Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004936.1 Hibiscus syriacus cultivar Beakdansim tig00011105_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: 67252
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2502 original size:63 final size:64
Alignment explanation
Indices: 2354--2503 Score: 180
Period size: 64 Copynumber: 2.4 Consensus size: 64
2344 AAGGTGTATT
* ** * *
2354 GATGCACAGGTAGTGCATCGATGTACTCTTTTAAAATATAAACATCGAATGTAATTAGTGCATC
1 GATGCACAAGTAGTGCATCGATGTACTCCATTAAAATATAAACATCGAATGCAATTAGTGCACC
* * * *
2418 GATGCATAAG-ACATGCATCGATGTATTCCATTAATAATA-AAACATCGAATGCATTTA-TGCAC
1 GATGCACAAGTA-GTGCATCGATGTACTCCATTAA-AATATAAACATCGAATGCAATTAGTGCAC
2480 C
64 C
2481 GATGCACAAGTAGTGCATCGATG
1 GATGCACAAGTAGTGCATCGATG
2504 CATACCTTCA
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
63 25 0.35
64 43 0.60
65 4 0.06
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (64 bp):
GATGCACAAGTAGTGCATCGATGTACTCCATTAAAATATAAACATCGAATGCAATTAGTGCACC
Found at i:2930 original size:29 final size:29
Alignment explanation
Indices: 2887--2967 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
2877 ATGAGAACAT
2887 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
* *
2917 GAGAAATGACATGATCTACATAATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
2946 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
2968 ACATATGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
28 6 0.13
29 36 0.77
30 5 0.11
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.19
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:7671 original size:21 final size:20
Alignment explanation
Indices: 7623--7675 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
7613 AAACTATTCG
** *
7623 TCAGTATCGATATTGGTCTC
1 TCAGTATCGATATTGACCCC
*
7643 TTAGTATCGATATTGAACCCC
1 TCAGTATCGATATTG-ACCCC
7664 TCAGTATCGATA
1 TCAGTATCGATA
7676 CACACCTGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (20 bp):
TCAGTATCGATATTGACCCC
Found at i:9476 original size:15 final size:15
Alignment explanation
Indices: 9452--9488 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
9442 TGTGGGGTAA
*
9452 GGTGCGCCCCCCTGC
1 GGTGCACCCCCCTGC
9467 GGTGCA-CCCCCTGC
1 GGTGCACCCCCCTGC
9481 GGTGCACC
1 GGTGCACC
9489 TTATGCTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.05, C:0.49, G:0.32, T:0.14
Consensus pattern (15 bp):
GGTGCACCCCCCTGC
Found at i:9478 original size:14 final size:14
Alignment explanation
Indices: 9459--9488 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
9449 TAAGGTGCGC
9459 CCCCCTGCGGTGCA
1 CCCCCTGCGGTGCA
9473 CCCCCTGCGGTGCA
1 CCCCCTGCGGTGCA
9487 CC
1 CC
9489 TTATGCTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.53, G:0.27, T:0.13
Consensus pattern (14 bp):
CCCCCTGCGGTGCA
Found at i:12354 original size:13 final size:13
Alignment explanation
Indices: 12336--12381 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
12326 AATGATAAAT
*
12336 AATAAAAAATTAC
1 AATAAAAAACTAC
*
12349 AAT-AAAAAGT-C
1 AATAAAAAACTAC
12360 TAATAAAAAACTAC
1 -AATAAAAAACTAC
12374 AATAAAAA
1 AATAAAAA
12382 GTACTAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 1 0.04
12 9 0.32
13 17 0.61
14 1 0.04
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.20
Consensus pattern (13 bp):
AATAAAAAACTAC
Found at i:12363 original size:25 final size:26
Alignment explanation
Indices: 12335--12388 Score: 92
Period size: 25 Copynumber: 2.1 Consensus size: 26
