Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005456.1 Hibiscus syriacus cultivar Beakdansim tig00012495_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: 46414
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Found at i:1981 original size:22 final size:22
Alignment explanation
Indices: 1953--1997 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1943 GACTTTGAGA
1953 AAACTATTTCTTTTTCCGGTGT
1 AAACTATTTCTTTTTCCGGTGT
1975 AAACTATTTCTTTTTCCGGTGT
1 AAACTATTTCTTTTTCCGGTGT
1997 A
1 A
1998 TGAAAAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.49
Consensus pattern (22 bp):
AAACTATTTCTTTTTCCGGTGT
Found at i:9554 original size:13 final size:13
Alignment explanation
Indices: 9536--9561 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9526 CTTAGTAAGT
9536 TTCGATATAATAA
1 TTCGATATAATAA
9549 TTCGATATAATAA
1 TTCGATATAATAA
9562 ATTCTTTATT
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:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
TTCGATATAATAA
Found at i:15024 original size:20 final size:21
Alignment explanation
Indices: 14988--15027 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
14978 GATTTTCGAA
14988 AAAAAATTATTTCGAAAATTC
1 AAAAAATTATTTCGAAAATTC
15009 AAAAAATCTA-TT-GAAAATT
1 AAAAAAT-TATTTCGAAAATT
15028 TGTGAGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 9 0.50
22 2 0.11
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (21 bp):
AAAAAATTATTTCGAAAATTC
Found at i:15422 original size:23 final size:22
Alignment explanation
Indices: 15391--15471 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 22
15381 AAACCCAAAA
15391 GATGCATCGATGCACATTCAAG
1 GATGCATCGATGCACATTCAAG
* * *
15413 GCATGCATCGGTGCACCTTCATG
1 G-ATGCATCGATGCACATTCAAG
* *
15436 G-TGTATTGATGCACATTCAAAGG
1 GATGCATCGATGCACATTC-AA-G
*
15459 GATGCATCAATGC
1 GATGCATCGATGC
15472 GCTGTTAAGT
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
21 13 0.30
22 2 0.05
23 21 0.48
24 8 0.18
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (22 bp):
GATGCATCGATGCACATTCAAG
Found at i:18923 original size:64 final size:63
Alignment explanation
Indices: 18855--19034 Score: 222
Period size: 65 Copynumber: 2.8 Consensus size: 63
18845 TTGGACCCTT
*
18855 AGTGCATCGGTGCACTAAG-AGTGCATCGATGCATAAAATGCATTCGATGTTTCA-AAATAGC-C
1 AGTGCATCGATGCA-T-AGTAGTGCATCGATGCATAAAATGCATTCGATGTTTCATAAA-A-CTC
18917 TG
62 TG
* *
18919 AGTGCATCGATGCATGGCTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACTCTG
1 AGTGCATCGATGCATAG-TAGTGCATCGATGCATAAAATGCATTCGATG-TTTCATAAAACTCTG
* * *
18984 AGTGCATCGATGCATAGTATGTGTATCGATGCATGAAATGCATTCTATGTT
1 AGTGCATCGATGCATAGTA-GTGCATCGATGCATAAAATGCATTCGATGTT
19035 CAATTTATTC
Statistics
Matches: 103, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 47 0.46
65 51 0.50
66 3 0.03
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (63 bp):
AGTGCATCGATGCATAGTAGTGCATCGATGCATAAAATGCATTCGATGTTTCATAAAACTCTG
Found at i:19959 original size:15 final size:16
Alignment explanation
Indices: 19935--19978 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
19925 AATAGTTAAG
19935 TAAA-TAAAAAATA-T
1 TAAATTAAAAAATATT
19949 TAAATTAAAAAATATT
1 TAAATTAAAAAATATT
19965 TAAACTTATAAAAA
1 TAAA-TTA-AAAAA
19979 AATAAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.15
15 9 0.35
16 5 0.19
17 3 0.12
18 5 0.19
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAATTAAAAAATATT
Found at i:22384 original size:15 final size:15
Alignment explanation
