Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005760.1 Hibiscus syriacus cultivar Beakdansim tig00013486_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: 75256
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:12537 original size:20 final size:20
Alignment explanation
Indices: 12479--12537 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
12469 AAATAACCAA
**
12479 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACGCGATTTC
* ***
12499 CAATTTCGCAACATAATTTC
1 CAAATTCGCAACGCGATTTC
12519 CAAATTCGCAACGCGATTT
1 CAAATTCGCAACGCGATTT
12538 TTGAATTCGC
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACGCGATTTC
Found at i:12544 original size:20 final size:20
Alignment explanation
Indices: 12521--12594 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
12511 ATAATTTCCA
* *
12521 AATTCGCAACGCGATTTTTG
1 AATTCGCGACGCGAATTTTG
**
12541 AATTCGCGACGTTAATTTTG
1 AATTCGCGACGCGAATTTTG
* *
12561 AATTCGCGACGCTAATTCTG
1 AATTCGCGACGCGAATTTTG
12581 AATTCGCGACGCGA
1 AATTCGCGACGCGA
12595 TTACCCAGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (20 bp):
AATTCGCGACGCGAATTTTG
Found at i:12656 original size:20 final size:20
Alignment explanation
Indices: 12581--12656 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
12571 GCTAATTCTG
*
12581 AATTCGCGACGCGATTAC-CCA
1 AATTCGCGACACGA--ACTCCA
*
12602 GATTCGCGACACGAACTCCA
1 AATTCGCGACACGAACTCCA
* * * *
12622 AAATCTCGACGCGAACTCCG
1 AATTCGCGACACGAACTCCA
*
12642 AATTCGCAACACGAA
1 AATTCGCGACACGAA
12657 TCCTGTTATG
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
19 2 0.05
20 29 0.67
21 12 0.28
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.16
Consensus pattern (20 bp):
AATTCGCGACACGAACTCCA
Found at i:12987 original size:21 final size:21
Alignment explanation
Indices: 12928--13124 Score: 131
Period size: 21 Copynumber: 9.7 Consensus size: 21
12918 CGGAATTAGT
* * *
12928 GTCGCGAATTTGGAG-TTCGA
1 GTCGCGAATCTGGAGAATCGC
* * *
12948 GTCACAAATCTAGAGAATCGC
1 GTCGCGAATCTGGAGAATCGC
*
12969 GTCGCTAATCTGG-GTAATCGC
1 GTCGCGAATCTGGAG-AATCGC
*
12990 GTCGAGAATCTGGAGAATCGC
1 GTCGCGAATCTGGAGAATCGC
* *
13011 GTCGCGAATC-GGA-ATTAGC
1 GTCGCGAATCTGGAGAATCGC
* *
13030 GTCGCGAAT-TCGAAAATCGC
1 GTCGCGAATCTGGAGAATCGC
*
13050 GTCGCGAAT-TCGGA-AATCAC
1 GTCGCGAATCT-GGAGAATCGC
* * *
13070 GTCGCGAATTTGGAG-TTTGC
1 GTCGCGAATCTGGAGAATCGC
* * *
13090 GTTGCGAATTTAGAGAATCGC
1 GTCGCGAATCTGGAGAATCGC
* *
13111 GTTGCGAATTTGGA
1 GTCGCGAATCTGGA
13125 AACTGTGTTG
Statistics
Matches: 141, Mismatches: 27, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
19 15 0.11
20 61 0.43
21 64 0.45
22 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (21 bp):
GTCGCGAATCTGGAGAATCGC
Found at i:13033 original size:19 final size:20
Alignment explanation
Indices: 13009--13099 Score: 87
Period size: 20 Copynumber: 4.6 Consensus size: 20
12999 CTGGAGAATC
13009 GCGTCGCGAA-TCGGAATTA
1 GCGTCGCGAATTCGGAATTA
* * *
13028 GCGTCGCGAATTCGAAAATC
1 GCGTCGCGAATTCGGAATTA
*
13048 GCGTCGCGAATTCGGAAATCA
1 GCGTCGCGAATTCGG-AATTA
* * *
13069 -CGTCGCGAATTTGGAGTTT
1 GCGTCGCGAATTCGGAATTA
*
13088 GCGTTGCGAATT
1 GCGTCGCGAATT
13100 TAGAGAATCG
Statistics
Matches: 57, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
19 12 0.21
20 43 0.75
21 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (20 bp):
GCGTCGCGAATTCGGAATTA
Found at i:13053 original size:20 final size:20
Alignment explanation
Indices: 12984--13079 Score: 104
Period size: 20 Copynumber: 4.8 Consensus size: 20