12325 AAATGATAAA
*
12335 TAATAAAAAATTACAATAAAAAGT-C
1 TAATAAAAAACTACAATAAAAAGTAC
12360 TAATAAAAAACTACAATAAAAAGTAC
1 TAATAAAAAACTACAATAAAAAGTAC
12386 TAA
1 TAA
12389 ATGCAAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.65, C:0.09, G:0.04, T:0.22
Consensus pattern (26 bp):
TAATAAAAAACTACAATAAAAAGTAC
Found at i:15749 original size:2 final size:2
Alignment explanation
Indices: 15742--15791 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
15732 AAAGAAAGTA
15742 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
15784 AT AT AT AT
1 AT AT AT AT
15792 TAAATGAGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16374 original size:324 final size:326
Alignment explanation
Indices: 15774--16391 Score: 790
Period size: 324 Copynumber: 1.9 Consensus size: 326
15764 ATATATATAT
* * *
15774 ATATATATATATATATATTAAATGAGTATTGGATTTTATTTAATGGATATTTATTATTTATTTAT
1 ATATATATATATATATATTAAATGAGTAATGGATTTGATTTAATGGACA-TTATTATTTATTTAT
* * * *
15839 ATATTCTCACATATAAGCAAGCTGGATCCTAACAGGATCCTACGGTAACAAAAGCAAGTCGAACC
65 ATAGTCTCACATATAAGCAAGCTGGATCCTAACAGGATCCTACGATAACAAAAGCAAGTCAAACA
* * * **
15904 ATCATAATGATATAGTAAAAGCAAGGGTCCTGCCCCATTTTCCTTCTCCCAAATCGGGTGGAAAC
130 ATCAGAATGATATAGTAAAAGCAAGGGACCTGCCCCATTTTCCTTCTCCCAAATCCGGCAGAAAC
* *
15969 ATAGAATCGTTGGGGGATTTTTTTTTACTTTTAAAATTTAAAAGTATATTGAGTTATGAATGGAT
195 ATAGAATCG-TGGGGGATTTTTTTTTACTTTTAAAATTCAAAAGTATATTGAGGTATGAATGGAT
* *
16034 TTTATGAATGTTTTTTACATGGATTCTAATTTATAAAAATGGGCTTTATTATTAAAAAATATATG
259 TTTAAGAATGTTTTTTACATGAATTCTAATTTATAAAAATGGGCTTTATTATTAAAAAATATATG
16099 CAC
324 CAC
16102 ATATATATATATATATATTAAATGAGTAATGGATTTGATTTAATGGACA-TA-TATTTATTTACT
1 ATATATATATATATATATTAAATGAGTAATGGATTTGATTTAATGGACATTATTATTTATTTA-T
* ** * *
16165 -TAGTCTTAGTTATAAGCAA-ATCGGATCCTAAC-GAGATCCTACGATAACAAAAGTAAGTCAAA
65 ATAGTCTCACATATAAGCAAGCT-GGATCCTAACAG-GATCCTACGATAACAAAAGCAAGTCAAA
* ** * * *
16227 CAAT-AGAGTGATAT-GATAAAAGCAAGGGACCTGCTTCATTTTTCTTCTCCTAAATCCGGCAGC
128 CAATCAGAATGATATAG-TAAAAGCAAGGGACCTGCCCCATTTTCCTTCTCCCAAATCCGGCAGA
* *
16290 AACATAGAATTC-T-GGTGATTTATTTTTTTACTTTTAAAATTCAAAAGTATATTGGGGTATGAA
192 AACATAGAA-TCGTGGGGGA-TT-TTTTTTTACTTTTAAAATTCAAAAGTATATTGAGGTATGAA
*
16353 T-GAGTTTTAAGAACT-TTTTTTACATGAATTCTACTTTAT
254 TGGA-TTTTAAGAA-TGTTTTTTACATGAATTCTAATTTAT
16392 TATTAAAAAA
Statistics
Matches: 251, Mismatches: 30, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
322 4 0.02
323 6 0.02
324 126 0.50
325 66 0.26
326 3 0.01
328 46 0.18
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (326 bp):
ATATATATATATATATATTAAATGAGTAATGGATTTGATTTAATGGACATTATTATTTATTTATA
TAGTCTCACATATAAGCAAGCTGGATCCTAACAGGATCCTACGATAACAAAAGCAAGTCAAACAA
TCAGAATGATATAGTAAAAGCAAGGGACCTGCCCCATTTTCCTTCTCCCAAATCCGGCAGAAACA
TAGAATCGTGGGGGATTTTTTTTTACTTTTAAAATTCAAAAGTATATTGAGGTATGAATGGATTT
TAAGAATGTTTTTTACATGAATTCTAATTTATAAAAATGGGCTTTATTATTAAAAAATATATGCA
C
Found at i:17025 original size:80 final size:80
Alignment explanation
Indices: 16887--17043 Score: 215
Period size: 80 Copynumber: 2.0 Consensus size: 80
16877 CTTTATTATT
* * * *
16887 TAACAGGTTTGGTAATATCAATTATTTAACAGGTTAATCTCATGTTCGGGTTAATAACAATCGGA
1 TAACAGGTCTGGTAATACCAATTATTTAACAGGTTAATCTCAGGTTCGAGTTAATAACAATCGGA
*
16952 TGTAGGTCAGGTCTA
66 TGCAGGTCAGGTCTA
* * * ** *
16967 TAACAGGTCTGGTAATACCAGTTATTTAACATGTTAATCTTAGGTTCGAGTTCGTAACAGTCGGA
1 TAACAGGTCTGGTAATACCAATTATTTAACAGGTTAATCTCAGGTTCGAGTTAATAACAATCGGA