Indices: 22360--22390 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
22350 TTGGGGTTAA
*
22360 TTTTAGCATTATACC
1 TTTTAACATTATACC
22375 TTTTAACATTATACC
1 TTTTAACATTATACC
22390 T
1 T
22391 ATAATAATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.19, G:0.03, T:0.48
Consensus pattern (15 bp):
TTTTAACATTATACC
Found at i:23794 original size:14 final size:14
Alignment explanation
Indices: 23771--23805 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
23761 GGAAAGAATG
*
23771 GAGTGACTGAGAAA
1 GAGTGGCTGAGAAA
*
23785 GAGTGGCTGATAAA
1 GAGTGGCTGAGAAA
23799 GAGTGGC
1 GAGTGGC
23806 AATAGTAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.40, T:0.17
Consensus pattern (14 bp):
GAGTGGCTGAGAAA
Found at i:24345 original size:182 final size:182
Alignment explanation
Indices: 24045--24520 Score: 697
Period size: 182 Copynumber: 2.6 Consensus size: 182
24035 CGATCCAAAT
* * * *
24045 TAAAAATGTATCGATCCA-TATCAATATAACATGTAAAAATATCGATAAAACCGGTCA-CGAAAA
1 TAAAAATGTATCGATCCACAAT-GATATAACAAGTAAAAATAT-GATAAAACCGGT-ATCGAAAT
* * * *
24108 GACAATACCGGTAAA-TCCTTACCAGATATATTGAACGTGTCAATACTTTAATATAAGGATCGAC
63 GATAAAACCGGTAAAGTGC-TACCAGATATATTGAAAGTGTCAATACTTTAATATAAGGATCGAC
* *
24172 ACTTTGTCAATTTAAAAGAGAAGCATTTTTAACGCCTATAAAGTGTCGATATTTTA
127 ACTTTGTCAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
*
24228 TAAAAATGTATCGATCCACAATGATATAACAAGTAAAAATATGACAAAACCGGTATCGAAATGAT
1 TAAAAATGTATCGATCCACAATGATATAACAAGTAAAAATATGATAAAACCGGTATCGAAATGAT
* * ** *
24293 AAAACCGGTAAAGAGCTACCAGATATATTTAAAGTGTCGGTACTTTAATATAAGTATCGACACTT
66 AAAACCGGTAAAGTGCTACCAGATATATTGAAAGTGTCAATACTTTAATATAAGGATCGACACTT
* *
24358 TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTA
131 TGTCAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
* * *
24410 TAAAAATGTATCGATCCACAATGATATAACAGGTAAAAATATGATAAAACTGGTATCAAAATGAT
1 TAAAAATGTATCGATCCACAATGATATAACAAGTAAAAATATGATAAAACCGGTATCGAAATGAT
*
24475 AAAACCGATAAAGTGCTACCAGATATATTGAAAGTGTCAATACTTT
66 AAAACCGGTAAAGTGCTACCAGATATATTGAAAGTGTCAATACTTT
24521 CATAAGTACG
Statistics
Matches: 263, Mismatches: 27, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
181 1 0.00
182 223 0.85
183 37 0.14
184 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.28
Consensus pattern (182 bp):
TAAAAATGTATCGATCCACAATGATATAACAAGTAAAAATATGATAAAACCGGTATCGAAATGAT
AAAACCGGTAAAGTGCTACCAGATATATTGAAAGTGTCAATACTTTAATATAAGGATCGACACTT
TGTCAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
Found at i:24464 original size:20 final size:20
Alignment explanation
Indices: 24429--24479 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
24419 ATCGATCCAC
*
24429 AATGATATAACAGGTA-AAA
1 AATGATAAAACAGGTATAAA
* *
24448 ATATGATAAAACTGGTATCAA
1 A-ATGATAAAACAGGTATAAA
24469 AATGATAAAAC
1 AATGATAAAAC
24480 CGATAAAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 23 0.85
21 3 0.11
ACGTcount: A:0.55, C:0.08, G:0.14, T:0.24
Consensus pattern (20 bp):
AATGATAAAACAGGTATAAA
Found at i:26742 original size:21 final size:21
Alignment explanation
Indices: 26716--26755 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
26706 CAATCAAGAA
26716 TCGAAGAGAAACTTGAGAGAG
1 TCGAAGAGAAACTTGAGAGAG
* *
26737 TCGAAGATACACTTGAGAG
1 TCGAAGAGAAACTTGAGAG
26756 GCATAAGGGG
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:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (21 bp):
TCGAAGAGAAACTTGAGAGAG
Found at i:26845 original size:33 final size:33
Alignment explanation
Indices: 26789--26854 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
