Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005102.1 Hibiscus syriacus cultivar Beakdansim tig00011469_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: 67212
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1201 original size:2 final size:2
Alignment explanation
Indices: 1194--1231 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1184 TAATTAAAGA
1194 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
1232 TAGCTCCACG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2193 original size:16 final size:16
Alignment explanation
Indices: 2157--2207 Score: 84
Period size: 16 Copynumber: 3.1 Consensus size: 16
2147 TAAAAACAAA
*
2157 TATATATTTAAACTTTT
1 TATATATTTAAAC-CTT
2174 TATATATTTAAACCTT
1 TATATATTTAAACCTT
2190 TATATATTTAAACCTT
1 TATATATTTAAACCTT
2206 TA
1 TA
2208 AATTTTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 20 0.61
17 13 0.39
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATATTTAAACCTT
Found at i:7398 original size:21 final size:21
Alignment explanation
Indices: 7372--7413 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
7362 TTTCCAAAGG
*
7372 GATGTACCGATGCACTCCCAT
1 GATGTACCGATGCACACCCAT
*
7393 GATGTATCGATGCACACCCAT
1 GATGTACCGATGCACACCCAT
7414 TTCGAATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (21 bp):
GATGTACCGATGCACACCCAT
Found at i:13662 original size:35 final size:35
Alignment explanation
Indices: 13621--13691 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
13611 GAACTTAGGA
13621 CTAGTTTTTGATTAGTTATAGGTTGAACTAAGTAT
1 CTAGTTTTTGATTAGTTATAGGTTGAACTAAGTAT
*
13656 CTAGTTTTTGATTAGTTCTAGGTTGAACTAAGTAT
1 CTAGTTTTTGATTAGTTATAGGTTGAACTAAGTAT
13691 C
1 C
13692 AGGCATTGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (35 bp):
CTAGTTTTTGATTAGTTATAGGTTGAACTAAGTAT
Found at i:15269 original size:10 final size:10
Alignment explanation
Indices: 15254--15284 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
15244 ATTTAGAACC
15254 TATGGATTAT
1 TATGGATTAT
*
15264 TATGGATGAT
1 TATGGATTAT
15274 TATGGATTAT
1 TATGGATTAT
15284 T
1 T
15285 TTGTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (10 bp):
TATGGATTAT
Found at i:17636 original size:26 final size:29
Alignment explanation
Indices: 17607--17670 Score: 91
Period size: 27 Copynumber: 2.3 Consensus size: 29
17597 TCTCTCTATG
17607 TTTTTCTTTCACCGAAAGGTTCTT-T-T-T
1 TTTTTCTTTCA-CGAAAGGTTCTTCTCTGT
17634 TTTTTCTTTCACGAAAGGTTC-TCTCTGT
1 TTTTTCTTTCACGAAAGGTTCTTCTCTGT
17662 TTTTTCTTT
1 TTTTTCTTT
17671 TCGTTTGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
25 1 0.03
26 11 0.32
27 12 0.35
28 10 0.29
ACGTcount: A:0.12, C:0.19, G:0.11, T:0.58
Consensus pattern (29 bp):
TTTTTCTTTCACGAAAGGTTCTTCTCTGT
Found at i:17637 original size:27 final size:28
Alignment explanation
Indices: 17596--17670 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 28
17586 GTTTTTTTGT
*
17596 TTCTCTCTATGTTTTTCTTTCACCGAAAGG
1 TTCTCTCTGT-TTTTTCTTTCA-CGAAAGG
*
17626 TTCT-T-TTTTTTTTCTTTCACGAAAGG
1 TTCTCTCTGTTTTTTCTTTCACGAAAGG
17652 TTCTCTCTGTTTTTTCTTT
1 TTCTCTCTGTTTTTTCTTT
17671 TCGTTTGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
26 11 0.27
27 12 0.29
28 13 0.32
29 1 0.02
30 4 0.10
ACGTcount: A:0.12, C:0.20, G:0.11, T:0.57
Consensus pattern (28 bp):
TTCTCTCTGTTTTTTCTTTCACGAAAGG
