Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008241.1 Hibiscus syriacus cultivar Beakdansim tig00110889_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: 1355325
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1310837 original size:13 final size:13
Alignment explanation
Indices: 1310808--1310848 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
1310798 CAGCAGCCCC
1310808 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
1310821 -CCCCCTTAGCAG
1 CCCCCCTTAGCAG
1310833 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
1310846 CCC
1 CCC
1310849 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.15, C:0.56, G:0.15, T:0.15
Consensus pattern (13 bp):
CCCCCCTTAGCAG
Found at i:1313952 original size:15 final size:16
Alignment explanation
Indices: 1313924--1313955 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1313914 AAAATCTTTC
1313924 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
1313940 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
1313955 T
1 T
1313956 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:1314730 original size:16 final size:16
Alignment explanation
Indices: 1314706--1314737 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1314696 TATCGCCGAC
*
1314706 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
1314722 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
1314738 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:1315160 original size:12 final size:12
Alignment explanation
Indices: 1315143--1315182 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
1315133 ACAGCAGCCC
1315143 CCCCCTTAGCAG
1 CCCCCTTAGCAG
1315155 CCCCCTTAGCAG
1 CCCCCTTAGCAG
1315167 CCCCCCTTAGCAG
1 -CCCCCTTAGCAG
1315180 CCC
1 CCC
1315183 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.15, C:0.55, G:0.15, T:0.15
Consensus pattern (12 bp):
CCCCCTTAGCAG
Found at i:1315171 original size:13 final size:13
Alignment explanation
Indices: 1315142--1315182 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
1315132 TACAGCAGCC
1315142 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
1315155 -CCCCCTTAGCAG
1 CCCCCCTTAGCAG
1315167 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
1315180 CCC
1 CCC
1315183 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.15, C:0.56, G:0.15, T:0.15
Consensus pattern (13 bp):
CCCCCCTTAGCAG
Found at i:1315562 original size:2 final size:2
Alignment explanation
Indices: 1315557--1315636 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
1315547 TAAAATGACA
1315557 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
1315599 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
1315637 TTTGTGCATG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1317395 original size:20 final size:20
Alignment explanation
Indices: 1317370--1317407 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1317360 ATTTTTATAA
* *
1317370 ACAAATAATTTTTTAATCTC
1 ACAAATAACTTATTAATCTC
1317390 ACAAATAACTTATTAATC
1 ACAAATAACTTATTAATC
1317408 ATAAATAATT
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:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (20 bp):
ACAAATAACTTATTAATCTC
Found at i:1321479 original size:2 final size:2
Alignment explanation
Indices: 1321472--1321496 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1321462 GTAAAATTTC
1321472 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
1321497 AAAGTTTAAA
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:1328974 original size:15 final size:15
Alignment explanation
Indices: 1328956--1328989 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1328946 GTGAAATTCT
*
1328956 AATTATTTAAATAAA
1 AATTATTCAAATAAA
*
1328971 AATTATTCATATAAA
1 AATTATTCAAATAAA
1328986 AATT
1 AATT
1328990 CATCGATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTATTCAAATAAA
Found at i:1333388 original size:29 final size:29
Alignment explanation
Indices: 1333346--1333404 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1333336 ACAGAGAGAC
1333346 ACTAGCTTGGTTATTATATTCATACCAGT
1 ACTAGCTTGGTTATTATATTCATACCAGT
1333375 ACTAGCTTGGTTATTATATTCATACCAGT
1 ACTAGCTTGGTTATTATATTCATACCAGT
1333404 A
1 A
1333405 TACTTGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.41
Consensus pattern (29 bp):
ACTAGCTTGGTTATTATATTCATACCAGT
Found at i:1334666 original size:21 final size:21
Alignment explanation
Indices: 1334640--1334681 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1334630 ATTTGAATAT