26779 AAATAGATAG
*
26789 AGTGGTGAAAGAAGTAAAAGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAAAAGTGTTAAGGGGTGA
* *
26822 AGTGGTGAAAGAAGCT-GAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAG-TAAAAGTGTTAAGGGGTGA
26855 TCTTAAGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.44, T:0.21
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAAAAGTGTTAAGGGGTGA
Found at i:28039 original size:4 final size:4
Alignment explanation
Indices: 28030--30022 Score: 3679
Period size: 4 Copynumber: 499.2 Consensus size: 4
28020 TAAGATATTG
28030 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28078 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28126 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28174 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28222 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28270 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28318 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28366 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28414 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28462 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28510 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28558 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28606 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28654 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28702 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28750 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28798 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28846 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28894 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28942 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
28990 GTAT GTAT GTAT GTAT GTAT GTAT G--T GTAT GTAT GTAT GTA- -TAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
29034 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GCAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * *
29082 GTAT GCAT GTAT CTAT GCAT GTAT GCAT GTAT GTAT GTAT GCAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * *
29130 GTAT GCAT GTAT GTAT GCAT GTAT CTAT GCAT GTAT GCAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
29178 GTAT GCAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
29226 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
29274 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
29322 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
29370 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * *
29418 GTAT GCAT GCAT GTAT GTAT GCAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
29466 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
29514 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
29562 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
29610 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* ** * * *
29658 GTAT GTAT ATAT GTAT ACAT GCAT GCAT GCAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* ** * * * * *
29706 ATAT GTAT ACAT GCAT GCAT GCAT GCAT GCAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
29754 GTAT GTAT GTAT ATAT GTAT GTAT ATAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
29802 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
29850 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
29898 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
29946 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