Found at i:17686 original size:20 final size:20
Alignment explanation
Indices: 17661--17700 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17651 GTTCTCTCTG
*
17661 TTTTTTCTTTTCGTTTGAAT
1 TTTTTTATTTTCGTTTGAAT
*
17681 TTTTTTATTTTTGTTTGAAT
1 TTTTTTATTTTCGTTTGAAT
17701 CAATTTGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.05, G:0.10, T:0.72
Consensus pattern (20 bp):
TTTTTTATTTTCGTTTGAAT
Found at i:18714 original size:24 final size:26
Alignment explanation
Indices: 18661--18714 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
18651 TATTTCGTTT
*
18661 TTTAAAATTTTATAGATATATATTAT
1 TTTAAAATTTTATAGATATATATTAC
18687 TTTAAAATTTTATTA-AT-T-TATTAC
1 TTTAAAATTTTA-TAGATATATATTAC
18711 TTTA
1 TTTA
18715 TAAAATTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 9 0.35
25 1 0.04
26 14 0.54
27 2 0.08
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
TTTAAAATTTTATAGATATATATTAC
Found at i:19023 original size:32 final size:33
Alignment explanation
Indices: 18987--19067 Score: 137
Period size: 32 Copynumber: 2.5 Consensus size: 33
18977 GCGTGTAAGC
18987 AATTCAATGGGCGAACCCCTGTTC-AAAACAAA
1 AATTCAATGGGCGAACCCCTGTTCAAAAACAAA
19019 AATTCAATGGGCGAACCCCTGTTCAAAAACAAA
1 AATTCAATGGGCGAACCCCTGTTCAAAAACAAA
* *
19052 AATCCATTGGGCGAAC
1 AATTCAATGGGCGAAC
19068 TAATAAAAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 24 0.52
33 22 0.48
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (33 bp):
AATTCAATGGGCGAACCCCTGTTCAAAAACAAA
Found at i:19395 original size:12 final size:13
Alignment explanation
Indices: 19378--19406 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
19368 TTTAATTGTG
19378 AAAATTAAAA-TT
1 AAAATTAAAATTT
19390 AAAATTAAAATTT
1 AAAATTAAAATTT
19403 AAAA
1 AAAA
19407 ATTTAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:21438 original size:85 final size:82
Alignment explanation
Indices: 21296--21573 Score: 236
Period size: 84 Copynumber: 3.3 Consensus size: 82
21286 AGGTGTCATC
* * * * *
21296 GAGCTTAATGGAATCGAACTCGACA-ATTTTGTTGACAGATAACCCTTATTGCCTTGAGCTATCC
1 GAGCTTAGTGTAATCGAACTCGA-AGGTTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATCC
* * * *
21360 TATAAATTTGATTTGCCTTT
65 TACAAA--TGATGTGACTTG
* *
21380 GAGCTTAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGC
1 GAGCTTAGTGTAATCGAACTCGAAGGT-TTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATCC
*
21445 TGCAAATGATGTGACTTG
65 TACAAATGATGTGACTTG
** * * * *
21463 GAGCCGAGTGTAATCGAACTCGAAGGTATTTGGTTGGCAGATAGCCCTTCTCA-ACTTAAGCTAT
1 GAGCTTAGTGTAATCGAACTCGAAGGT-TTT-GTTGACAGATAACCCTTCT-AGCCTTGAGCTAT
* * * * *
21527 GCTGCAAATGGTGTGCCTTC
63 CCTACAAATGATGTGACTTG
* * * *
21547 GAGCTGAGCGTAGTCGAACCCGAAGGT
1 GAGCTTAGTGTAATCGAACTCGAAGGT
21574 CTTTTGTGTT
Statistics
Matches: 163, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
83 38 0.23
84 87 0.53
85 38 0.23
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (82 bp):
GAGCTTAGTGTAATCGAACTCGAAGGTTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATCCT
ACAAATGATGTGACTTG
Found at i:21653 original size:21 final size:20
Alignment explanation
Indices: 21620--21716 Score: 70
Period size: 20 Copynumber: 5.2 Consensus size: 20
21610 TGTTTCAGAG
21620 AAACTGTCTCAAGAGAGACA
1 AAACTGTCTCAAGAGAGACA
*
21640 AAACTTGTTTC-A-AGAG---
1 AAAC-TGTCTCAAGAGAGACA