17032 TGCAGGTCAGGT
66 TGCAGGTCAGGT
17044 TTGTGTTATC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (80 bp):
TAACAGGTCTGGTAATACCAATTATTTAACAGGTTAATCTCAGGTTCGAGTTAATAACAATCGGA
TGCAGGTCAGGTCTA
Found at i:17248 original size:51 final size:51
Alignment explanation
Indices: 17191--17295 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
17181 TGTTTTAACT
17191 CAAATCGATTTCAATAAGATTTGCAAGTAAAATCAACTTTTTACATCCTAC
1 CAAATCGATTTCAATAAGATTTGCAAGTAAAATCAACTTTTTACATCCTAC
17242 CAAATCGATTTCAATAAGATTTGCAAGTAAAATCAACTTTTTACATCCTAC
1 CAAATCGATTTCAATAAGATTTGCAAGTAAAATCAACTTTTTACATCCTAC
17293 CAA
1 CAA
17296 TTGTATAATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (51 bp):
CAAATCGATTTCAATAAGATTTGCAAGTAAAATCAACTTTTTACATCCTAC
Found at i:22200 original size:20 final size:19
Alignment explanation
Indices: 22165--22208 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
22155 CAGGTACAAC
22165 AAAAAACTAAAAAAAAATT
1 AAAAAACTAAAAAAAAATT
*
22184 AAAAAA-TAAAGATAAAACTT
1 AAAAAACTAAA-A-AAAAATT
22204 AAAAA
1 AAAAA
22209 GTGTTGTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 7 0.32
20 11 0.50
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (19 bp):
AAAAAACTAAAAAAAAATT
Found at i:23032 original size:21 final size:21
Alignment explanation
Indices: 23006--23055 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
22996 ATTTGGGTAC
23006 TAAACAATCAAA-CGATTGCTA
1 TAAACAAT-AAACCGATTGCTA
23027 TAAACAA-AAACCGATTGCTA
1 TAAACAATAAACCGATTGCTA
23047 TAAAACAAT
1 T-AAACAAT
23056 GCACCAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 3 0.12
20 10 0.38
21 13 0.50
ACGTcount: A:0.52, C:0.18, G:0.08, T:0.22
Consensus pattern (21 bp):
TAAACAATAAACCGATTGCTA
Found at i:24332 original size:31 final size:31
Alignment explanation
Indices: 24290--24366 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
24280 AAAAATTAAA
*
24290 AATTTAAGTACTAAAACGGACCAAAACTGAT
1 AATTTATGTACTAAAACGGACCAAAACTGAT
*
24321 AATTTATGTACTAAAACGGATCAAAACTGAT
1 AATTTATGTACTAAAACGGACCAAAACTGAT
24352 AATTTATGTACTAAA
1 AATTTATGTACTAAA
24367 CGAATAACTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.29
Consensus pattern (31 bp):
AATTTATGTACTAAAACGGACCAAAACTGAT
Found at i:24445 original size:2 final size:2
Alignment explanation
Indices: 24440--24475 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24430 AACGTAAATA
24440 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
24476 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28268 original size:24 final size:24
Alignment explanation
Indices: 28213--28268 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
28203 CATGACCTAG
* *
28213 ATTTTATTCTGATTTCTGATCTGA
1 ATTTTGTTCTGATATCTGATCTGA
* * * *
28237 AGTCTGTTCTGATATCTTATTTGA
1 ATTTTGTTCTGATATCTGATCTGA
28261 ATTTTGTT
1 ATTTTGTT
28269 TTAATTTCTC
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.11, G:0.14, T:0.55
Consensus pattern (24 bp):
ATTTTGTTCTGATATCTGATCTGA
Found at i:29704 original size:25 final size:25
Alignment explanation
Indices: 29676--29730 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
29666 GTTCATTGGA
29676 TTATTGATACATGTCAACATTTTAG
1 TTATTGATACATGTCAACATTTTAG
29701 TTATTGATACATGTCAACATTTTAG
1 TTATTGATACATGTCAACATTTTAG
29726 TTATT
1 TTATT
29731 AATCTTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (25 bp):
TTATTGATACATGTCAACATTTTAG
Found at i:36745 original size:21 final size:22
Alignment explanation