*
1334640 TATGAAGGGGTATCAATTCCC
1 TATGAAGGGGTACCAATTCCC
*
1334661 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCAATTCCC
1334682 CCCATTCTGG
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:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCAATTCCC
Found at i:1334743 original size:21 final size:21
Alignment explanation
Indices: 1334710--1334749 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1334700 TTTTTGCATA
*
1334710 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1334732 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1334750 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1335060 original size:21 final size:21
Alignment explanation
Indices: 1335034--1335075 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1335024 CCAGAATGGG
*
1335034 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1335055 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1335076 ATATTCAAAT
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:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1335258 original size:20 final size:19
Alignment explanation
Indices: 1335188--1335258 Score: 71
Period size: 20 Copynumber: 3.9 Consensus size: 19
1335178 AACCATGCAA
1335188 GGGGGAATCTGTA-CCC--
1 GGGGGAATCTGTACCCCTG
1335204 -GGGGAATC-GATACCCCTG
1 GGGGGAATCTG-TACCCCTG
*
1335222 GGGGGAATCTGTTCCCCTTG
1 GGGGGAATCTGTACCCC-TG
*
1335242 GGGGGAATTTGTACCCC
1 GGGGGAATCTGTACCCC
1335259 CTGGACAATC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 1 0.02
15 10 0.22
16 3 0.07
19 13 0.29
20 18 0.40
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.23
Consensus pattern (19 bp):
GGGGGAATCTGTACCCCTG
Found at i:1338273 original size:34 final size:32
Alignment explanation
Indices: 1338220--1338289 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1338210 CCTTACAAAC
* *
1338220 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
*
1338252 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
1338286 TCCC
1 TCCC
1338290 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:1338598 original size:21 final size:21
Alignment explanation
Indices: 1338572--1338613 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1338562 CCAGAATGGG
*
1338572 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1338593 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1338614 ATATTCAAAT
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:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1338747 original size:15 final size:15
Alignment explanation
Indices: 1338727--1338782 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
1338717 AACCATATAG
1338727 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
1338742 GGGGAATC-GATACCCC
1 GGGGAATCTG-TA-CCC
*
1338758 TGGGGGAATCTGTTCCC
1 --GGGGAATCTGTACCC
1338775 GGGGAATC
1 GGGGAATC
1338783 GATACCCCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 1 0.03
15 18 0.51
16 3 0.09
17 3 0.09
18 9 0.26
19 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.36, T:0.20
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:1338805 original size:35 final size:33
Alignment explanation
Indices: 1338726--1338809 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
1338716 AAACCATATA
*
1338726 GGGGGAATCTGTACCCGGGGAATCGATACCCCT
1 GGGGGAATCTGTTCCCGGGGAATCGATACCCCT
1338759 GGGGGAATCTGTTCCCGGGGAATCGATACCCCCT
1 GGGGGAATCTGTTCCCGGGGAATCGATA-CCCCT
1338793 GGGGGGAATCTGTTCCC
1 -GGGGGAATCTGTTCCC
1338810 CCTGGGGGGA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 27 0.56
34 5 0.10
35 16 0.33
ACGTcount: A:0.18, C:0.27, G:0.35, T:0.20
Consensus pattern (33 bp):
GGGGGAATCTGTTCCCGGGGAATCGATACCCCT
Found at i:1338810 original size:19 final size:20
Alignment explanation
Indices: 1338775--1338834 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
1338765 ATCTGTTCCC
1338775 GGGGAATC-GATACCCCCTGG
1 GGGGAATCTG-TACCCCCTGG
*
1338795 GGGGAATCTGTTCCCCCTGG
1 GGGGAATCTGTACCCCCTGG
1338815 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
1338835 AGAATCTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 36 0.97
21 1 0.03
ACGTcount: A:0.15, C:0.30, G:0.35, T:0.20
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTGG
Found at i:1338841 original size:18 final size:19
Alignment explanation
Indices: 1338785--1338842 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
1338775 GGGGAATCGA
*
1338785 TACCCCCTGGGGGGAATCTG
1 TACCCCCT-GGGAGAATCTG
* *
1338805 TTCCCCCTGGGGGGAATCTG