21656 AAACTGTCTCAAGAGAGACA
1 AAACTGTCTCAAGAGAGACA
* *
21676 AAACTTTTTTC-A-AGAG---
1 AAAC-TGTCTCAAGAGAGACA
*
21692 AAACTGTCTCAAGAGAGCCA
1 AAACTGTCTCAAGAGAGACA
21712 AAACT
1 AAACT
21717 TAGTTCCAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 24
0.66 0.07 0.27
Matches are distributed among these distances:
15 9 0.15
16 10 0.17
17 8 0.14
19 8 0.14
20 15 0.25
21 9 0.15
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.22
Consensus pattern (20 bp):
AAACTGTCTCAAGAGAGACA
Found at i:21658 original size:36 final size:36
Alignment explanation
Indices: 21610--22103 Score: 415
Period size: 36 Copynumber: 14.1 Consensus size: 36
21600 CAAAGGTTGG
*
21610 TGTTTC-AGAGAAACTGTCTCAAGAGAGACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
21645 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
*
21682 T-TTTCAAGAGAAACTGTCTCAAGAGAGCCAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * *
21718 AGTTCCAAAAGAAACTGTTTCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
21754 TGTTTAAAG-GAAAACATAT-TC-------ACAGATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
*
21783 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC--AATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
21817 TGATTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
21853 TGTTTCAAGAAAAACTGTCT-ATAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCA-AGAGAGACAAAA-TT
* * * * *
21890 AGTTCCAAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
21927 TGTTCCAAG-GAAA-----T----AGAGTCAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
21953 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * * *
21989 TGTTTTAAGAGAAAATATCTCATGAGAGGCAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
22025 TGTTTTAAGATAAACTGTCTCAAGAGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
** *
22062 TGTTTTGAGAGAATCTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
22099 TGTTT
1 TGTTT
22104 TGAGTAAATT
Statistics
Matches: 372, Mismatches: 56, Indels: 60
0.76 0.11 0.12
Matches are distributed among these distances:
26 15 0.04
27 4 0.01
28 2 0.01
29 19 0.05
30 2 0.01
32 1 0.00
34 32 0.09
35 12 0.03
36 179 0.48
37 83 0.22
38 22 0.06
39 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:21857 original size:99 final size:101
Alignment explanation
Indices: 21683--21867 Score: 241
Period size: 99 Copynumber: 1.8 Consensus size: 101
21673 ACAAAACTTT
* *
21683 TTTCAAGAGAAACTGTCTCAAGAGAGCCAAAACTTAGTTCCAAAAGAAACTGTTTCAAGGGAGAC
1 TTTCAAGAGAAACTGTCTCAAGAGAG-CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGAC
* *
21748 GAAATTTGTTTAAAGGAAAACATATTCACAGATTTTG
65 AAAATTTGTTTAAAGAAAAACATATTCACAGATTTTG
* * * **
21785 TTTCAAGGGAAACTGTCTCAAGAGAG-ACAA-TTTGATT-CAAGGGAAACTGTCTCAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCAAGAGAGCAAAACTTAG-TTCCAAAAGAAACTGTCTCAAGAGAGAC
*
21847 AAAATTTGTTTCAAGAAAAAC
65 AAAATTTGTTTAAAGAAAAAC
21868 TGTCTATAGA
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
99 42 0.58
100 5 0.07
102 25 0.35
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (101 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGCAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACA
AAATTTGTTTAAAGAAAAACATATTCACAGATTTTG
Found at i:22024 original size:172 final size:173
Alignment explanation