Indices: 36721--36774 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
36711 CCCTTGCTAG
36721 GTATCGATACATC-TTCAATGT
1 GTATCGATACATCTTTCAATGT
* * *
36742 GTATCAATACCCTCTTTGAATGT
1 GTATCGATA-CATCTTTCAATGT
36765 GTATCGATAC
1 GTATCGATAC
36775 CCCTAGATGG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 8 0.30
22 4 0.15
23 15 0.56
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (22 bp):
GTATCGATACATCTTTCAATGT
Found at i:38726 original size:13 final size:13
Alignment explanation
Indices: 38697--38731 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
38687 TGAGAGTAAT
*
38697 TTTTCAAAATTGA
1 TTTTCAAAAATGA
38710 -TTTCAAAAATGA
1 TTTTCAAAAATGA
38722 TTTTCAAAAA
1 TTTTCAAAAA
38732 GAAAATCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:39044 original size:25 final size:25
Alignment explanation
Indices: 39005--39070 Score: 125
Period size: 25 Copynumber: 2.7 Consensus size: 25
38995 AACCTTAATC
39005 GAGCCAAAAA-AAGTTTTATATAAG
1 GAGCCAAAAACAAGTTTTATATAAG
39029 GAGCCAAAAACAAGTTTTATATAAG
1 GAGCCAAAAACAAGTTTTATATAAG
39054 GAGCCAAAAACAAGTTT
1 GAGCCAAAAACAAGTTT
39071 CGAATGAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 10 0.24
25 31 0.76
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.23
Consensus pattern (25 bp):
GAGCCAAAAACAAGTTTTATATAAG
Found at i:41554 original size:18 final size:18
Alignment explanation
Indices: 41507--41556 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
41497 GCGGAAGCAT
* *
41507 AAGATGCCGATGTTGATA
1 AAGATGACGATTTTGATA
41525 AAGATGACGATTTTGATA
1 AAGATGACGATTTTGATA
* *
41543 AATATGATGATTTT
1 AAGATGACGATTTT
41557 TTTTGCATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (18 bp):
AAGATGACGATTTTGATA
Found at i:42992 original size:23 final size:24
Alignment explanation
Indices: 42948--42994 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
42938 TACTACTAAA
*
42948 AAATATGTTAAATAAAATAAAAGT
1 AAATATGTTAAATAAAAAAAAAGT
42972 AAATATG-TAAA-AAAGAAAAAAGT
1 AAATATGTTAAATAAA-AAAAAAGT
42995 TAGTATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 11 0.52
24 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (24 bp):
AAATATGTTAAATAAAAAAAAAGT
Found at i:44934 original size:31 final size:28
Alignment explanation
Indices: 44899--44974 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 28
44889 AGATAAAATT
*
44899 TGTTTCAAGAGAAATTGATTCAAACATTTTG
1 TGTTTCAAGAGAAATT--TTCAAA-ATTTTA
*
44930 TGTTTCAAGGGAAACGTTTTCAAAATTTTA
1 TGTTTCAAGAGAAA--TTTTCAAAATTTTA
44960 TGTTTCAAGAGAAAT
1 TGTTTCAAGAGAAAT
44975 CGTCTCAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 1 0.03
30 18 0.45
31 19 0.47
33 2 0.05
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (28 bp):
TGTTTCAAGAGAAATTTTCAAAATTTTA
Found at i:45025 original size:36 final size:36
Alignment explanation
Indices: 44977--45045 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
44967 AGAGAAATCG
* *
44977 TCTCAAGGGAGACAAAATTTGTTCCAAGGGAAACTA
1 TCTCAAGAGAGACAAAATTTATTCCAAGGGAAACTA
*
45013 TCTCAAGAGAGACAAAATTTATTTCAAGGGAAA
1 TCTCAAGAGAGACAAAATTTATTCCAAGGGAAA
45046 TGTTTTCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.23
Consensus pattern (36 bp):
TCTCAAGAGAGACAAAATTTATTCCAAGGGAAACTA
Found at i:45081 original size:101 final size:100
Alignment explanation
Indices: 44932--45127 Score: 306
Period size: 101 Copynumber: 1.9 Consensus size: 100
44922 ACATTTTGTG
