Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006404.1 Hibiscus syriacus cultivar Beakdansim tig00015441_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: 99634
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1772 original size:16 final size:16
Alignment explanation
Indices: 1746--1790 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
1736 TAATATTGAA
1746 ACTCG-ACTCGAAAAG
1 ACTCGAACTCGAAAAG
1761 ACTCGAACTCGAAAAG
1 ACTCGAACTCGAAAAG
*
1777 ACTCAAACTC-AAAA
1 ACTCGAACTCGAAAA
1791 AAAAAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.47, C:0.27, G:0.13, T:0.13
Consensus pattern (16 bp):
ACTCGAACTCGAAAAG
Found at i:11262 original size:33 final size:33
Alignment explanation
Indices: 11220--11332 Score: 131
Period size: 33 Copynumber: 3.4 Consensus size: 33
11210 TCCAACATGT
11220 TATAATTTCAGTTAATAAGGATTTGAATAAGTA
1 TATAATTTCAGTTAATAAGGATTTGAATAAGTA
* *** *
11253 TATAATTTCAGTAAATCACTCTCATTGGAA-AATGT-
1 TATAATTTCAGTTAAT-A--AGGATTTGAATAA-GTA
11288 TATAATTTCAGTTAATAAGGATTTGAATAAGTA
1 TATAATTTCAGTTAATAAGGATTTGAATAAGTA
11321 TATAATTTCAGT
1 TATAATTTCAGT
11333 AAATCACTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
32 8 0.12
33 29 0.45
34 2 0.03
35 17 0.27
36 8 0.12
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (33 bp):
TATAATTTCAGTTAATAAGGATTTGAATAAGTA
Found at i:11299 original size:35 final size:35
Alignment explanation
Indices: 11253--11363 Score: 131
Period size: 35 Copynumber: 3.2 Consensus size: 35
11243 TGAATAAGTA
11253 TATAATTTCAGTAAATCACTCTCATTGGAAAATGT
1 TATAATTTCAGTAAATCACTCTCATTGGAAAATGT
* *** *
11288 TATAATTTCAGTTAAT-A--AGGATTTGAATAA-GT
1 TATAATTTCAGTAAATCACTCTCATTGGAA-AATGT
11320 ATATAATTTCAGTAAATCACTCTCATTGGAAAATGT
1 -TATAATTTCAGTAAATCACTCTCATTGGAAAATGT
11356 TATAATTT
1 TATAATTT
11364 GTTTAAAGTG
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
32 8 0.13
33 17 0.28
34 2 0.03
35 25 0.42
36 8 0.13
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.40
Consensus pattern (35 bp):
TATAATTTCAGTAAATCACTCTCATTGGAAAATGT
Found at i:11325 original size:68 final size:68
Alignment explanation
Indices: 11216--11363 Score: 296
Period size: 68 Copynumber: 2.2 Consensus size: 68
11206 GACATCCAAC
11216 ATGTTATAATTTCAGTTAATAAGGATTTGAATAAGTATATAATTTCAGTAAATCACTCTCATTGG
1 ATGTTATAATTTCAGTTAATAAGGATTTGAATAAGTATATAATTTCAGTAAATCACTCTCATTGG
11281 AAA
66 AAA
11284 ATGTTATAATTTCAGTTAATAAGGATTTGAATAAGTATATAATTTCAGTAAATCACTCTCATTGG
1 ATGTTATAATTTCAGTTAATAAGGATTTGAATAAGTATATAATTTCAGTAAATCACTCTCATTGG
11349 AAA
66 AAA
11352 ATGTTATAATTT
1 ATGTTATAATTT
11364 GTTTAAAGTG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 80 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (68 bp):
ATGTTATAATTTCAGTTAATAAGGATTTGAATAAGTATATAATTTCAGTAAATCACTCTCATTGG
AAA
Found at i:20935 original size:8 final size:7
Alignment explanation
Indices: 20922--20987 Score: 50
Period size: 8 Copynumber: 9.3 Consensus size: 7
20912 GTAAAAAATA
20922 AAATAATT
1 AAATAA-T
20930 AAATAA-
1 AAATAAT
20936 AAA-AAT
1 AAATAAT
*
20942 AAAAAAAT
1 -AAATAAT
20950 AAATAAT
1 AAATAAT
20957 ACAATAATT
1 A-AATAA-T
20966 AAATAATT
1 AAATAA-T
20974 AAAT-A-
1 AAATAAT
20979 AAATAAT
1 AAATAAT
20986 AA
1 AA
20988 CAAAATATTA
Statistics
Matches: 50, Mismatches: 1, Indels: 15
0.76 0.02 0.23