1 TACCCCCT-GGGAGAATCTG
1338825 TACCCCCT-GGAGAATCTG
1 TACCCCCTGGGAGAATCTG
1338843 ATTTTTCTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
18 9 0.26
20 26 0.74
ACGTcount: A:0.16, C:0.31, G:0.31, T:0.22
Consensus pattern (19 bp):
TACCCCCTGGGAGAATCTG
Found at i:1339427 original size:135 final size:130
Alignment explanation
Indices: 1339183--1339440 Score: 417
Period size: 135 Copynumber: 1.9 Consensus size: 130
1339173 CCTGAATCCA
* *
1339183 ACCCAATCCGAACATTACCTGTAGAAAAACTCGACCGACCCCGATTCGAACCCAATTTTAAAAAA
1 ACCCAACCCGAACATTACCTGTAGAAAAACTCGACCGACCCCGACTCGAACCCAATTTTAAAAAA
*
1339248 AATCTCCGACCCAATCGGGTTGGGTCAGGTCGAAACCCATAAGATTCGATCCCATTTTGAATTCG
66 AAACTCCGACCCAATCGGGTTGGGTCAGGTCGAAACCCATAAGATTCGATCCCATTTTGAATTCG
*
1339313 ACCCAACCCGAACATTACCTGTAGAAAAACTTGACCGACCCCGACTCGAACCCAATTTTTTTTAA
1 ACCCAACCCGAACATTACCTGTAGAAAAACTCGACCGACCCCGACTCGAACCCAA----TTTT-A
* *
1339378 AAAAAAAACTCCGACTCAATCGGGTTGGGTCAGGTCGAAACCCATAAGATTCGGTCCCATTTT
61 AAAAAAAACTCCGACCCAATCGGGTTGGGTCAGGTCGAAACCCATAAGATTCGATCCCATTTT
1339441 CATTCCCAGG
Statistics
Matches: 117, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
130 52 0.44
134 4 0.03
135 61 0.52
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (130 bp):
ACCCAACCCGAACATTACCTGTAGAAAAACTCGACCGACCCCGACTCGAACCCAATTTTAAAAAA
AAACTCCGACCCAATCGGGTTGGGTCAGGTCGAAACCCATAAGATTCGATCCCATTTTGAATTCG
Found at i:1339901 original size:32 final size:32
Alignment explanation
Indices: 1339865--1339955 Score: 80
Period size: 31 Copynumber: 2.8 Consensus size: 32
1339855 AAGAGTAAAA
1339865 TATATAAATAATCTCTAAACTTTTAAAAAATT
1 TATATAAATAATCTCTAAACTTTTAAAAAATT
** * * *
1339897 TATAT-TTTTATCACTTAACTTTT--AAAATT
1 TATATAAATAATCTCTAAACTTTTAAAAAATT
*
1339926 TAAAATATAAATAATCTCTAAACATTTAAA
1 T---ATATAAATAATCTCTAAACTTTTAAA
1339956 CCTTTAGTTC
Statistics
Matches: 42, Mismatches: 11, Indels: 9
0.68 0.18 0.15
Matches are distributed among these distances:
29 7 0.17
31 13 0.31
32 9 0.21
33 12 0.29
35 1 0.02
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (32 bp):
TATATAAATAATCTCTAAACTTTTAAAAAATT
Found at i:1340716 original size:26 final size:27
Alignment explanation
Indices: 1340679--1340731 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1340669 TGATGATGAG
1340679 AAATATTTTATA-ATTTAAAAAATTAT
1 AAATATTTTATATATTTAAAAAATTAT
* *
1340705 AAAT-TTTATATATTTTTGAAAAATTAT
1 AAATATTT-TATATATTTAAAAAATTAT
1340732 TGACTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 3 0.13
26 8 0.35
27 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
AAATATTTTATATATTTAAAAAATTAT
Found at i:1347407 original size:29 final size:30
Alignment explanation
Indices: 1347337--1347396 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1347327 AAATTTAAGG
1347337 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1347368 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1347397 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1347506 original size:21 final size:21
Alignment explanation
Indices: 1347480--1347528 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1347470 TGTCAAAGTA
*
1347480 CATCCATGCACCCCTGCAGTG
1 CATCCATGCACCCCTACAGTG
*
1347501 CATCCATGCATCCCTACAGTG
1 CATCCATGCACCCCTACAGTG
1347522 CATCCAT
1 CATCCAT
1347529 ACACATGCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.41, G:0.14, T:0.22
Consensus pattern (21 bp):
CATCCATGCACCCCTACAGTG
Found at i:1347623 original size:20 final size:20
Alignment explanation
Indices: 1347598--1347668 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
1347588 GCAATTAGTC
1347598 CATCGATGCATCCTTCTGTG
1 CATCGATGCATCCTTCTGTG
***
1347618 CATCGATGCATCAAGGCTGTG
1 CATCGATGCATC-CTTCTGTG
1347639 CATCGATGCATCCTGT-TGTG
1 CATCGATGCATCCT-TCTGTG
*
1347659 CATCCATGCA
1 CATCGATGCA
1347669 CGAAGGCTGC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 25 0.60
21 17 0.40
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.30
Consensus pattern (20 bp):
CATCGATGCATCCTTCTGTG
Found at i:1347643 original size:41 final size:41
Alignment explanation
Indices: 1347598--1347677 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
1347588 GCAATTAGTC
*
1347598 CATCGATGCATCCT-TCTGTGCATCGATGCATC-AAGGCTGTG
1 CATCGATGCATCCTGT-TGTGCATCCATGCA-CGAAGGCTGTG
1347639 CATCGATGCATCCTGTTGTGCATCCATGCACGAAGGCTG
1 CATCGATGCATCCTGTTGTGCATCCATGCACGAAGGCTG
1347678 CAACGGCTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
40 1 0.03
41 34 0.94
42 1 0.03
