Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005538.1 Hibiscus syriacus cultivar Beakdansim tig00012817_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: 62936
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:1076 original size:20 final size:20
Alignment explanation
Indices: 1051--1135 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
1041 TTCAAGCCTT
1051 GATGCATCGATGCATGGCAG
1 GATGCATCGATGCATGGCAG
1071 GATGCATC---G-AT----G
1 GATGCATCGATGCATGGCAG
*
1083 -ATGCATCGATTCATGGCAG
1 GATGCATCGATGCATGGCAG
* *
1102 GATGCATCGATTCATGGTAG
1 GATGCATCGATGCATGGCAG
1122 GATGCATCGATGCA
1 GATGCATCGATGCA
1136 CTAAGTGAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
11 7 0.13
12 1 0.02
15 2 0.04
16 2 0.04
17 1 0.02
19 1 0.02
20 39 0.74
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (20 bp):
GATGCATCGATGCATGGCAG
Found at i:1086 original size:31 final size:31
Alignment explanation
Indices: 1050--1112 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
1040 GTTCAAGCCT
1050 TGATGCATCGATGCATGGCAGGATGCATCGA
1 TGATGCATCGATGCATGGCAGGATGCATCGA
*
1081 TGATGCATCGATTCATGGCAGGATGCATCGA
1 TGATGCATCGATGCATGGCAGGATGCATCGA
1112 T
1 T
1113 TCATGGTAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (31 bp):
TGATGCATCGATGCATGGCAGGATGCATCGA
Found at i:1344 original size:29 final size:30
Alignment explanation
Indices: 1311--1367 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1301 AACTTTGAAT
1311 AATTCAATT-AAGTCCAAAAACATTTTGTA
1 AATTCAATTCAAGTCCAAAAACATTTTGTA
*
1340 AATTCAATTCAAGTCCAAAAATATTTTG
1 AATTCAATTCAAGTCCAAAAACATTTTG
1368 CCTTAAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (30 bp):
AATTCAATTCAAGTCCAAAAACATTTTGTA
Found at i:3534 original size:3 final size:3
Alignment explanation
Indices: 3526--3559 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
3516 TCTAGAGTCC
3526 TCT TCT TCTT TCT TCT TCT TCTT TCT TCT TCT TC
1 TCT TCT TC-T TCT TCT TCT TC-T TCT TCT TCT TC
3560 ATACGTGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:3542 original size:13 final size:13
Alignment explanation
Indices: 3526--3559 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
3516 TCTAGAGTCC
3526 TCTTCTTCTTTCT
1 TCTTCTTCTTTCT
3539 TCTTCTTCTTTCT
1 TCTTCTTCTTTCT
3552 TCTTCTTC
1 TCTTCTTC
3560 ATACGTGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (13 bp):
TCTTCTTCTTTCT
Found at i:4054 original size:21 final size:21
Alignment explanation
Indices: 4012--4054 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4002 TTTCTGAGCT
* *
4012 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
4033 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
4054 A
1 A
4055 ACGAATATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:4107 original size:20 final size:20
Alignment explanation
Indices: 4082--4119 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4072 GAATGCTAGA
*
4082 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
4102 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
4120 TAATGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:4706 original size:100 final size:102
Alignment explanation
Indices: 4589--4803 Score: 398
Period size: 102 Copynumber: 2.1 Consensus size: 102
4579 AGTAAGGGTC
*
4589 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGT-GACACATACT
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTAGACACATACT
4653 TGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
4690 TATGT-GTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGT-AGACACATAC