Matches are distributed among these distances:
5 6 0.12
6 4 0.08
7 13 0.26
8 25 0.50
9 2 0.04
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATAAT
Found at i:20964 original size:36 final size:36
Alignment explanation
Indices: 20913--20994 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 36
20903 TTTATAACTG
20913 TAAAAAATAAAATAATTAAATAAAAAAATAAAAAAA
1 TAAAAAATAAAATAATTAAATAAAAAAATAAAAAAA
* * ** *
20949 TAAATAATACAATAATTAAATAATTAAATAAAATAA
1 TAAAAAATAAAATAATTAAATAAAAAAATAAAAAAA
20985 TAACAAAATA
1 TAA-AAAATA
20995 TTAAATATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 34 0.87
37 5 0.13
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (36 bp):
TAAAAAATAAAATAATTAAATAAAAAAATAAAAAAA
Found at i:20993 original size:16 final size:15
Alignment explanation
Indices: 20916--20994 Score: 53
Period size: 16 Copynumber: 5.4 Consensus size: 15
20906 ATAACTGTAA
20916 AAAATAAAATAATTA-
1 AAAATAAAATAA-TAC
*
20931 AATAAAAAAATAA-A-
1 AA-AATAAAATAATAC
20945 AAAAT-AAATAATAC
1 AAAATAAAATAATAC
*
20959 AATAATTAAATAAT--
1 AA-AATAAAATAATAC
*
20973 TAAATAAAATAATAAC
1 AAAATAAAATAAT-AC
20989 AAAATA
1 AAAATA
20995 TTAAATATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
12 6 0.12
13 13 0.25
14 6 0.12
15 5 0.10
16 21 0.41
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAATAAAATAATAC
Found at i:21009 original size:17 final size:18
Alignment explanation
Indices: 20979--21012 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20969 TAATTAAATA
20979 AAATAATAACAAAATATT
1 AAATAATAACAAAATATT
*
20997 AAAT-ATAATAAAATAT
1 AAATAATAACAAAATAT
21013 AACTTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAATAACAAAATATT
Found at i:25255 original size:2 final size:2
Alignment explanation
Indices: 25248--25272 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25238 TTATAGTTGA
25248 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 A
25273 AACTATAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25316 original size:25 final size:25
Alignment explanation
Indices: 25288--25338 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
25278 TAGTTAATAT
25288 AGGATTTAAAGTGAAATGAGTTTAA
1 AGGATTTAAAGTGAAATGAGTTTAA
25313 AGGATTTAAAGTGAAATGAGTTTAA
1 AGGATTTAAAGTGAAATGAGTTTAA
25338 A
1 A
25339 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.31
Consensus pattern (25 bp):
AGGATTTAAAGTGAAATGAGTTTAA
Found at i:25380 original size:27 final size:27
Alignment explanation
Indices: 25333--25387 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
25323 GTGAAATGAG
*
25333 TTTAAAATTTTTATATTTTTAAAATAA
1 TTTAAAATTTTTATATCTTTAAAATAA
* *
25360 TTTAATATTTTCTATA-CTTTATAATAA
1 TTTAAAATTTT-TATATCTTTAAAATAA
25387 T
1 T
25388 GAAAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTAAAATTTTTATATCTTTAAAATAA
Found at i:28949 original size:35 final size:35
Alignment explanation
Indices: 28903--28990 Score: 167
Period size: 35 Copynumber: 2.5 Consensus size: 35
28893 CTATAGTTTA
28903 ATATATATATATAGTAAATACCAATTGATAACTAT
1 ATATATATATATAGTAAATACCAATTGATAACTAT
28938 ATATATATATATAGTAAATACCAATTGATAACTAT
1 ATATATATATATAGTAAATACCAATTGATAACTAT
*
28973 ATATATATATATATTAAA
1 ATATATATATATAGTAAA
28991 CTATAGTTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.39
Consensus pattern (35 bp):