Indices: 21610--22058 Score: 642
Period size: 172 Copynumber: 2.6 Consensus size: 173
21600 CAAAGGTTGG
* *
21610 TGTTTC-AGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
* * *
21674 CAAAACTTT-TTTCAAGAGAAACTGTCTCAAGAGAGCCAAAACTTAGTTCCAAAAGAAACTGTTT
66 CAAAA-TTTGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCT
* * *
21738 CAAGGGAGACGAAATTTGTTTAAAGGAAAACATATTCACAGATTT
130 CAAGGGAGACGAAATTTGTTCAAAGGAAAACAGAGT-ACAGATTT
* *
21783 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC--AATTTGATTCAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
21846 CAAAATTTGTTTCAAGAAAAACTGTCT-ATAGAGAGACAAAACTTAGTTCCAAAAAGAAACTGTC
66 CAAAATTTGTTTCAAGAAAAACTGTCTCA-AGAGAGACAAAACTTAGTTCC-AAAAGAAACTGTC
* *
21910 TCAAGGGAGACGAAATTTGTTCCAAGG-AAATAGAGT-CAGATTT
129 TCAAGGGAGACGAAATTTGTTCAAAGGAAAACAGAGTACAGATTT
* * * * *
21953 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATATCTCATGAGAGG
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
* *
22018 CAAAATTTGTTTTAAGATAAACTGTCTCAAGAGAGACAAAA
66 CAAAATTTGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAA
22059 TTTTGTTTTG
Statistics
Matches: 248, Mismatches: 21, Indels: 15
0.87 0.07 0.05
Matches are distributed among these distances:
170 37 0.15
171 4 0.02
172 141 0.57
173 44 0.18
174 22 0.09
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (173 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
CAAAATTTGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTC
AAGGGAGACGAAATTTGTTCAAAGGAAAACAGAGTACAGATTT
Found at i:27946 original size:40 final size:40
Alignment explanation
Indices: 27902--27982 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
27892 TCGAAAATTT
27902 ACATATAAAACTCATAAAAATTAACCTTTCATCACTAAAA
1 ACATATAAAACTCATAAAAATTAACCTTTCATCACTAAAA
27942 ACATATAAAACTCATAAAAATTAACCTTTCATCACTAAAA
1 ACATATAAAACTCATAAAAATTAACCTTTCATCACTAAAA
27982 A
1 A
27983 TTCCCAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (40 bp):
ACATATAAAACTCATAAAAATTAACCTTTCATCACTAAAA
Found at i:27982 original size:21 final size:21
Alignment explanation
Indices: 27916--27984 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
27906 ATAAAACTCA
27916 TAAAAATTAACCTTTCATCAC
1 TAAAAATTAACCTTTCATCAC
**
27937 TAAAAACATATAA---AAC-TCA-
1 T-AAAA-AT-TAACCTTTCATCAC
27956 TAAAAATTAACCTTTCATCAC
1 TAAAAATTAACCTTTCATCAC
27977 TAAAAATT
1 TAAAAATT
27985 CCCAAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
16 3 0.08
17 2 0.06
18 4 0.11
19 2 0.06
20 6 0.17
21 10 0.28
22 4 0.11
23 2 0.06
24 3 0.08
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAAATTAACCTTTCATCAC
Found at i:35363 original size:44 final size:46
Alignment explanation
Indices: 35243--35368 Score: 159
Period size: 47 Copynumber: 2.8 Consensus size: 46
35233 TATATAATCT
*
35243 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
35288 CTTATCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
35335 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
35369 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 23 0.32
45 9 0.13
46 2 0.03
47 37 0.52
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:36719 original size:246 final size:245
Alignment explanation
Indices: 36285--36778 Score: 904
Period size: 246 Copynumber: 2.0 Consensus size: 245
36275 TTCAAATGCT