4754 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
65 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
4792 TATGTGGTCCTT
1 TATGTGGTCCTT
4804 ATGGACATTA
Statistics
Matches: 110, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
100 47 0.43
101 5 0.05
102 52 0.47
103 6 0.05
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (102 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTAGACACATACT
TGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:4854 original size:21 final size:21
Alignment explanation
Indices: 4828--4869 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4818 ATGGCACTAC
4828 GGTGCAATTCTACGCGGCACT
1 GGTGCAATTCTACGCGGCACT
*
4849 GGTGCAATTCTACGTGGCACT
1 GGTGCAATTCTACGCGGCACT
4870 TAGGTACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.26
Consensus pattern (21 bp):
GGTGCAATTCTACGCGGCACT
Found at i:11001 original size:20 final size:20
Alignment explanation
Indices: 10976--11013 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10966 GAATGCTAGA
*
10976 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
10996 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
11014 TAATGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:11668 original size:103 final size:103
Alignment explanation
Indices: 11489--11706 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
11479 GTAGAGGGTC
* *
11489 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGAACATATATGTAATCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
11554 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
11592 TATGTGGTCCTTCGGAACATATATGTAATCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGAACATATATGTAATCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
11657 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
11695 TATATGGTCCTT
1 TATGTGGTCCTT
11707 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGAACATATATGTAATCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:11756 original size:23 final size:23
Alignment explanation
Indices: 11723--11785 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
11713 ATTATTATAT
11723 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
11746 GGCACTCCGGTGCAATTTTACGT
1 GGCACTACGGTGCAATTCTACGC
11769 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
11786 ATATGAGCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:18262 original size:20 final size:20
Alignment explanation
Indices: 18237--18282 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
18227 TCAATCCTAG
* *
18237 AATTTAAAGTTAGAATGTTA
1 AATTTAAAGTTAGAAAGTGA
**
18257 AATTTATGGTTAGAAAGTGA
1 AATTTAAAGTTAGAAAGTGA
18277 AATTTA
1 AATTTA
18283 GACCATTTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.39
Consensus pattern (20 bp):
AATTTAAAGTTAGAAAGTGA
Found at i:19805 original size:2 final size:2
Alignment explanation
Indices: 19794--19824 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
19784 TATGAATTAG
19794 TA TA -A 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
19825 ATTTATGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:20135 original size:43 final size:44
Alignment explanation
Indices: 20074--20161 Score: 151
Period size: 43 Copynumber: 2.0 Consensus size: 44
20064 ATGAGATTTG
*
20074 TTATAGATGTGAACTATAAAAACAACAAACCA-TAAACATTACA
1 TTATAGATGTGAACTATAAAAACAACAAACCATTAAACATGACA
*
20117 TTATAGATGTGAACTATAAAAACAACAAACTATTAAACATGACA
1 TTATAGATGTGAACTATAAAAACAACAAACCATTAAACATGACA
20161 T
1 T
20162 GAAGCATACC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 31 0.74
44 11 0.26