ATATATATATATAGTAAATACCAATTGATAACTAT
Found at i:30772 original size:2 final size:2
Alignment explanation
Indices: 30765--30823 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
30755 TAGATTACAA
30765 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
30807 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
30824 ATTATTTTAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31562 original size:12 final size:12
Alignment explanation
Indices: 31537--31577 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
31527 AAAAAGGTTG
* *
31537 TTTTAAAATAAT
1 TTTTAAAGTTAT
31549 TTTTAAAGTTATT
1 TTTTAAAGTTA-T
31562 TTTTAAAGTTAT
1 TTTTAAAGTTAT
31574 TTTT
1 TTTT
31578 TTAAAATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 14 0.54
13 12 0.46
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (12 bp):
TTTTAAAGTTAT
Found at i:31582 original size:14 final size:13
Alignment explanation
Indices: 31548--31578 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
31538 TTTAAAATAA
31548 TTTTTAAAGTTAT
1 TTTTTAAAGTTAT
31561 TTTTTAAAGTTAT
1 TTTTTAAAGTTAT
31574 TTTTT
1 TTTTT
31579 TAAAATACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (13 bp):
TTTTTAAAGTTAT
Found at i:36769 original size:28 final size:29
Alignment explanation
Indices: 36700--36775 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
36690 AGACTTTCAT
*
36700 GTGTTGAAATTGATGATATGTCACATGTCAA
1 GTGTTGAAAGTGATG--ATGTCACATGTCAA
*
36731 GTGTCT-AAAGTGATGATGTCACATGTCAC
1 GTGT-TGAAAGTGATGATGTCACATGTCAA
36760 GT-TTGAAAGTGATGAT
1 GTGTTGAAAGTGATGAT
36776 ATTACATATG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
27 1 0.02
28 12 0.29
29 15 0.37
31 12 0.29
32 1 0.02
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (29 bp):
GTGTTGAAAGTGATGATGTCACATGTCAA
Found at i:36782 original size:28 final size:29
Alignment explanation
Indices: 36700--36782 Score: 89
Period size: 28 Copynumber: 2.8 Consensus size: 29
36690 AGACTTTCAT
*
36700 GTGTTGAAATTGATGATATGTCACATGTCAA
1 GTGTTGAAAGTGATGATAT-T-ACATGTCAA
* * *
36731 GTGTCT-AAAGTGATGATGTCACATGTCAC
1 GTGT-TGAAAGTGATGATATTACATGTCAA
36760 GT-TTGAAAGTGATGATATTACAT
1 GTGTTGAAAGTGATGATATTACAT
36783 ATGTTGTGTG
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
27 1 0.02
28 17 0.39
29 10 0.23
31 15 0.34
32 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (29 bp):
GTGTTGAAAGTGATGATATTACATGTCAA
Found at i:42090 original size:3 final size:3
Alignment explanation
Indices: 42082--42152 Score: 83
Period size: 3 Copynumber: 24.0 Consensus size: 3
42072 AAAATATTTG
* * **
42082 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TGA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42126 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
42153 ATAACGAACG
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
2 3 0.05
3 55 0.90
4 3 0.05
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:42380 original size:43 final size:44
Alignment explanation
Indices: 42333--42696 Score: 244
Period size: 43 Copynumber: 8.5 Consensus size: 44
42323 CTCATACGCA
* *
42333 ATGAAGAGGTCTGGTCATCTAAGGG-TGACACGGCTCATACGTG
1 ATGAGGAGGTCTGGTCATCTAAGGGATGACACGGCTCCTACGTG
* * * * *
42376 ATGAAGAGATCTGG---TCT-GGGGATGACACGGTTCCTACATG
1 ATGAGGAGGTCTGGTCATCTAAGGGATGACACGGCTCCTACGTG
* * *