12974 TAATCTGGGT
* * *
12984 AATCGCGTCGAGAATCTGGAG
1 AATCGCGTCGCGAAT-TCGAA
*
13005 AATCGCGTCGCGAA-TCGGA
1 AATCGCGTCGCGAATTCGAA
* *
13024 ATTAGCGTCGCGAATTCGAA
1 AATCGCGTCGCGAATTCGAA
*
13044 AATCGCGTCGCGAATTCGGA
1 AATCGCGTCGCGAATTCGAA
*
13064 AATCACGTCGCGAATT
1 AATCGCGTCGCGAATT
13080 TGGAGTTTGC
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
19 14 0.22
20 36 0.57
21 13 0.21
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (20 bp):
AATCGCGTCGCGAATTCGAA
Found at i:13063 original size:40 final size:39
Alignment explanation
Indices: 12963--13079 Score: 119
Period size: 40 Copynumber: 2.9 Consensus size: 39
12953 AAATCTAGAG
* * * * * *
12963 AATCGCGTCGCTAATCTGGGTAATCGCGTCGAGAATCTGGAG
1 AATCGCGTCGCGAATC--GGAAATCACGTCGCGAAT-TCGAA
*
13005 AATCGCGTCGCGAATCGG-AATTAGCGTCGCGAATTCGAA
1 AATCGCGTCGCGAATCGGAAATCA-CGTCGCGAATTCGAA
13044 AATCGCGTCGCGAATTCGGAAATCACGTCGCGAATT
1 AATCGCGTCGCGAA-TCGGAAATCACGTCGCGAATT
13080 TGGAGTTTGC
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
39 20 0.31
40 26 0.40
41 4 0.06
42 15 0.23
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.22
Consensus pattern (39 bp):
AATCGCGTCGCGAATCGGAAATCACGTCGCGAATTCGAA
Found at i:13096 original size:20 final size:20
Alignment explanation
Indices: 13045--13162 Score: 94
Period size: 20 Copynumber: 5.8 Consensus size: 20
13035 GAATTCGAAA
* * *
13045 ATCGCGTCGCGAATTCGGAA
1 ATCGCGTTGCGAATTTGGAG
* *
13065 ATCACGTCGCGAATTTGGAG
1 ATCGCGTTGCGAATTTGGAG
* * *
13085 TTTGCGTTGCGAATTTAGAG
1 ATCGCGTTGCGAATTTGGAG
13105 AATCGCGTTGCGAATTTGGA-
1 -ATCGCGTTGCGAATTTGGAG
* * * *
13125 AACTGTGTTGCGAAATTAGAG
1 ATC-GCGTTGCGAATTTGGAG
*
13146 TTCGCGTTGCGAATTTG
1 ATCGCGTTGCGAATTTG
13163 TTGGTTATTT
Statistics
Matches: 75, Mismatches: 20, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
19 2 0.03
20 56 0.75
21 17 0.23
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.31
Consensus pattern (20 bp):
ATCGCGTTGCGAATTTGGAG
Found at i:13118 original size:61 final size:60
Alignment explanation
Indices: 12984--13161 Score: 164
Period size: 61 Copynumber: 2.9 Consensus size: 60
12974 TAATCTGGGT
* * * * *
12984 AATCGCGTCGAGAA-TCTGGAGAATCGCGTCGCGAATCGGAATTAGCGTCGCGAA-TTCGAA
1 AATCGCGTCGCGAATTC-GGA-AATCGCGTCGCGAATTGGAGTTAGCGTTGCGAATTTAGAA
* * *
13044 AATCGCGTCGCGAATTCGGAAATCACGTCGCGAATTTGGAGTTTGCGTTGCGAATTTAGAG
1 AATCGCGTCGCGAATTCGGAAATCGCGTCGCGAA-TTGGAGTTAGCGTTGCGAATTTAGAA
* * * * * *
13105 AATCGCGTTGCGAATTTGGAAA-CTGTGTTGCGAAATTAGAGTTCGCGTTGCGAATTT
1 AATCGCGTCGCGAATTCGGAAATC-GCGTCGCG-AATTGGAGTTAGCGTTGCGAATTT
13162 GTTGGTTATT
Statistics
Matches: 98, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
59 13 0.13
60 32 0.33
61 51 0.52
62 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (60 bp):
AATCGCGTCGCGAATTCGGAAATCGCGTCGCGAATTGGAGTTAGCGTTGCGAATTTAGAA
Found at i:13120 original size:41 final size:41
Alignment explanation
Indices: 13064--13162 Score: 119
Period size: 41 Copynumber: 2.4 Consensus size: 41
13054 CGAATTCGGA
* * *** *
13064 AATCACGTCGCGAATTTGGAGTTTGCGTTGCGAATTTAGAG
1 AATCGCGTTGCGAATTTGGAAACTGCGTTGCGAAATTAGAG
*
13105 AATCGCGTTGCGAATTTGGAAACTGTGTTGCGAAATTAGAG
1 AATCGCGTTGCGAATTTGGAAACTGCGTTGCGAAATTAGAG
*
13146 -TTCGCGTTGCGAATTTG
1 AATCGCGTTGCGAATTTG
13163 TTGGTTATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
40 16 0.32
41 34 0.68
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.32
Consensus pattern (41 bp):
AATCGCGTTGCGAATTTGGAAACTGCGTTGCGAAATTAGAG
Found at i:16860 original size:6 final size:6