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.25
Consensus pattern (44 bp):
TTATAGATGTGAACTATAAAAACAACAAACCATTAAACATGACA
Found at i:20666 original size:3 final size:3
Alignment explanation
Indices: 20658--20723 Score: 60
Period size: 3 Copynumber: 22.0 Consensus size: 3
20648 CCCCATCATT
* * * * * * *
20658 CTC CTC CTC TTC ATC ATC ATC CTC ATC CTC ATC CTC CTC CTC ATC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
*
20706 CTC CTC ATC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC
20724 GTCATCATCA
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.11, C:0.55, G:0.00, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:20671 original size:30 final size:30
Alignment explanation
Indices: 20635--20733 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 30
20625 CTTGTCGTCA
* *
20635 TCTTCATCGTCATCCCCATCATTC-TCCTCC
1 TCTTCATCATCATCCCCATC-CTCATCCTCC
*
20665 TCTTCATCATCATCCTCATCCTCATCCTCC
1 TCTTCATCATCATCCCCATCCTCATCCTCC
* * * * * *
20695 TCCTCATCCTCCTCCTCATCCTCCTCCTCG
1 TCTTCATCATCATCCCCATCCTCATCCTCC
*
20725 TCATCATCA
1 TCTTCATCA
20734 CTATCAACAA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 2 0.03
30 56 0.97
ACGTcount: A:0.14, C:0.48, G:0.02, T:0.35
Consensus pattern (30 bp):
TCTTCATCATCATCCCCATCCTCATCCTCC
Found at i:20683 original size:6 final size:6
Alignment explanation
Indices: 20632--20723 Score: 78
Period size: 6 Copynumber: 15.3 Consensus size: 6
20622 ATCCTTGTCG
* * * * * * *
20632 TCATCT TCATCG TCATCC CCATCAT TC-TCC TCCTCT TCATCA TCATCC
1 TCATCC TCATCC TCATCC TCATC-C TCATCC TCATCC TCATCC TCATCC
* * *
20680 TCATCC TCATCC TCCTCC TCATCC TCCTCC TCATCC TCCTCC TC
1 TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC TC
20724 GTCATCATCA
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
5 2 0.03
6 66 0.96
7 1 0.01
ACGTcount: A:0.13, C:0.50, G:0.01, T:0.36
Consensus pattern (6 bp):
TCATCC
Found at i:22685 original size:14 final size:14
Alignment explanation
Indices: 22666--22696 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
22656 CAAAATTATT
22666 TAAATAAATTCAAA
1 TAAATAAATTCAAA
*
22680 TAAATAAATTCTAA
1 TAAATAAATTCAAA
22694 TAA
1 TAA
22697 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATAAATTCAAA
Found at i:22947 original size:16 final size:15
Alignment explanation
Indices: 22928--22972 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
22918 AATTAATTAC
22928 TTAAATAATAAAAAA
1 TTAAATAATAAAAAA
*
22943 TTTAATGAATAAAAAA
1 TTAAAT-AATAAAAAA
* *
22959 ATAAATTATAAAAA
1 TTAAATAATAAAAA
22973 TAATTATACC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
TTAAATAATAAAAAA
Found at i:25046 original size:16 final size:16
Alignment explanation
Indices: 25027--25072 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
25017 AATAAAAGTG
25027 CACGAACATAAACGAA
1 CACGAACATAAACGAA
*
25043 CACGAACATAAATGAA
1 CACGAACATAAACGAA
25059 CACGAACATAAACG
1 CACGAACATAAACG
25073 TTGGAGACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.54, C:0.24, G:0.13, T:0.09
Consensus pattern (16 bp):
CACGAACATAAACGAA
Found at i:25305 original size:24 final size:24
Alignment explanation
Indices: 25276--25333 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
25266 AAAAAATTAA
25276 GAGCTCGATTAAAACTCGAGACTC
1 GAGCTCGATTAAAACTCGAGACTC
25300 GAGCTCGATTAAAACTCGAGACTC
1 GAGCTCGATTAAAACTCGAGACTC
25324 GAGCTCGATT
1 GAGCTCGATT
25334 CAGAGCTCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (24 bp):
GAGCTCGATTAAAACTCGAGACTC
Found at i:25341 original size:12 final size:12
Alignment explanation