42416 ATGAGGACGG-CTGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
1 ATGAGGA-GGTCTGGTCATCT-AAGG-GATGACACGGCTCCTACGTG
* * *
42462 ATGAGGACGG-CTGGTTATCT-ATGGTTGACACGGCTCCTACGTG
1 ATGAGGA-GGTCTGGTCATCTAAGGGATGACACGGCTCCTACGTG
* * * * *
42505 ATGAAGAGATCTGG---TCT-GGGGATGACACGGTTCCTACATG
1 ATGAGGAGGTCTGGTCATCTAAGGGATGACACGGCTCCTACGTG
* * *
42545 ATGAGGACGG-CTGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
1 ATGAGGA-GGTCTGGTCATCT-AAGG-GATGACACGGCTCCTACGTG
* * * *
42591 ATGAGGACGG-CTGGTTATCT-ATGGTTGACACGGCTCATACGTG
1 ATGAGGA-GGTCTGGTCATCTAAGGGATGACACGGCTCCTACGTG
* * * *
42634 ATGAGGAGATCTGG---TCT-GGGGAATGACACGACTCATACGTG
1 ATGAGGAGGTCTGGTCATCTAAGGG-ATGACACGGCTCCTACGTG
*
42675 ATGAGGAGATCTGGTCATCTAA
1 ATGAGGAGGTCTGGTCATCTAA
42697 AGGAGTTATG
Statistics
Matches: 258, Mismatches: 41, Indels: 42
0.76 0.12 0.12
Matches are distributed among these distances:
39 3 0.01
40 64 0.25
41 33 0.13
42 2 0.01
43 73 0.28
44 7 0.03
45 4 0.02
46 72 0.28
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (44 bp):
ATGAGGAGGTCTGGTCATCTAAGGGATGACACGGCTCCTACGTG
Found at i:42418 original size:40 final size:41
Alignment explanation
Indices: 42358--42678 Score: 186
Period size: 46 Copynumber: 7.5 Consensus size: 41
42348 CATCTAAGGG
* * *
42358 TGACACGGCTCATACGTGATGAAGA-GATCTGG-TCTGGGGA
1 TGACACGGTTCCTACGTGATGAAGACG-GCTGGATCTGGGGA
* * *
42398 TGACACGGTTCCTACATGATGAGGACGGCTGGCCATCTAAAGGTGA
1 TGACACGGTTCCTACGTGATGAAGACGGCTGG--ATCT---GGGGA
* * ** *
42444 TAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
1 TGACACGGTTCCTACGTGATGAAGACGGCTGG--ATCTGGGGA
* *
42487 TGACACGGCTCCTACGTGATGAAGA-GATCTGG-TCTGGGGA
1 TGACACGGTTCCTACGTGATGAAGACG-GCTGGATCTGGGGA
* * *
42527 TGACACGGTTCCTACATGATGAGGACGGCTGGCCATCTAAAGGTGA
1 TGACACGGTTCCTACGTGATGAAGACGGCTGG--ATCT---GGGGA
* * ** *
42573 TAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
1 TGACACGGTTCCTACGTGATGAAGACGGCTGG--ATCTGGGGA
* * * *
42616 TGACACGGCTCATACGTGATGAGGA-GATCTGG-TCTGGGGAA
1 TGACACGGTTCCTACGTGATGAAGACG-GCTGGATCTGGGG-A
** *
42657 TGACACGACTCATACGTGATGA
1 TGACACGGTTCCTACGTGATGA
42679 GGAGATCTGG
Statistics
Matches: 222, Mismatches: 42, Indels: 33
0.75 0.14 0.11
Matches are distributed among these distances:
40 61 0.27
41 23 0.10
42 2 0.01
43 60 0.27
46 76 0.34
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (41 bp):
TGACACGGTTCCTACGTGATGAAGACGGCTGGATCTGGGGA
Found at i:42467 original size:46 final size:45
Alignment explanation
Indices: 42400--42640 Score: 232
Period size: 46 Copynumber: 5.5 Consensus size: 45
42390 TCTGGGGATG
*
42400 ACACGGTTCCTACATGATGAGGACGGCTGGCCATCTAAAGGTGATA
1 ACACGGTTCCTACGTGATGAGGACGGCTGGCCATCT-AAGGTGATA
** * *
42446 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT--TG
1 ACACGGTTCCTACGTGATGAGGACGGCTGGCCATCTAAGGTGATA
* * * * *
42489 ACACGGCTCCTACGTGATGAAGA-GATCTGG---TCT--GGGGATG
1 ACACGGTTCCTACGTGATGAGGACG-GCTGGCCATCTAAGGTGATA
*
42529 ACACGGTTCCTACATGATGAGGACGGCTGGCCATCTAAAGGTGATA
1 ACACGGTTCCTACGTGATGAGGACGGCTGGCCATCT-AAGGTGATA
** * *
42575 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT--TG
1 ACACGGTTCCTACGTGATGAGGACGGCTGGCCATCTAAGGTGATA
* *
42618 ACACGGCTCATACGTGATGAGGA
1 ACACGGTTCCTACGTGATGAGGA
42641 GATCTGGTCT
Statistics
Matches: 163, Mismatches: 22, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