44932 TTTCAAGGGAAACGTTTTCAAAATTTTATGTTTCAAGAGAAATCGTCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAACGTTTTC-AAATTTTATGTTTCAAGAGAAATCGTCTCAAGGGAGACAAAATTT
*
44997 GTTCCAAGGGAAACTATCTCAAGAGAGACAAAATTTA
65 ATTCCAAGGG-AACTATCTCAAGAGAGACAAAATTTA
*
45034 TTTCAAGGGAAATGTTTTC-AATGTTTATGTTTCAAGAGAAA-CTGTCTCAAGGGAGACAAAATT
1 TTTCAAGGGAAACGTTTTCAAAT-TTTATGTTTCAAGAGAAATC-GTCTCAAGGGAGACAAAATT
* *
45097 TATTTCAAGGGAACTGTCTCAAGAGAGACAA
64 TATTCCAAGGGAACTATCTCAAGAGAGACAA
45128 TGGTGAGCAG
Statistics
Matches: 88, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
100 23 0.26
101 47 0.53
102 18 0.20
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (100 bp):
TTTCAAGGGAAACGTTTTCAAATTTTATGTTTCAAGAGAAATCGTCTCAAGGGAGACAAAATTTA
TTCCAAGGGAACTATCTCAAGAGAGACAAAATTTA
Found at i:45449 original size:107 final size:107
Alignment explanation
Indices: 45250--46046 Score: 1292
Period size: 107 Copynumber: 7.5 Consensus size: 107
45240 TGTATTGTTC
* * * *
45250 CGAGTCTAATATCCTCCGCCGTGAAGTTGAAATTGGCTCT-AGAACT-GGGAATTTGTTTGTTGA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-AACTGGGGAAATTGTTTGTTGA
* *
45313 CAACCAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCT
65 CAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
**
45356 CGAGTCCAATATCCTTTACTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGAC
* * * *
45421 AACCAGTCGTCCCTTCCCTGTGATGTTGAACTTGTATTGTCT
66 AACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * *
45463 TGAGTCCAATATTCTTCGATGTGAAGTTGAAATTGGCTCTGAAACTGGGAAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGAC
* *
45528 AACCAGCCGTCCCTTCGATGTGAAGTTGAACTTGCGTTGTCT
66 AACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
*
45570 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGAT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGAC
* *
45635 AACCAACCGTCCCTTCGCTGTGAAGTTGAACTTGTATTGTCT
66 AACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * *
45677 CGAGTCCAATATCATTCGTTGTGAAGTTAAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGAC
*
45742 AACCAGTCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
66 AACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * *
45784 CAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAACTGGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGAC
* *
45849 AACCAGCCATCCCTTCGCTGTGAAGTTGAACTTATGTTGTCT
66 AACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
45891 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGAC
*
45956 AACCAACCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
66 AACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
45998 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGG
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGG
46047 AAGCCCCTTC
Statistics
Matches: 636, Mismatches: 53, Indels: 3
0.92 0.08 0.00
Matches are distributed among these distances:
106 39 0.06
107 597 0.94
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (107 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGAC
AACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
Found at i:46543 original size:32 final size:32
Alignment explanation
Indices: 46502--46576 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
46492 TTTGCATTAG
** * *
46502 GATGTTGAATCCCCAACGATGCCCCAATATTC
1 GATGTTGAATCCAAAAAGATGCCCCAAAATTC
* *
46534 GATGTTGAATCTAAAAAGATGCCCCAAAATTT
1 GATGTTGAATCCAAAAAGATGCCCCAAAATTC
46566 GATGTTGAATC
1 GATGTTGAATC