Indices: 25324--25364 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
25314 CTCGAGACTC
25324 GAGCTCGATTCA
1 GAGCTCGATTCA
25336 GAGCTCGATTCA
1 GAGCTCGATTCA
25348 GAGCTCGATTCA
1 GAGCTCGATTCA
25360 -AGCTC
1 GAGCTC
25365 AACATTGCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 5 0.17
12 24 0.83
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (12 bp):
GAGCTCGATTCA
Found at i:31276 original size:11 final size:10
Alignment explanation
Indices: 31255--31313 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
31245 TCAATTTTTT
31255 AAAATCAATA
1 AAAATCAATA
31265 AAAATGCAATA
1 AAAAT-CAATA
31276 AAAA--AATTA
1 AAAATCAA-TA
* *
31285 AAAGTGAATA
1 AAAATCAATA
*
31295 AAATTCAATA
1 AAAATCAATA
31305 AAAAT-AATA
1 AAAATCAATA
31314 TAAAGCTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
8 2 0.05
9 9 0.22
10 19 0.46
11 11 0.27
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (10 bp):
AAAATCAATA
Found at i:31286 original size:29 final size:30
Alignment explanation
Indices: 31253--31317 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
31243 ATTCAATTTT
31253 TTAAAA-TCAATAAAAATGCAATAAAAA-AA
1 TTAAAAGTCAAT-AAAATGCAATAAAAATAA
* *
31282 TTAAAAGTGAATAAAATTCAATAAAAATAA
1 TTAAAAGTCAATAAAATGCAATAAAAATAA
31312 TATAAA
1 T-TAAA
31318 GCTAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 20 0.65
30 7 0.23
31 4 0.13
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (30 bp):
TTAAAAGTCAATAAAATGCAATAAAAATAA
Found at i:31306 original size:20 final size:20
Alignment explanation
Indices: 31254--31309 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
31244 TTCAATTTTT
31254 TAAAATCAATAAAAATGCAA
1 TAAAATCAATAAAAATGCAA
* *
31274 TAAAA-AAATTAAAAGTG-AA
1 TAAAATCAA-TAAAAATGCAA
31293 TAAAATTCAATAAAAAT
1 TAAAA-TCAATAAAAAT
31310 AATATAAAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 9 0.31
20 18 0.62
21 2 0.07
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.23
Consensus pattern (20 bp):
TAAAATCAATAAAAATGCAA
Found at i:33509 original size:20 final size:22
Alignment explanation
Indices: 33462--33515 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 22
33452 CAAAATGATG
33462 TCAAAAACCACTTGGTTTTAGC
1 TCAAAAACCACTTGGTTTTAGC
33484 TC-AAAA-CACTTGGTTTTAGC
1 TCAAAAACCACTTGGTTTTAGC
33504 -CAAAAAACCACT
1 TC-AAAAACCACT
33516 ATCAGTCTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.03
20 14 0.48
21 8 0.28
22 6 0.21
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (22 bp):
TCAAAAACCACTTGGTTTTAGC
Found at i:35965 original size:20 final size:20
Alignment explanation
Indices: 35942--35989 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
35932 AGGTGTGTTG
35942 AAGCTATTGTGAGCAAAATC
1 AAGCTATTGTGAGCAAAATC
35962 AAGCTATTGTGAGCAAAATC
1 AAGCTATTGTGAGCAAAATC
35982 AAGCTATT
1 AAGCTATT
35990 TTGGAGCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (20 bp):
AAGCTATTGTGAGCAAAATC
Found at i:41836 original size:22 final size:23
Alignment explanation
Indices: 41811--41853 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
41801 AAAAATACAC
41811 ATATAAAAA-AATATAATTTTTT
1 ATATAAAAATAATATAATTTTTT
*
41833 ATATAAAAATTATATAATTTT
1 ATATAAAAATAATATAATTTT
41854 AAAATCTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATAAAAATAATATAATTTTTT
Found at i:42049 original size:39 final size:38
Alignment explanation
Indices: 41972--42070 Score: 121
Period size: 39 Copynumber: 2.6 Consensus size: 38
41962 TAAAAGAACT
*
41972 TATT-TGAT-AAATAATTTAAAAATTAAGAATTTAAAA
1 TATTATGATAAAATAATTTAAAAAGTAAGAATTTAAAA
* *