38 2 0.01
40 29 0.18
41 1 0.01
42 1 0.01
43 51 0.31
45 8 0.05
46 71 0.44
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (45 bp):
ACACGGTTCCTACGTGATGAGGACGGCTGGCCATCTAAGGTGATA
Found at i:42573 original size:129 final size:129
Alignment explanation
Indices: 42343--42699 Score: 590
Period size: 129 Copynumber: 2.8 Consensus size: 129
42333 ATGAAGAGGT
* * *
42343 CTGGTCATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTT
1 CTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTT
42408 CCTACATGATGAGGACGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
66 CCTACATGATGAGGACGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
*
42472 CTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTT
1 CTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTT
42537 CCTACATGATGAGGACGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
66 CCTACATGATGAGGACGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
* **
42601 CTGGTTATCTATGGTTGACACGGCTCATACGTGATGAGGAGATCTGGTCTGGGGAATGACACGAC
1 CTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGG-ATGACACGGT
* * * *
42666 TCATACGTGATGAGGA-GATCTGGTCATCTAAAGG
65 TCCTACATGATGAGGACG-GCTGGCCATCTAAAGG
42700 AGTTATGGTT
Statistics
Matches: 214, Mismatches: 12, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
129 178 0.83
130 36 0.17
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (129 bp):
CTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTT
CCTACATGATGAGGACGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
Found at i:42845 original size:63 final size:62
Alignment explanation
Indices: 42777--42894 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 62
42767 TTTCAAAAGC
*
42777 AACTGTCTCAAAAGAGACAAAATTTTGTTTCAAA-GGAAATGA-CTCAAAGATTGTTTAAAGGAA
1 AACTGTCTCAAAAGAGACAAAA-TTCGTTT-AAAGGGAAATGATCTCAAAGA-TGTTTAAAGGAA
* *
42840 AACTGTCTCGAATGAGACAAAATTCGTTTAAAGGGAAATGATCTCAAAGATGTTT
1 AACTGTCTCAAAAGAGACAAAATTCGTTTAAAGGGAAATGATCTCAAAGATGTTT
42895 GTTTTGTTTC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
61 3 0.06
62 19 0.38
63 28 0.56
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (62 bp):
AACTGTCTCAAAAGAGACAAAATTCGTTTAAAGGGAAATGATCTCAAAGATGTTTAAAGGAA
Found at i:43132 original size:30 final size:30
Alignment explanation
Indices: 43086--43151 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
43076 AGAGACAAAA
* *
43086 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTTTTTCAAAAGAAACAAACTCAAAGAT
*
43116 TTTTTTTTCAAAAGAAACAATCTCAAAGAT
1 TTTTTTTTCAAAAGAAACAAACTCAAAGAT
43146 TTTTTT
1 TTTTTT
43152 ACAAAATTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (30 bp):
TTTTTTTTCAAAAGAAACAAACTCAAAGAT
Found at i:43212 original size:50 final size:53
Alignment explanation
Indices: 43137--43237 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 53
43127 AAGAAACAAT
*
43137 CTCAAAGATTTTTTTACAAAATTGTCT-AA-AGAGACAAAACTTTGTTTCAGA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
43188 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
43238 AAAGATTCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 16 0.35
51 10 0.22
52 20 0.43
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.34
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:43532 original size:36 final size:35
Alignment explanation