36285 TTTACAAAAGCATAAATACATTTAAGTACCCCAACTATGCAATTGTTGTACTTAAATCACCAATC
1 TTTACAAAAGCATAAATACATTTAAGTACCCCAACTATGCAATTGTTGTACTTAAATCACCAATC
36350 ATTTCAATCTTCCCAAATAATCAATTTCACATCTAACACTCATTTCAATTCCCGAACAACAATTT
66 ATTTCAATCTTCCCAAATAATCAA--TCACATCTAACACTCATTTCAATTCCCGAACAACAATTT
36415 CCAGCATAATACATCAATTATACAACTCTTACAACAACCCATTAATTTTCCAGAATTCAGACAAC
129 CCAGCATAATACATCAATTATACAACTCTTACAACAACCCATTAATTTTCCAGAATTCAGACAAC
36480 TCGCACTACCCTTAAAGAATCATTATTCTGTATTG-ATAGACACTCGAATTC
194 TCGCACTACCCTTAAAGAATCATTATTCTGTATTGAATAGACACTCGAATTC
36531 TTTACAAAAGCATAAATACATTTAAGTACCCCAACTATGCAATTGTTGTACTTAAATCACCAATC
1 TTTACAAAAGCATAAATACATTTAAGTACCCCAACTATGCAATTGTTGTACTTAAATCACCAATC
36596 ATTTCAATCTTCCCAAAATAATC-A-CACATCTAACCACTCATTTCAATTCCCGAACAACAATTT
66 ATTTCAATCTTCCC-AAATAATCAATCACATCTAA-CACTCATTTCAATTCCCGAACAACAATTT
36659 CCAGCATAATACATCAATTATACAACTCTTACACAACAACCCATTAATTTTCCAGAATTCAGACA
129 CCAGCATAATACATCAATTATACAACTCTT--ACAACAACCCATTAATTTTCCAGAATTCAGACA
36724 ACTCGCACTACCCTTAAAGAATCATTATTCTGTATTGATATAGACACTCGAATTC
192 ACTCGCACTACCCTTAAAGAATCATTATTCTGTATTGA-ATAGACACTCGAATTC
36779 AATTCCGTTT
Statistics
Matches: 242, Mismatches: 0, Indels: 10
0.96 0.00 0.04
Matches are distributed among these distances:
243 9 0.04
244 59 0.24
246 150 0.62
247 8 0.03
248 16 0.07
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (245 bp):
TTTACAAAAGCATAAATACATTTAAGTACCCCAACTATGCAATTGTTGTACTTAAATCACCAATC
ATTTCAATCTTCCCAAATAATCAATCACATCTAACACTCATTTCAATTCCCGAACAACAATTTCC
AGCATAATACATCAATTATACAACTCTTACAACAACCCATTAATTTTCCAGAATTCAGACAACTC
GCACTACCCTTAAAGAATCATTATTCTGTATTGAATAGACACTCGAATTC
Found at i:39606 original size:22 final size:23
Alignment explanation
Indices: 39580--39640 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
39570 TTAGTGTAGA
* *
39580 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
39602 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
39625 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
39641 CCCCCACAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:41467 original size:95 final size:94
Alignment explanation
Indices: 41302--41484 Score: 314
Period size: 95 Copynumber: 1.9 Consensus size: 94
41292 TGTAAATATC
* *
41302 TTTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGACA
1 TTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGACA
*
41367 GCTCAAGCTTTATTGTATAGTATAATCACA
66 ACTCAAGCTTTATTGTATA-TATAATCACA
41397 TTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTG-CTCTAGAGGGAC
1 TTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCT-TAGAGGGAC
41461 AACTCAAGCTTTATTGTATATATA
65 AACTCAAGCTTTATTGTATATATA
41485 TAATATTATA
Statistics
Matches: 84, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
94 6 0.07
95 78 0.93
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (94 bp):
TTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGACA
ACTCAAGCTTTATTGTATATATAATCACA
Found at i:44794 original size:21 final size:21
Alignment explanation
Indices: 44770--44819 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
44760 TTCAAATCCT
*
44770 GATACATTTTATTTCCACCTA
1 GATACATCTTATTTCCACCTA
*
44791 GATACATCTTATTTTCACCTAA
1 GATACATCTTATTTCCACCT-A
44813 GA-ACATC
1 GATACATC
44820 ATCAAAGGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (21 bp):
GATACATCTTATTTCCACCTA