42008 TATTATGATAAAATAATTTAAGAAAGTAATAATTTTAAA
1 TATTATGATAAAATAATTTAA-AAAGTAAGAATTTAAAA
* * *
42047 TATTACGGTAAAATAATTTGAAAA
1 TATTATGATAAAATAATTTAAAAA
42071 TTAGAAATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
36 4 0.07
37 4 0.07
38 14 0.26
39 32 0.59
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (38 bp):
TATTATGATAAAATAATTTAAAAAGTAAGAATTTAAAA
Found at i:46299 original size:47 final size:47
Alignment explanation
Indices: 46254--46506 Score: 375
Period size: 47 Copynumber: 5.4 Consensus size: 47
46244 TACATTTAAA
* * *
46254 TTATGACATCCTTTTATACCTTAATGCATCCTTTCATGCATTTTA-A
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGT
*
46300 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTGT
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGT
* *
46347 TTATGGCATCCTTTCATGCCTTAATACATCCTTTCATGCATTTTAGT
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGT
* * *
46394 TTATGGCATCATTTCATGCCTTAATGCATCATTTCATGCATTTTAGT
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGT
** *
46441 TTATGACATCCTTTCAAACTTTAATGCATCCTTTCATGCATTTTAGT
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGT
46488 TTATTG-CATCCTTTCATGC
1 TTA-TGACATCCTTTCATGC
46507 ATTTTAGTTT
Statistics
Matches: 187, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
46 42 0.22
47 143 0.76
48 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.45
Consensus pattern (47 bp):
TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGT
Found at i:46331 original size:20 final size:20
Alignment explanation
Indices: 46260--46432 Score: 85
Period size: 20 Copynumber: 7.7 Consensus size: 20
46250 TAAATTATGA
* *
46260 CATCCTTTTATACCTTAATG
1 CATCCTTTCATGCCTTAATG
*
46280 CATCCTTTCATGCATTTTAATTATG
1 CATCCTTTCATGC--CTT-A--ATG
46305 ACATCCTTTCATGCCTTAATG
1 -CATCCTTTCATGCCTTAATG
* *
46326 CATCCTTTCATGCATTTTTGTTTATGG
1 CATCCTTTCATGC------CTTAAT-G
*
46353 CATCCTTTCATGCCTTAATA
1 CATCCTTTCATGCCTTAATG
*
46373 CATCCTTTCATGCATTTTAGTTTATGG
1 CATCCTTTCATGC--CTTA----AT-G
*
46400 CATCATTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
*
46420 CATCATTTCATGC
1 CATCCTTTCATGC
46433 ATTTTAGTTT
Statistics
Matches: 120, Mismatches: 13, Indels: 40
0.69 0.08 0.23
Matches are distributed among these distances:
20 51 0.43
21 9 0.08
22 5 0.04
23 2 0.02
24 2 0.02
25 6 0.05
26 19 0.16
27 26 0.22
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.45
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:46363 original size:27 final size:27
Alignment explanation
Indices: 46325--46574 Score: 196
Period size: 27 Copynumber: 10.3 Consensus size: 27
46315 ATGCCTTAAT
*
46325 GCATCCTTTCATGCATTTTTGTTTATG
1 GCATCCTTTCATGCATTTTAGTTTATG
*
46352 GCATCCTTTCATGC--CTTA----AT-
1 GCATCCTTTCATGCATTTTAGTTTATG
*
46372 ACATCCTTTCATGCATTTTAGTTTATG
1 GCATCCTTTCATGCATTTTAGTTTATG
* *
46399 GCATCATTTCATGC--CTTA----AT-
1 GCATCCTTTCATGCATTTTAGTTTATG
*
46419 GCATCATTTCATGCATTTTAGTTTATG
1 GCATCCTTTCATGCATTTTAGTTTATG
* * *
46446 ACATCCTTTCA--AACTTTA----AT-
1 GCATCCTTTCATGCATTTTAGTTTATG
*
46466 GCATCCTTTCATGCATTTTAGTTTATT
1 GCATCCTTTCATGCATTTTAGTTTATG
46493 GCATCCTTTCATGCATTTTAGTTTATG
1 GCATCCTTTCATGCATTTTAGTTTATG
*
46520 GCATCCTTTCATGC--CTTA----AT-
1 GCATCCTTTCATGCATTTTAGTTTATG
*
46540 ACATCCTTTCATGCATTTTAGTTTATG
1 GCATCCTTTCATGCATTTTAGTTTATG
46567 GCATCCTT
1 GCATCCTT
46575 AATTATGGAT
Statistics
Matches: 175, Mismatches: 20, Indels: 56
0.70 0.08 0.22
Matches are distributed among these distances:
20 50 0.29
21 8 0.05
22 14 0.08
25 13 0.07
26 8 0.05
27 82 0.47
ACGTcount: A:0.21, C:0.22, G:0.11, T:0.46