46577 TTCAAAGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.28
Consensus pattern (32 bp):
GATGTTGAATCCAAAAAGATGCCCCAAAATTC
Found at i:46577 original size:32 final size:32
Alignment explanation
Indices: 46519--46588 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
46509 AATCCCCAAC
*
46519 GATGCCCCAATATTCGATGTTGAATCTAAAAA
1 GATGCCCCAAAATTCGATGTTGAATCTAAAAA
* **
46551 GATGCCCCAAAATTTGATGTTGAATCTTCAAA
1 GATGCCCCAAAATTCGATGTTGAATCTAAAAA
46583 GATGCC
1 GATGCC
46589 ATCATTGTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (32 bp):
GATGCCCCAAAATTCGATGTTGAATCTAAAAA
Found at i:47683 original size:12 final size:10
Alignment explanation
Indices: 47668--47725 Score: 55
Period size: 10 Copynumber: 5.5 Consensus size: 10
47658 TTTTCCTTTA
47668 TTTTTGTTTCTC
1 TTTTT-TTT-TC
47680 TTTTTTTTTC
1 TTTTTTTTTC
*
47690 TTTTCTCTTTGC
1 TTTT-T-TTTTC
*
47702 -TTTTTTCTC
1 TTTTTTTTTC
47711 TTTTTTTTTC
1 TTTTTTTTTC
47721 TTTTT
1 TTTTT
47726 GTTCTGATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 3 0.08
10 20 0.51
11 7 0.18
12 9 0.23
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:47705 original size:21 final size:19
Alignment explanation
Indices: 47681--47730 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
47671 TTGTTTCTCT
47681 TTTTTTTTCTTTTCTCTTTGC
1 TTTTTTTTCTTTT-T-TTTGC
* *
47702 TTTTTTCTCTTTTTTTTTC
1 TTTTTTTTCTTTTTTTTGC
*
47721 TTTTTGTTCT
1 TTTTTTTTCT
47731 GATTGAATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 12 0.48
20 1 0.04
21 12 0.48
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (19 bp):
TTTTTTTTCTTTTTTTTGC
Found at i:47709 original size:14 final size:13
Alignment explanation
Indices: 47690--47728 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
47680 TTTTTTTTTC
47690 TTTTCTCTTTGCTT
1 TTTTCTCTTTG-TT
47704 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
*
47716 TTTTCTTTTTGTT
1 TTTTCTCTTTGTT
47729 CTGATTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 11 0.48
13 2 0.09
14 10 0.43
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.79
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:57515 original size:42 final size:42
Alignment explanation
Indices: 57452--57541 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
57442 CATTCAACGT
*
57452 TCCAACAATTGAAAAAGATCAACCCTCTACCGCACTCACCGA
1 TCCAACAATTGAAAAAGATCAACCCACTACCGCACTCACCGA
* *
57494 TCCAACAATTGAAAAATATCAATCCACTACCGCACTCACCGA
1 TCCAACAATTGAAAAAGATCAACCCACTACCGCACTCACCGA
*
57536 ACCAAC
1 TCCAAC
57542 TGCTTCATCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.17
Consensus pattern (42 bp):
TCCAACAATTGAAAAAGATCAACCCACTACCGCACTCACCGA
Found at i:58751 original size:11 final size:11
Alignment explanation
Indices: 58735--58765 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
58725 AATGAAAATG
58735 GTAAATAAACA
1 GTAAATAAACA
58746 GTAAATAAACA
1 GTAAATAAACA
*
58757 GAAAATAAA
1 GTAAATAAA
58766 ATAAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.06, G:0.10, T:0.16
Consensus pattern (11 bp):
GTAAATAAACA
Found at i:62576 original size:20 final size:20
Alignment explanation
Indices: 62540--62584 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
62530 GATAAAAAGT
*
62540 AAAAGTTAAAAATGAAATAG
1 AAAAGTTAAAAATGAAAGAG
*
62560 AAAAGTTAAGGAA-GAAAGAG
1 AAAAGTTAA-AAATGAAAGAG
62580 AAAAG
1 AAAAG
62585 AAAAAGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.13
Consensus pattern (20 bp):
AAAAGTTAAAAATGAAAGAG
Done.