Found at i:48070 original size:18 final size:19
Alignment explanation
Indices: 48043--48084 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
48033 CGGTCCAAAA
* *
48043 CGGTCTGAA-CGGGTTGAC
1 CGGTCCGAACCGGGATGAC
48061 CGGTCCGAACCGGGATGAC
1 CGGTCCGAACCGGGATGAC
48080 CGGTC
1 CGGTC
48085 TGACCCAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.17, C:0.29, G:0.38, T:0.17
Consensus pattern (19 bp):
CGGTCCGAACCGGGATGAC
Found at i:48124 original size:18 final size:18
Alignment explanation
Indices: 48092--48136 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
48082 GTCTGACCCA
48092 ACCCGTTGA-CCGACCAG
1 ACCCGTTGACCCGACCAG
*
48109 ACCCGTTGACCCGACCCG
1 ACCCGTTGACCCGACCAG
*
48127 ACCCGGTGAC
1 ACCCGTTGAC
48137 ATTCTGGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.20, C:0.44, G:0.24, T:0.11
Consensus pattern (18 bp):
ACCCGTTGACCCGACCAG
Found at i:48289 original size:29 final size:28
Alignment explanation
Indices: 48131--48292 Score: 141
Period size: 29 Copynumber: 5.8 Consensus size: 28
48121 GACCCGACCC
* *
48131 GGTGACATTCTGGGAATTATTATGAAAAA
1 GGTGACATTTTGGGAATT-TTTTGAAAAA
*
48160 GGTGATATTTTGGGAATTTTTGTGAAAAA
1 GGTGACATTTTGGGAATTTTT-TGAAAAA
* * * **
48189 TGTGACATTCT-AG-ATTTTTT-TTAAA
1 GGTGACATTTTGGGAATTTTTTGAAAAA
* *
48214 GATGACATTTCGGGAATTTTTGTGAAAAA
1 GGTGACATTTTGGGAATTTTT-TGAAAAA
* *
48243 TGTGACATTCTGGGAATTATTTTGAAAAA
1 GGTGACATTTTGGGAATT-TTTTGAAAAA
**
48272 GGTGACATTTTGATAATTTTT
1 GGTGACATTTTGGGAATTTTT
48293 GAATGTGGAC
Statistics
Matches: 103, Mismatches: 24, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
25 10 0.10
26 2 0.02
27 12 0.12
28 7 0.07
29 69 0.67
30 3 0.03
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.41
Consensus pattern (28 bp):
GGTGACATTTTGGGAATTTTTTGAAAAA
Found at i:49396 original size:26 final size:26
Alignment explanation
Indices: 49317--49385 Score: 120
Period size: 26 Copynumber: 2.7 Consensus size: 26
49307 AGGGTAACTA
49317 TTTTATGAGATTTACTGCAGTACAAT
1 TTTTATGAGATTTACTGCAGTACAAT
*
49343 TTTTATGAGATTTATTGCAGTACAAT
1 TTTTATGAGATTTACTGCAGTACAAT
*
49369 TTTTATGAGATATACTG
1 TTTTATGAGATTTACTG
49386 GACTATGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (26 bp):
TTTTATGAGATTTACTGCAGTACAAT
Found at i:55543 original size:19 final size:19
Alignment explanation
Indices: 55519--55595 Score: 102
Period size: 19 Copynumber: 4.1 Consensus size: 19
55509 TTAATTGGTT
* *
55519 AACCGGCTTGACCGGTCTG
1 AACCGGGTTGACCGATCTG
*
55538 AACC-GGTCTGACCGATCCG
1 AACCGGGT-TGACCGATCTG
55557 AACCGGGTTGACCGATCTG
1 AACCGGGTTGACCGATCTG
*
55576 AACCGGGTTGACCGGTCTG
1 AACCGGGTTGACCGATCTG
55595 A
1 A
55596 CCCGACCCGT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
18 2 0.04
19 46 0.90
20 3 0.06
ACGTcount: A:0.19, C:0.30, G:0.31, T:0.19
Consensus pattern (19 bp):
AACCGGGTTGACCGATCTG
Found at i:55544 original size:10 final size:10
Alignment explanation
Indices: 55529--55595 Score: 54
Period size: 10 Copynumber: 7.0 Consensus size: 10
55519 AACCGGCTTG
55529 ACCGGTCTGA
1 ACCGGTCTGA
55539 ACCGGTCTG-
1 ACCGGTCTGA
* *
55548 ACCGATCCGA
1 ACCGGTCTGA
55558 ACCGGGT-TG-
1 ACC-GGTCTGA
*
55567 ACCGATCTGA
1 ACCGGTCTGA
55577 ACCGGGT-TG-
1 ACC-GGTCTGA
55586 ACCGGTCTGA
1 ACCGGTCTGA
55596 CCCGACCCGT
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
8 5 0.11
9 17 0.39