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.28
Consensus pattern (41 bp):
CATCGATGCATCCTGTTGTGCATCCATGCACGAAGGCTGTG
Found at i:1347819 original size:20 final size:22
Alignment explanation
Indices: 1347781--1347820 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1347771 TTTGAGTAGA
1347781 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1347803 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1347821 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1349106 original size:3 final size:3
Alignment explanation
Indices: 1349094--1349123 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1349084 TGAAGAAAGG
1349094 GAA G-A GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1349124 GAGGAGGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1350968 original size:29 final size:30
Alignment explanation
Indices: 1350899--1350957 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1350889 AATTTAAGGC
1350899 AAAATGGTTTTTGGACTTGAATTGAATTTAA
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAA
1350930 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
1350958 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAA
Found at i:1351064 original size:21 final size:21
Alignment explanation
Indices: 1351038--1351157 Score: 140
Period size: 21 Copynumber: 5.7 Consensus size: 21
1351028 AGGGTGTCAA
*
1351038 AGTGCATCCATGCACCCTTGC
1 AGTGCATCCATGCACCCATGC
*
1351059 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCATGC
1351080 AGTGCATCCATGCATCCC-TGC
1 AGTGCATCCATGCA-CCCATGC
1351101 AGTGCATCCATGCA--CATGCAC
1 AGTGCATCCATGCACCCATG--C
* *
1351122 TAGTGCATCGATGCA-TCATGC
1 -AGTGCATCCATGCACCCATGC
1351143 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1351158 TCAAACACCG
Statistics
Matches: 89, Mismatches: 3, Indels: 14
0.84 0.03 0.13
Matches are distributed among these distances:
18 1 0.01
19 2 0.02
20 13 0.15
21 53 0.60
22 16 0.18
23 4 0.04
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCATGC
Found at i:1351093 original size:13 final size:14
Alignment explanation
Indices: 1351090--1351157 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 14
1351080 AGTGCATCCA
*
1351090 TGCATCCCTGCA-G
1 TGCATCCATGCACG
*
1351103 TGCATCCATGCACA
1 TGCATCCATGCACG
*
1351117 TGCA-CTAGTGCATCG
1 TGCATCCA-TGCA-CG
1351132 ATGCAT-CATGCA-G
1 -TGCATCCATGCACG
1351145 TGCATCCATGCAC
1 TGCATCCATGCAC
1351158 TCAAACACCG
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
12 5 0.12
13 20 0.47
14 8 0.19
15 5 0.12
16 5 0.12
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (14 bp):
TGCATCCATGCACG
Found at i:1351400 original size:20 final size:22
Alignment explanation
Indices: 1351362--1351401 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1351352 TTTGAGTAGA
1351362 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1351384 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1351402 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1352547 original size:125 final size:125
Alignment explanation
Indices: 1352325--1352580 Score: 406
Period size: 125 Copynumber: 2.0 Consensus size: 125
1352315 TAACAACTAA
1352325 ATCTTACTAACAGTATATCATTGAAAGGCTCAAGCTATAAAATCTATTGCTTTGCATTAGTGAGT
1 ATCTTACTAACAGTATATCATTGAAAGGCTCAAGCTATAAAATCTATTGCTTTGCATTAGTGAGT
* * *
1352390 ATACTAGTATACTCACTCTTTACTCTATGGTAGACATCATGGTTCTTCTGAGGGTTCTAC
66 ATACTAGTATACTCACTCTCTACTCTATGGTAGACATCATGGTGCGTCTGAGGGTTCTAC
* * * * *
1352450 ATCTTACTAACATTATGTCACTT-AAAGGCTCAAGCTATCAAGTCTATTGCTTTGCTTTAGTGAG
1 ATCTTACTAACAGTATATCA-TTGAAAGGCTCAAGCTATAAAATCTATTGCTTTGCATTAGTGAG
* *
1352514 TATACTCGTATACTCACTCTCTACTCTATGGTAGACATCATGGTGCGTCTGAGGGTTCTAT
65 TATACTAGTATACTCACTCTCTACTCTATGGTAGACATCATGGTGCGTCTGAGGGTTCTAC
1352575 ATCTTA
1 ATCTTA
1352581 GAGCTCACAC
Statistics
Matches: 120, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
125 118 0.98
126 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (125 bp):
ATCTTACTAACAGTATATCATTGAAAGGCTCAAGCTATAAAATCTATTGCTTTGCATTAGTGAGT
ATACTAGTATACTCACTCTCTACTCTATGGTAGACATCATGGTGCGTCTGAGGGTTCTAC
Found at i:1354067 original size:22 final size:23
Alignment explanation
Indices: 1354039--1354099 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
1354029 CAGCTTGTAT
*
1354039 AAATGCATCGAAGTGCA-CGTAG
1 AAATGCACCGAAGTGCAGCGTAG
*
1354061 AATTGCACCGAAGTGCAGCGTAG
1 AAATGCACCGAAGTGCAGCGTAG
*
1354084 AAATGCACCAAAGTGC
1 AAATGCACCGAAGTGC
1354100 CATATAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCAGCGTAG
Done.