Indices: 43448--43578 Score: 126
Period size: 36 Copynumber: 3.7 Consensus size: 35
43438 GAGAAAATGA
* *
43448 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGAC-AAATTTGTTTTTAGAGAAAT
* **
43482 AGTCTCAAATGAGACAACATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAA-ATTTGTTTTTAGAGAAAT
43518 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA-
1 TGTCTCAAGCGAGACAAA-TTTGTTTTTAGAGAAAT
* *
43552 CGATCTCAAGCGAGATCAACTTTGTTT
1 TG-TCTCAAGCGAGA-CAAATTTGTTT
43579 AATGTGAAAC
Statistics
Matches: 81, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
33 2 0.02
34 18 0.22
35 30 0.37
36 31 0.38
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAATTTGTTTTTAGAGAAAT
Found at i:51857 original size:3 final size:3
Alignment explanation
Indices: 51849--51916 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
51839 AAAATATTTG
* * **
51849 TAA TAA TAAA TAA TAA TAA TAA TAA -GA TGA CGA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
51894 TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
51917 CGAACGAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 3 0.05
3 52 0.90
4 3 0.05
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:56371 original size:14 final size:12
Alignment explanation
Indices: 56342--56368 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
56332 ATACGTAAAT
56342 AAAGAAGAGAAA
1 AAAGAAGAGAAA
56354 AAAGAAGAGAAA
1 AAAGAAGAGAAA
56366 AAA
1 AAA
56369 AAGCTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAGAAGAGAAA
Found at i:56761 original size:28 final size:28
Alignment explanation
Indices: 56713--56766 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
56703 TGAAAATGAG
* *
56713 TTTAAATTTTTTATATTTTTAAAATATA
1 TTTAAATTTTCTATATCTTTAAAATATA
*
56741 TTTAATATTTTCTATA-CTTTATAATA
1 TTTAA-ATTTTCTATATCTTTAAAATA
56767 ATGAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 13 0.59
29 9 0.41
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTAAATTTTCTATATCTTTAAAATATA
Found at i:58171 original size:32 final size:31
Alignment explanation
Indices: 58131--58193 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
58121 TCCTCTATTG
* *
58131 GAGCTTTCGGCAGCAATTACTTCTGCTTCTT
1 GAGCTTTCGACAGCAACTACTTCTGCTTCTT
* *
58162 GAGCTTTTCGACAGCAACTGCTTCTTCTTCTT
1 GAGC-TTTCGACAGCAACTACTTCTGCTTCTT
58194 TTACCAACCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.16, C:0.27, G:0.17, T:0.40
Consensus pattern (31 bp):
GAGCTTTCGACAGCAACTACTTCTGCTTCTT
Found at i:58810 original size:15 final size:13
Alignment explanation
Indices: 58782--58807 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58772 ATTTCAGGAA
58782 AAAAAAAAGATTT
1 AAAAAAAAGATTT
58795 AAAAAAAAGATTT
1 AAAAAAAAGATTT
58808 TTATAAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
AAAAAAAAGATTT
Found at i:59544 original size:15 final size:15
Alignment explanation
Indices: 59524--59560 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
59514 CTCGAGCTCA
59524 AGTCGAGTCAACTCG
1 AGTCGAGTCAACTCG
59539 AGTCGAGTCAACTCG
1 AGTCGAGTCAACTCG
59554 AGTCGAG
1 AGTCGAG
59561 CTTTGACCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.27, C:0.24, G:0.30, T:0.19
Consensus pattern (15 bp):
AGTCGAGTCAACTCG
Found at i:62454 original size:14 final size:14
Alignment explanation