29994 GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
30023 AAAGGACATT
Statistics
Matches: 1941, Mismatches: 44, Indels: 8
0.97 0.02 0.00
Matches are distributed among these distances:
2 4 0.00
4 1937 1.00
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:30621 original size:19 final size:19
Alignment explanation
Indices: 30597--30645 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
30587 AATGTAGGGT
*
30597 TAATTTTTTATAAGATTTA
1 TAATTTTGTATAAGATTTA
30616 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
30635 TAATTTTGTAT
1 TAATTTTGTAT
30646 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:32091 original size:251 final size:251
Alignment explanation
Indices: 31647--32100 Score: 680
Period size: 251 Copynumber: 1.8 Consensus size: 251
31637 TAACGACCCA
* * *
31647 AAAAACATCGAAACCTATAATTATAATGTAATGGGTAATTTTTCAATATAACTGGTATAAATATA
1 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATATAACCGGTATAAATATA
* * * *
31712 CTGGTTTTATGAAAAATATGTCTACAACATTTATCGACACTTATTAGTATTGTGTCGATACTTTT
66 CCGGTTTTATGAAAAATATGTCTACAACATGTATCGACACTTATTAATATTGTGTCGATAATTTT
* * * *
31777 TGTCCAGAATGGATGCCAAAAAGGGTGAACCTACAAAGTGTCGATATATTTTCATAGAGTGTCGA
131 TGTCCAGAATGAATGCCAAAAAGGGTGAACCTACAAAGTGTCGATACATTTTCAAAAAGTGTCGA
31842 T-CCAAAAGGGTTGCACGCATAAAATGTCGATACATTTATTAAAAGAGTCGATCCC
196 TCCCAAAAGGGTTGCACGCATAAAATGTCGATACATTTATTAAAAGAGTCGATCCC
* * *
31897 AAAAATATCGAAGCCCATAATTATAATGTAATAGGTAATTTTGT-AATATAACCGGTATACATAT
1 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTT-TCAATATAACCGGTATAAATAT
* * * *
31961 ACCGGTTTTATGAGAGAATATGTCTATAATATGTATTGACACTTATTAATATTGTGTCGATAATT
65 ACCGGTTTTATGA-AAAATATGTCTACAACATGTATCGACACTTATTAATATTGTGTCGATAATT
* *
32026 TTTGTCCATAATGAATGCCAAAAAGGGTGAACGC-ATAAAGTGTCGATACATTTTCAAAAAGTGT
129 TTTGTCCAGAATGAATGCCAAAAAGGGTGAAC-CTACAAAGTGTCGATACATTTTCAAAAAGTGT
32090 CGATCCCAAAA
193 CGATCCCAAAA
32101 ACATTGAAAC
Statistics
Matches: 180, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
250 68 0.38
251 105 0.58
252 7 0.04
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.33
Consensus pattern (251 bp):
AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATATAACCGGTATAAATATA
CCGGTTTTATGAAAAATATGTCTACAACATGTATCGACACTTATTAATATTGTGTCGATAATTTT
TGTCCAGAATGAATGCCAAAAAGGGTGAACCTACAAAGTGTCGATACATTTTCAAAAAGTGTCGA
TCCCAAAAGGGTTGCACGCATAAAATGTCGATACATTTATTAAAAGAGTCGATCCC
Found at i:34072 original size:200 final size:196
Alignment explanation
Indices: 33672--34373 Score: 675
Period size: 200 Copynumber: 3.5 Consensus size: 196
33662 ACCTAAATAT
* * * *
33672 GTGTTGATACATTT-TATACAAGTATCGA-CCCAAAAAACATCAAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTAT-TAAAAGTATCGATCCC-AAAAACATCGAAACCGATAATTATAATGTAA
* * ** * *
33735 TAGGTAAATTAACAATGTAAATGGTATAAATATACCGG-TTAATTAGAAAATAGGTCAACATAAT
64 TAGGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTC-ACATAAT
* * * * *
33799 GTATCGACACTTGTGTAATTTGTGTTGATACTTATTGTCCAGGATGAATGCACAAACGAGATGC-
128 GTATCGACACTTGT-TAATTTGTGTCGATACTT-TTGTCCAGAATGAATCCA-AAAAG-GGTGCA
33863 ACGCATAAA
189 AC-CATAAA
* *
33872 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAATATCGAAACCGATAATTATAATGTATTA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * *
33937 GGTAAATTTACAATGTAACCGATATAAATATATCGGTTTTATGATAAAATAGGTCAGCATAAAGT
66 GGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCA-CATAATGT
*
34002 ATCGACACTTGATAAATTTGTGTCGATACTTTTGGTCCAGAATGAATACCAAAAAGGGTGCAACC