Alignment explanation
Indices: 16849--16877 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
16839 TCGTATATGA
16849 ATAATT ATAATT ATAATT ATAATT ATAAT
1 ATAATT ATAATT ATAATT ATAATT ATAAT
16878 CAATCATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATAATT
Found at i:23586 original size:29 final size:29
Alignment explanation
Indices: 23543--23602 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
23533 AATTTTCACC
*
23543 AAACTAAATTGATGTAAGCAATGACATCA
1 AAACTAAATTAATGTAAGCAATGACATCA
23572 AAACTAAATTAATGTAAGCAATGACATCA
1 AAACTAAATTAATGTAAGCAATGACATCA
23601 AA
1 AA
23603 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.52, C:0.13, G:0.12, T:0.23
Consensus pattern (29 bp):
AAACTAAATTAATGTAAGCAATGACATCA
Found at i:28263 original size:29 final size:29
Alignment explanation
Indices: 28223--28290 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
28213 AATTTTCACC
28223 AAACTAAATTGATGTAAGCAATGACATCA
1 AAACTAAATTGATGTAAGCAATGACATCA
28252 AAACTAAATTGATGTAAGCAATGACATCA
1 AAACTAAATTGATGTAAGCAATGACATCA
28281 AAACTAAATT
1 AAACTAAATT
28291 AATTATGCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (29 bp):
AAACTAAATTGATGTAAGCAATGACATCA
Found at i:30306 original size:32 final size:30
Alignment explanation
Indices: 30270--30345 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
30260 GGGGCCGTGG
*
30270 GGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
30301 TGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 -GGCCTACCTAAGAAACATCTCAGGGCCGCA
30332 GAGCCTACCTAAGA
1 G-GCCTACCTAAGA
30346 GTCACATTAG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
30 1 0.03
31 23 0.64
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.25, T:0.16
Consensus pattern (30 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:31227 original size:7 final size:7
Alignment explanation
Indices: 31215--31252 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
31205 GTCAAAGAAA
31215 GTCAACG
1 GTCAACG
31222 GTCAACG
1 GTCAACG
31229 GTCAACG
1 GTCAACG
31236 GTCAACG
1 GTCAACG
31243 GTCAACG
1 GTCAACG
31250 GTC
1 GTC
31253 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:31270 original size:22 final size:22
Alignment explanation
Indices: 31242--31284 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
31232 AACGGTCAAC
31242 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
31264 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
31285 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:31320 original size:9 final size:9
Alignment explanation
Indices: 31281--31379 Score: 72
Period size: 9 Copynumber: 10.3 Consensus size: 9
31271 GGTCGGGTCG
*
31281 GGTCAGACC
1 GGTCAAACC
*
31290 GGTCAAACT
1 GGTCAAACC
* *
31299 GATTCAGACC
1 G-GTCAAACC
31309 GGTCAAACC
1 GGTCAAACC
*
31318 GGTTCGAACC
1 GG-TCAAACC
*
31328 GGTTGAAACC
1 GG-TCAAACC
31338 GGTCAAACC
1 GGTCAAACC
31347 GGTCAGAACC
1 GGTCA-AACC
* *
31357 GGTTGAAAACT
1 GG-T-CAAACC
31368 GGTCAAACC
1 GGTCAAACC
31377 GGT
1 GGT
31380 TTCCAGCAGC
Statistics
Matches: 70, Mismatches: 15, Indels: 10
0.74 0.16 0.11
Matches are distributed among these distances:
9 34 0.49
10 29 0.41
11 6 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:31328 original size:19 final size:19
Alignment explanation
Indices: 31287--31380 Score: 77
Period size: 19 Copynumber: 4.8 Consensus size: 19
31277 GTCGGGTCAG
* *
31287 ACCGGTCAAACTGATTC-A
1 ACCGGTCAAACCGGTTCGA
31305 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
* *