Indices: 62423--62461 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
62413 GAAAAATGGT
62423 GAAAAATA-TTAAA
1 GAAAAATATTTAAA
* *
62436 AAAAAATATTTACA
1 GAAAAATATTTAAA
62450 GAAAAATATTTA
1 GAAAAATATTTA
62462 GGAAATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (14 bp):
GAAAAATATTTAAA
Found at i:62466 original size:13 final size:13
Alignment explanation
Indices: 62423--62466 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
62413 GAAAAATGGT
*
62423 GAAAAATATTAAA
1 GAAAAATATTTAA
*
62436 AAAAAATATTTACA
1 GAAAAATATTTA-A
*
62450 GAAAAATATTTAG
1 GAAAAATATTTAA
62463 GAAA
1 GAAA
62467 TTATAATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (13 bp):
GAAAAATATTTAA
Found at i:63669 original size:19 final size:20
Alignment explanation
Indices: 63617--63670 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
63607 GCGATTTTTT
* *
63617 TTCGCAACGCGATTTTTCAAA
1 TTCGCAACGCGAATCTT-AAA
**
63638 TTCGCAAAACGAATCTT-AA
1 TTCGCAACGCGAATCTTAAA
63657 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
63671 TCTCTTTTCG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 14 0.52
21 13 0.48
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (20 bp):
TTCGCAACGCGAATCTTAAA
Found at i:64053 original size:20 final size:20
Alignment explanation
Indices: 64028--64083 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
64018 AAAGAGGAGC
64028 TTGCGAAAAGAAAATTCGCG
1 TTGCGAAAAGAAAATTCGCG
*** *
64048 TTGCGAATTTAAAAATCGCG
1 TTGCGAAAAGAAAATTCGCG
*
64068 TTACGAAAAAGAAAAT
1 TTGCG-AAAAGAAAAT
64084 CGTGTTACGA
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (20 bp):
TTGCGAAAAGAAAATTCGCG
Found at i:64102 original size:21 final size:20
Alignment explanation
Indices: 64078--64120 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
64068 TTACGAAAAA
*
64078 GAAAATCGTGTTACGAATTTG
1 GAAAAT-GTGTTACGAAATTG
* *
64099 GAAACTGTGTTGCGAAATTG
1 GAAAATGTGTTACGAAATTG
64119 GA
1 GA
64121 GTTCGCGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (20 bp):
GAAAATGTGTTACGAAATTG
Found at i:65391 original size:47 final size:48
Alignment explanation
Indices: 65300--65415 Score: 114
Period size: 47 Copynumber: 2.4 Consensus size: 48
65290 AGGGGTACAG
* * *
65300 CGCGGATA-AGGGGTCGCGCCTTACCTTTAATTCTGAATTATATAT-AG-
1 CGCGG-TACAGGGGCCGCGCCATACCTTTAA-TCTGAATAATATATAAGA
*
65347 CGCGGTGCAGGGGCCGCGCCATACCTTTAA-CTGATATAATTATATAAGA
1 CGCGGTACAGGGGCCGCGCCATACCTTTAATCTGA-ATAA-TATATAAGA
**
65396 CGCGGTACAGGTACCGCGCC
1 CGCGGTACAGGGGCCGCGCC
65416 TTGTATTACT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
45 4 0.07
46 4 0.07
47 30 0.53
48 2 0.04
49 17 0.30
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (48 bp):
CGCGGTACAGGGGCCGCGCCATACCTTTAATCTGAATAATATATAAGA
Found at i:66187 original size:35 final size:33
Alignment explanation
Indices: 66104--66188 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
66094 ATAATTTTAA
*
66104 AATACAACAAACTTACAATAAGTATCAAATGGT
1 AATACAACAAAATTACAATAAGTATCAAATGGT
* * *
66137 AATTGATAACCAAATTACAATAACTGATATTAAATGGT
1 AA-T-ACAACAAAATTACAATAA--G-TATCAAATGGT
66175 AATA-AACAAAATTA
1 AATACAACAAAATTA
66189 ACTGAAATAC
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 2 0.05
38 12 0.29
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (33 bp):
AATACAACAAAATTACAATAAGTATCAAATGGT
Done.