130 ATCGACACTTG-TTAATTTGTGTCGATACTTTT-GTCCAGAATGAAT-CCAAAAAGGGTGCAACC
34067 ATAAA
192 ATAAA
* * ** * *
34072 GTGTCGATACATTTATAAAAAATATCGATCCCGGAAACATCGAAACAC-ATAAGTATAATTTAAT
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAAC-CGATAATTATAATGTAAT
* * * * *
34136 AGGTAAATTTTCAATATAACCGGTATAAATATACCGATTTTATGAGAGAATATGTCTAAATAATG
65 AGGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTC-ACATAATG
** * **
34201 TATCGACACGTTGTTAGGTTGTGTCGATACTTTTTTTCCAAAATGAAATATGAATGCCCAACCA-
129 TATCGACAC-TTGTTAATTTGTGTCGATAC-TTTTGTCC---A-G--A-ATGAAT--CCAAAAAG
*
34265 GGTGCAAGCATAAA
183 GGTGCAACCATAAA
*** * * *
34279 GTGTCGATACA--TA-TAAAATTGTATCGATTTAAAAAATATCGTAACCGATAATAATAATGTAA
1 GTGTCGATACATTTATTAAAA--GTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAA
*
34341 TAGGTAAATTTACAATATTACCGGTATAAATAT
64 TAGGTAAATTTACAATATAACCGGTATAAATAT
34374 GTCGGTTTAC
Statistics
Matches: 418, Mismatches: 61, Indels: 40
0.81 0.12 0.08
Matches are distributed among these distances:
200 230 0.55
201 80 0.19
202 3 0.01
203 1 0.00
204 5 0.01
205 3 0.01
206 61 0.15
207 30 0.07
208 5 0.01
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (196 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCACATAATGTA
TCGACACTTGTTAATTTGTGTCGATACTTTTGTCCAGAATGAATCCAAAAAGGGTGCAACCATAA
A
Found at i:34446 original size:23 final size:23
Alignment explanation
Indices: 34390--34446 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
34380 TTACTTTGAA
* *
34390 AATATGTCAATATAAGCGCTACCT
1 AATATGT-TATATAAGAGCTACCT
* **
34414 ATTACATTATATAAGAGCTACCT
1 AATATGTTATATAAGAGCTACCT
34437 AATATGTTAT
1 AATATGTTAT
34447 TGTACTTGAT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.35
Consensus pattern (23 bp):
AATATGTTATATAAGAGCTACCT
Found at i:38981 original size:18 final size:17
Alignment explanation
Indices: 38947--38979 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38937 AAAAAATTGT
*
38947 GTCTGTGACTGTTTTTA
1 GTCTGCGACTGTTTTTA
38964 GTCTGCGACTGTTTTT
1 GTCTGCGACTGTTTTT
38980 TAAAGTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.15, G:0.24, T:0.52
Consensus pattern (17 bp):
GTCTGCGACTGTTTTTA
Found at i:39772 original size:11 final size:11
Alignment explanation
Indices: 39756--39781 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39746 GCACAGTAGT
39756 CTTTTACTTGG
1 CTTTTACTTGG
39767 CTTTTACTTGG
1 CTTTTACTTGG
39778 CTTT
1 CTTT
39782 CGTCAACCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.19, G:0.15, T:0.58
Consensus pattern (11 bp):
CTTTTACTTGG
Found at i:41582 original size:48 final size:48
Alignment explanation
Indices: 41506--41599 Score: 134
Period size: 48 Copynumber: 2.0 Consensus size: 48
41496 TATTATTGTC
41506 AAATAATGAAACATATTCTATGTGAACTCAACAATTAAACTCTTTTTA
1 AAATAATGAAACATATTCTATGTGAACTCAACAATTAAACTCTTTTTA
* * * * * *
41554 AAATAATGAAATATGTTTTATGTTAACTCAGCAATTAATCTCTTTT
1 AAATAATGAAACATATTCTATGTGAACTCAACAATTAAACTCTTTT
41600 AGCTTAGATA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.39
Consensus pattern (48 bp):
AAATAATGAAACATATTCTATGTGAACTCAACAATTAAACTCTTTTTA
Found at i:44179 original size:20 final size:20
Alignment explanation
Indices: 44154--44200 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
44144 CTCTACACTC
*
44154 TTCCACTCCCTTCCATAAGG
1 TTCCACACCCTTCCATAAGG
* *
44174 TTCCACACTCTTTCATAAGG
1 TTCCACACCCTTCCATAAGG
44194 TTCCACA
1 TTCCACA
44201 TATCTCCAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.36, G:0.09, T:0.32
Consensus pattern (20 bp):
TTCCACACCCTTCCATAAGG
Done.