Consensus pattern (27 bp):
GCATCCTTTCATGCATTTTAGTTTATG
Found at i:46503 original size:74 final size:74
Alignment explanation
Indices: 46418--46574 Score: 251
Period size: 74 Copynumber: 2.1 Consensus size: 74
46408 CATGCCTTAA
* * *
46418 TGCATCATTTCATGCATTTTAGTTTATGACATCCTTTCAAACTTTAATGCATCCTTTCATGCATT
1 TGCATCCTTTCATGCATTTTAGTTTATGACATCCTTTCAAACCTTAATACATCCTTTCATGCATT
46483 TTAGTTTAT
66 TTAGTTTAT
* **
46492 TGCATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATACATCCTTTCATGCATT
1 TGCATCCTTTCATGCATTTTAGTTTATGACATCCTTTCAAACCTTAATACATCCTTTCATGCATT
46557 TTAGTTTAT
66 TTAGTTTAT
*
46566 GGCATCCTT
1 TGCATCCTT
46575 AATTATGGAT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.46
Consensus pattern (74 bp):
TGCATCCTTTCATGCATTTTAGTTTATGACATCCTTTCAAACCTTAATACATCCTTTCATGCATT
TTAGTTTAT
Found at i:47041 original size:19 final size:20
Alignment explanation
Indices: 46974--47044 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 20
46964 GGCTCCTCAT
*
46974 TATCGATACCCTTACTATGG
1 TATCGATACCCATACTATGG
* *
46994 TATTGATACTACCATACTATAG
1 TATCGATAC--CCATACTATGG
* *
47016 TACCGATACCC-TATTATGG
1 TATCGATACCCATACTATGG
47035 TATCGATACC
1 TATCGATACC
47045 ATTTTTGCAT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 15 0.37
20 10 0.24
22 16 0.39
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (20 bp):
TATCGATACCCATACTATGG
Found at i:48922 original size:16 final size:16
Alignment explanation
Indices: 48875--48923 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
48865 AAAAATAAAA
48875 TTGAAAGTTAAAGTAA-
1 TTGAAAGTT-AAGTAAT
48891 TT-AAA-TTAGGAGTAAT
1 TTGAAAGTTA--AGTAAT
48907 TTGAAAGTTAAGTAAT
1 TTGAAAGTTAAGTAAT
48923 T
1 T
48924 AAATTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.04
14 2 0.07
15 8 0.29
16 11 0.39
17 3 0.11
18 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (16 bp):
TTGAAAGTTAAGTAAT
Found at i:52826 original size:28 final size:28
Alignment explanation
Indices: 52807--52861 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
52797 ACTCAGTTTC
*
52807 ATATTTTTTTATTTTTAAACTAAATTTA
1 ATATTTTTATATTTTTAAACTAAATTTA
*
52835 ATATTTTTATATTTTTAAACAAAATTT
1 ATATTTTTATATTTTTAAACTAAATTT
52862 TATAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (28 bp):
ATATTTTTATATTTTTAAACTAAATTTA
Found at i:55195 original size:20 final size:20
Alignment explanation
Indices: 55170--55207 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
55160 TAAAATACAA
55170 AATGAGATAGAAATAAGGCT
1 AATGAGATAGAAATAAGGCT
55190 AATGAGATAGAAATAAGG
1 AATGAGATAGAAATAAGG
55208 AATCATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.26, T:0.18
Consensus pattern (20 bp):
AATGAGATAGAAATAAGGCT
Found at i:61253 original size:17 final size:17
Alignment explanation
Indices: 61233--61267 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
61223 TAAAAAAAGA
61233 AAAT-AAATAAGTAAAAT
1 AAATAAAATAA-TAAAAT
61250 AAATAAAATAATAAAAT
1 AAATAAAATAATAAAAT
61267 A
1 A
61268 CTAATGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (17 bp):
AAATAAAATAATAAAAT
Found at i:61333 original size:9 final size:9
Alignment explanation
Indices: 61289--61333 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
61279 AGAAAAAAGT
*
61289 AATAAAATA
1 AATAAAACA
*
61298 AATAAAATA
1 AATAAAACA
*
61307 AATAAGACAA
1 AATAAAAC-A
61317 AATAAAACA
1 AATAAAACA
61326 AATAAAAC
1 AATAAAAC
61334 CTAAGAATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
9 24 0.75
10 8 0.25
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.16
Consensus pattern (9 bp):
AATAAAACA
Done.