31325 ACCGGTTGAAACCGG-TCAA
1 ACCGG-TCAAACCGGTTCGA
31344 ACCGGTCAGAACCGGTT-GAAA
1 ACCGGTCA-AACCGGTTCG--A
*
31365 ACTGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
31381 TCCAGCAGCC
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.03
19 34 0.55
20 18 0.29
21 8 0.13
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.18
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:31341 original size:29 final size:31
Alignment explanation
Indices: 31306--31380 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
31296 ACTGATTCAG
31306 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
31335 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
31365 ACTGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
31381 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:31378 original size:20 final size:21
Alignment explanation
Indices: 31342--31380 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31332 GAAACCGGTC
31342 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
31363 AAACTGGTCA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
31381 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:37667 original size:63 final size:62
Alignment explanation
Indices: 37552--37684 Score: 146
Period size: 63 Copynumber: 2.1 Consensus size: 62
37542 ACAACGTTAC
* * ** *
37552 CCTAAGGAAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTA
1 CCTAA-GAAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATATCAGGGCCGCAGAGCCTA
*
37615 CCTAAGAACACATCTTAGGGCC-GCATG-GCCTACCCGAGA-ATGATATCAGGGCCGCAGAGCCT
1 CCTAAGAA-ACATCTTAGGGCCTG-A-GAGCCTACCCAAGATA-GATATCAGGGCCGCAGAGCCT
37677 A
62 A
37678 CCTAAGA
1 CCTAAGA
37685 GTCACATTAG
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
62 5 0.08
63 54 0.90
64 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (62 bp):
CCTAAGAAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATATCAGGGCCGCAGAGCCTA
Found at i:38567 original size:7 final size:7
Alignment explanation
Indices: 38555--38585 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
38545 GTCAAAGAAA
38555 GTCAACG
1 GTCAACG
38562 GTCAACG
1 GTCAACG
*
38569 GTCAACA
1 GTCAACG
38576 GTCAACG
1 GTCAACG
38583 GTC
1 GTC
38586 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:38598 original size:17 final size:17
Alignment explanation
Indices: 38576--38635 Score: 75
Period size: 17 Copynumber: 3.2 Consensus size: 17
38566 ACGGTCAACA
38576 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
38593 GTCAACGGTCGGGTCGGGTCG
1 GTCAACGGTCGGGTC--G--G
38614 AGTCAACGGTCGGGTCGG
1 -GTCAACGGTCGGGTCGG
38632 GTCA
1 GTCA
38636 GACCGGTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
17 19 0.50
18 1 0.03
19 1 0.03
20 1 0.03
21 1 0.03
22 15 0.39
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.18
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGG
Found at i:38610 original size:22 final size:22
Alignment explanation
Indices: 38582--38634 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
38572 AACAGTCAAC
*
38582 GGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGAGTCAACGGTCG
38604 GGTCGGGTCGAGTCAACGGTCG
1 GGTCGGGTCGAGTCAACGGTCG
38626 GGTCGGGTC
1 GGTCGGGTC
38635 AGACCGGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCGGGTCGAGTCAACGGTCG
Found at i:38649 original size:9 final size:9
Alignment explanation
Indices: 38631--38758 Score: 121
Period size: 9 Copynumber: 13.3 Consensus size: 9
38621 GGTCGGGTCG
*
38631 GGTCAGACC
1 GGTCAAACC
38640 GGTCAAACC
1 GGTCAAACC
