCAAATAATCAAAT
1 AAAAAAATAAAATAATAAAAT
39397 AA
1 AA
39399 TCAAATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAAAAATAAAATAATAAAAT
Found at i:39398 original size:16 final size:16
Alignment explanation
Indices: 39377--39407 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
39367 TAATAAAATA
39377 AAATAATCAAATAATC
1 AAATAATCAAATAATC
39393 AAATAATCAAATAAT
1 AAATAATCAAATAAT
39408 TAATACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAATCAAATAATC
Found at i:45005 original size:12 final size:12
Alignment explanation
Indices: 44988--45013 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44978 TTCCTGCTTA
44988 CTTGTATTAGTT
1 CTTGTATTAGTT
45000 CTTGTATTAGTT
1 CTTGTATTAGTT
45012 CT
1 CT
45014 GGTGTCCTAA
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:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (12 bp):
CTTGTATTAGTT
Found at i:49767 original size:2 final size:2
Alignment explanation
Indices: 49760--49841 Score: 150
Period size: 2 Copynumber: 42.0 Consensus size: 2
49750 ATATGTATTA
49760 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
49802 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49842 TTCATATTAA
Statistics
Matches: 78, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 76 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49857 original size:14 final size:14
Alignment explanation
Indices: 49762--49853 Score: 52
Period size: 14 Copynumber: 6.7 Consensus size: 14
49752 ATGTATTAAT
*
49762 ATATATATATATAT-
1 ATATATA-ATATTTC
*
49776 ATATATATATATAT-
1 ATATATA-ATATTTC
*
49790 ATATATATATATAT-
1 ATATATA-ATATTTC
* *
49804 ATATATATTATAT-
1 ATATATAATATTTC
*
49817 ATATATATATATAT-
1 ATATATA-ATATTTC
49831 ATATATAATATTTC
1 ATATATAATATTTC
49845 ATAT-TAATA
1 ATATATAATA
49854 ATTTTGATTA
Statistics
Matches: 73, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
13 22 0.30
14 51 0.70
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATAATATTTC
Found at i:51746 original size:36 final size:33
Alignment explanation
Indices: 51706--51776 Score: 90
Period size: 36 Copynumber: 2.1 Consensus size: 33
51696 TGTGTTAAGG
*
51706 AAAAAAAA-TACAAATTTTACATACCTATTATTTTTA
1 AAAAAAAATTA-AAATTTTA-A-ACCT-TTATTCTTA
51742 AAAAAAAATTAAAATTTTAAACCTTTATTCTTA
1 AAAAAAAATTAAAATTTTAAACCTTTATTCTTA
51775 AA
1 AA
51777 TTTCTGCATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
33 10 0.30
34 4 0.12
35 1 0.03
36 16 0.48
37 2 0.06
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (33 bp):
AAAAAAAATTAAAATTTTAAACCTTTATTCTTA
Found at i:56089 original size:3 final size:3
Alignment explanation
Indices: 56081--56105 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
56071 TAGTTTATAA
56081 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
56106 AATTCTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:56526 original size:2 final size:2
Alignment explanation
Indices: 56519--56552 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
56509 ATTTATAACG
56519 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
56553 CTTAAATAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56940 original size:2 final size:2
Alignment explanation
Indices: 56933--56958 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56923 ATAATTGTAC
56933 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
56959 AATTTATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60200 original size:2 final size:2
Alignment explanation
Indices: 60193--60218 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
60183 GATCTTATTC
60193 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
60219 TTACACATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60809 original size:17 final size:18
Alignment explanation
Indices: 60789--60823 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
60779 ATTTAAAATA
60789 AAAATAA-AAATATATTC
1 AAAATAAGAAATATATTC
*
60806 AAAATAAGTAATATATTC
1 AAAATAAGAAATATATTC
60824 TCTTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAATAAGAAATATATTC
Done.