10 18 0.41
11 4 0.09
ACGTcount: A:0.19, C:0.30, G:0.31, T:0.19
Consensus pattern (10 bp):
ACCGGTCTGA
Found at i:55551 original size:9 final size:9
Alignment explanation
Indices: 55527--55597 Score: 56
Period size: 9 Copynumber: 7.6 Consensus size: 9
55517 TTAACCGGCT
55527 TGACCGGTC
1 TGACCGGTC
55536 TGAACCGGTC
1 TG-ACCGGTC
*
55546 TGACCGATC
1 TGACCGGTC
*
55555 CGAACCGGGT-
1 TG-ACC-GGTC
*
55565 TGACCGATC
1 TGACCGGTC
55574 TGAACCGGGT-
1 TG-ACC-GGTC
55584 TGACCGGTC
1 TGACCGGTC
55593 TGACC
1 TGACC
55598 CGACCCGTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
8 5 0.10
9 22 0.45
10 18 0.37
11 4 0.08
ACGTcount: A:0.18, C:0.31, G:0.31, T:0.20
Consensus pattern (9 bp):
TGACCGGTC
Found at i:55616 original size:17 final size:18
Alignment explanation
Indices: 55594--55639 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 18
55584 TGACCGGTCT
*
55594 GACCCGACCCGTTAA-TC
1 GACCCGACCCGTTAACCC
55611 GACCCGACCCGTTAACCC
1 GACCCGACCCGTTAACCC
55629 GACCCGACCCG
1 GACCCGACCCG
55640 GTGACATTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.22, C:0.48, G:0.20, T:0.11
Consensus pattern (18 bp):
GACCCGACCCGTTAACCC
Found at i:55695 original size:29 final size:27
Alignment explanation
Indices: 55639--55818 Score: 157
Period size: 29 Copynumber: 6.3 Consensus size: 27
55629 GACCCGACCC
*
55639 GGTGACATTCTAGGAATTATTTTGAAAAA
1 GGTGACATTCT-GGGATT-TTTTGAAAAA
* *
55668 TGTGACATTTTGGGATTTTTGTGAAAAAA
1 GGTGACATTCTGGGATTTTT-TG-AAAAA
* *
55697 TGTGACATTCT-GGATTTTTTTAAAAAA
1 GGTGACATTCTGGGA-TTTTTTGAAAAA
** * *
55724 AATGACATT-TCGGGAATTTTGTGAAAAG
1 GGTGACATTCT-GGG-ATTTTTTGAAAAA
*
55752 GGTGACATTCTGGGAATTATTTTGAGAAA
1 GGTGACATTCTGGG-ATT-TTTTGAAAAA
55781 GGTGACATTCTGGGTATTATTTTGAAAAA
1 GGTGACATTCTGGG-ATT-TTTTGAAAAA
55810 GGTGACATT
1 GGTGACATT
55819 TTGGTAATTT
Statistics
Matches: 126, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
26 1 0.01
27 15 0.12
28 36 0.29
29 74 0.59
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (27 bp):
GGTGACATTCTGGGATTTTTTGAAAAA
Found at i:55744 original size:56 final size:56
Alignment explanation
Indices: 55639--55827 Score: 175
Period size: 56 Copynumber: 3.3 Consensus size: 56
55629 GACCCGACCC
* ** * *
55639 GGTGACATTCTAGGAATTATTTTGAAAAATGTGACATTTTGGGATTTTTGTGAAAAAA
1 GGTGACATTCT-GGAATTATTTTAAAAAAAATGACATTTCGGGAATTTTGTG-AAAAA
* * *
55697 TGTGACATTCTGG-ATTTTTTTAAAAAAAATGACATTTCGGGAATTTTGTGAAAAG
1 GGTGACATTCTGGAATTATTTTAAAAAAAATGACATTTCGGGAATTTTGTGAAAAA
* * ** * *
55752 GGTGACATTCTGGGAATTATTTTGAGAAAGGTGACA-TTCTGGGTATTATTTTGAAAAA
1 GGTGACATTCT-GGAATTATTTTAAAAAAAATGACATTTC-GGGAATT-TTGTGAAAAA
*
55810 GGTGACATTTTGGTAATT
1 GGTGACATTCTGG-AATT
55828 TTCGAATGTG
Statistics
Matches: 108, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
55 14 0.13
56 36 0.33
57 26 0.24
58 32 0.30
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.38
Consensus pattern (56 bp):
GGTGACATTCTGGAATTATTTTAAAAAAAATGACATTTCGGGAATTTTGTGAAAAA
Found at i:57533 original size:55 final size:55
Alignment explanation
Indices: 57466--57814 Score: 500
Period size: 55 Copynumber: 6.3 Consensus size: 55
57456 TTTATTAAGA
* * *
57466 TGCACACATAGTGCCTTTACGGTTATTCATCAATTCATGATGAATTCTGTGGTTT
1 TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGTTT
*
57521 TGCACACTTAGTGCCTGTACTGTTATTCATCAACTCATGATGAATTCTGTGGTTT