* *
38649 GATTCAGACC
1 G-GTCAAACC
38659 GGTCAAACC
1 GGTCAAACC
*
38668 GGTTCGAACC
1 GG-TCAAACC
*
38678 GGTTGAAACC
1 GG-TCAAACC
38688 GGTCAAACC
1 GGTCAAACC
38697 GGTCAGAACC
1 GGTCA-AACC
*
38707 GGTTGAAACC
1 GG-TCAAACC
38717 GGTCAAACC
1 GGTCAAACC
38726 GGTCAGAACC
1 GGTCA-AACC
*
38736 GGTTGAAAACC
1 GG-T-CAAACC
38747 GGTCAAACC
1 GGTCAAACC
38756 GGT
1 GGT
38759 TTCCAGCAGC
Statistics
Matches: 99, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
9 47 0.47
10 42 0.42
11 9 0.09
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:38655 original size:19 final size:19
Alignment explanation
Indices: 38633--38738 Score: 110
Period size: 19 Copynumber: 5.5 Consensus size: 19
38623 TCGGGTCGGG
*
38633 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
38652 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
38671 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
38690 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* *
38710 TGAAACCGGTCAAACCGG-
1 TCAGACCGGTCAAACCGGT
38728 TCAGAACCGGT
1 TCAG-ACCGGT
38739 TGAAAACCGG
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
18 5 0.07
19 50 0.68
20 19 0.26
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.15
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:38677 original size:10 final size:9
Alignment explanation
Indices: 38656--38758 Score: 80
Period size: 10 Copynumber: 10.7 Consensus size: 9
38646 ACCGATTCAG
*
38656 ACCGGTCAA
1 ACCGGTCGA
38665 ACCGGTTCGA
1 ACCGG-TCGA
*
38675 ACCGGTTGAA
1 ACCGGTCG-A
*
38685 ACCGGTCAA
1 ACCGGTCGA
38694 ACCGGTCAGA
1 ACCGGTC-GA
*
38704 ACCGGTTGAA
1 ACCGGTCG-A
*
38714 ACCGGTCAA
1 ACCGGTCGA
38723 ACCGGTCAGA
1 ACCGGTC-GA
*
38733 ACCGGTTGAAA
1 ACCGGTCG--A
*
38744 ACCGGTCAA
1 ACCGGTCGA
38753 ACCGGT
1 ACCGGT
38759 TTCCAGCAGC
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
9 32 0.43
10 36 0.48
11 7 0.09
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
ACCGGTCGA
Found at i:50541 original size:21 final size:22
Alignment explanation
Indices: 50511--50551 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
50501 ACAAGTGTCG
*
50511 TAATTGTCAA-ATAAATAAACA
1 TAATTCTCAATATAAATAAACA
*
50532 TAATTCTCAATTTAAATAAA
1 TAATTCTCAATATAAATAAA
50552 TAAAATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (22 bp):
TAATTCTCAATATAAATAAACA
Found at i:51206 original size:18 final size:19
Alignment explanation
Indices: 51175--51220 Score: 76
Period size: 18 Copynumber: 2.5 Consensus size: 19
51165 TAGCGGTGTG
*
51175 AAAAGAAAATAATGAAAGA
1 AAAATAAAATAATGAAAGA
51194 AAAATAAAA-AATGAAAGA
1 AAAATAAAATAATGAAAGA
51212 AAAATAAAA
1 AAAATAAAA
51221 CTTTAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (19 bp):
AAAATAAAATAATGAAAGA
Found at i:59626 original size:22 final size:22
Alignment explanation
Indices: 59600--59666 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 22
59590 TGGCATATGA
*
59600 AATTTGTCCCGAAGGACCTGTG
1 AATTTGTCCCGAATGACCTGTG
*
59622 AATTTGTCCCGAATGACCTATG
1 AATTTGTCCCGAATGACCTGTG
* *
59644 -AGTTGTCCCGATTGACCTGTG
1 AATTTGTCCCGAATGACCTGTG
59665 AA
1 AA
59667 ACCCTCGACT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 18 0.46
22 21 0.54
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (22 bp):
AATTTGTCCCGAATGACCTGTG
Found at i:59651 original size:21 final size:22
Alignment explanation
Indices: 59603--59666 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 22
59593 CATATGAAAT
* * *
59603 TTGTCCCGAAGGACCTGTGAAT
1 TTGTCCCGAATGACCTATGAAG
59625 TTGTCCCGAATGACCTATG-AG
1 TTGTCCCGAATGACCTATGAAG
* *
59646 TTGTCCCGATTGACCTGTGAA
1 TTGTCCCGAATGACCTATGAA
59667 ACCCTCGACT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 18 0.50
22 18 0.50
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (22 bp):
TTGTCCCGAATGACCTATGAAG
Found at i:61156 original size:64 final size:66
Alignment explanation
Indices: 61042--61166 Score: 175
Period size: 64 Copynumber: 1.9 Consensus size: 66
61032 TAATGAAGGT
* * *
61042 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTTAATGGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCAATGTTTTCTATTTAATGGG
61106 G
66 G
* *
61107 ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCATGTTCAATGTTTTCTATTTAA
1 ATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCATATTCAATGTTTTCTATTTAA
61167 ATTCATGCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
63 1 0.02
64 27 0.51
65 25 0.47
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (66 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCAATGTTTTCTATTTAATGGG
G
Found at i:61175 original size:64 final size:62
Alignment explanation
Indices: 61042--61202 Score: 162
Period size: 64 Copynumber: 2.5 Consensus size: 62
61032 TAATGAAGGT
* * * * *
61042 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCATATTCAATGTTTCTATTTAAT-GGC
* *
61107 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCATGTTCAATGTTTTCTATTTAAAT-TC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCATATTCAATG-TTTCTATTT-AATGGC
* * *
61171 ATGCATTGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
61203 CCTTAAACAA
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
63 1 0.01
64 54 0.66
65 24 0.29
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCATATTCAATGTTTCTATTTAATGGC
Found at i:72268 original size:17 final size:19
Alignment explanation
Indices: 72211--72275 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 19
72201 TCTCTACGGT
*
72211 GGATGAATCGACCGAAGGA
1 GGATGAATCGATCGAAGGA
*
72230 GG-TGAA-CGA-CAGAAGAA
1 GGATGAATCGATC-GAAGGA
72247 GGATGAA-CGATCG-AGGA
1 GGATGAATCGATCGAAGGA
72264 GGATGAATCGAT
1 GGATGAATCGAT
72276 GTAGAACGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 1 0.03
17 20 0.50
18 16 0.40
19 3 0.08
ACGTcount: A:0.38, C:0.12, G:0.37, T:0.12
Consensus pattern (19 bp):
GGATGAATCGATCGAAGGA
Found at i:73713 original size:116 final size:115
Alignment explanation
Indices: 73551--73846 Score: 540
Period size: 116 Copynumber: 2.6 Consensus size: 115
73541 TTGCAGTATA
73551 ACTATTAATTTCCAACACCTAAAACACGATAAGTTAACCATTTATCCACCACAAAAATTAAACAT
1 ACTATTAATTTCCAACACCTAAAACACGATAAGTTAACCATTTATCCACCACAAAAATTAAACAT
73616 GGCATTGAAGTTTTGTTTGAAAAGTCTAATGTAATAGCTTAGAAAGAATAGT
66 GGCATTGAAGTTTTGTTTGAAAAGTCTAATGTAATAGCTTAGAAAG-A-AGT
73668 ACTATTAATTTCCAACACCT-AAACACGATAAGTTAACCATTTATCCACCACAAAAATTAAACAT
1 ACTATTAATTTCCAACACCTAAAACACGATAAGTTAACCATTTATCCACCACAAAAATTAAACAT
73732 GGCATTGAAGTTTTGTTTGAAAAGTCTAATGTAATAGCTTAGAAAGAAGT
66 GGCATTGAAGTTTTGTTTGAAAAGTCTAATGTAATAGCTTAGAAAGAAGT
* * *
73782 ACTATTAATTTCTAACACCTAAAACACGATATGTTAACCATTTATCCACCGCAAAAATTAAACAT
1 ACTATTAATTTCCAACACCTAAAACACGATAAGTTAACCATTTATCCACCACAAAAATTAAACAT
73847 AAAAGTCTAA
Statistics
Matches: 175, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
114 22 0.13
115 43 0.25
116 90 0.51
117 20 0.11
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (115 bp):
ACTATTAATTTCCAACACCTAAAACACGATAAGTTAACCATTTATCCACCACAAAAATTAAACAT
GGCATTGAAGTTTTGTTTGAAAAGTCTAATGTAATAGCTTAGAAAGAAGT
Done.