1 TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGTTT
* * * * * * *
57576 TGTACACTTAGTGTCTATACAGTTATTCATCAACTCATTATGAATTTTGTTGTTT
1 TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGTTT
* *
57631 TGCACACTTAGTGCCTGTACGATTATTCATCAACTCATGATGAATTATGTGGTTT
1 TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGTTT
* * * *
57686 TGCACACTTAGTGCATGTACGCTAATTCATCAACTCATGATGAATTCTATGGTTT
1 TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGTTT
* * * *
57741 TGCACATTTAGTGCATGTACGATTATTCATCAACTCATGATGAATTCCGTGGTTT
1 TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGTTT
*
57796 TGTACACTTAGTGCCTGTA
1 TGCACACTTAGTGCCTGTA
57815 GTACACATAG
Statistics
Matches: 262, Mismatches: 32, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 262 1.00
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (55 bp):
TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGTTT
Found at i:58184 original size:22 final size:19
Alignment explanation
Indices: 58142--58212 Score: 79
Period size: 19 Copynumber: 3.5 Consensus size: 19
58132 TGGCTCCTCA
* *
58142 GTATCGATACCCATACCATG
1 GTATCGATA-CTATACTATG
58162 GTATCGATACTAATATACTATG
1 GTATCGATAC---TATACTATG
*
58184 GTAACGATACTATACTATG
1 GTATCGATACTATACTATG
58203 GTATCGATAC
1 GTATCGATAC
58213 CATTTTTGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 19 0.43
20 9 0.20
22 16 0.36
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (19 bp):
GTATCGATACTATACTATG
Found at i:64193 original size:81 final size:81
Alignment explanation
Indices: 64095--64587 Score: 752
Period size: 81 Copynumber: 6.1 Consensus size: 81
64085 AAGCATTTAG
* * *
64095 TCTTTTACTCAAAGGTATTTAACATTTTATCTAACTGGCATAATTGACACCTTTATGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
64160 ACATCTAGGCCATTAA
66 ACAACTAGGCCATTAA
* *
64176 TCTTTTACTCAAAGGTATTTAACCTTTCATGTAACTGACATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
64241 ACAACTAGGCCATTAA
66 ACAACTAGGCCATTAA
* * *
64257 TCTTTTACTCAAAGTTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTATGTCAAATAC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
64322 ACAGCTAGGCCATTAA
66 ACAACTAGGCCATTAA
* * *
64338 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCACAATTGACATCTTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
64403 ACAACTAGGCCATTAA
66 ACAACTAGGCCATTAA
** *
64419 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTACATAATTGACAGCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
* *
64484 ACACCTAGGCCATAAA
66 ACAACTAGGCCATTAA
* * * * * *
64500 TCTTTTACTCAAAGGTATTTAACATTTTATCTAATTGGCATAATTGACACATTTCTATCCAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
64565 ACAACTAGGTCATTAA
66 ACAACTAGGCCATTAA
*
64581 TATTTTA
1 TCTTTTA
64588 TTTAGAACAG
Statistics
Matches: 373, Mismatches: 39, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 373 1.00
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
ACAACTAGGCCATTAA
Found at i:66667 original size:21 final size:21
Alignment explanation
Indices: 66637--66676 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
66627 TATAAGATGA
*
66637 TATAACACATGTGAGCTAATG
1 TATAACACATATGAGCTAATG
*
66658 TATAAGACATATGAGCTAA
1 TATAACACATATGAGCTAA
66677 ATTTAATGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (21 bp):
TATAACACATATGAGCTAATG
Done.