Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003638.1 Hibiscus syriacus cultivar Beakdansim tig00007708_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: 39111
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:598 original size:20 final size:19
Alignment explanation
Indices: 575--642 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
565 GAAACTTAAA
575 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
595 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
615 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
634 ATCGCAACG
1 ATCGCAACG
643 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:650 original size:14 final size:14
Alignment explanation
Indices: 631--688 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
621 ATGCGAAATG
631 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
645 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
661 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
677 AAAATCGCAACG
1 AAAATCGCAACG
689 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:673 original size:32 final size:33
Alignment explanation
Indices: 615--693 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
605 GGAAATGGCT
*
615 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
648 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
680 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
694 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:772 original size:33 final size:32
Alignment explanation
Indices: 700--776 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
690 GAAACACAAA
700 TCGCATTGCGATTTTGTCGTTGAGATTTCATT
1 TCGCATTGCGATTTTGTCGTTGAGATTTCATT
* *
732 TCACATTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTGTCGTTGAGA-TTTCATT
765 TCGCATTGCGAT
1 TCGCATTGCGAT
777 AGCCATTTCG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 23 0.56
33 18 0.44
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.45
Consensus pattern (32 bp):
TCGCATTGCGATTTTGTCGTTGAGATTTCATT
Found at i:811 original size:20 final size:19
Alignment explanation
Indices: 761--814 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
751 TTGCGATTTT
*
761 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
780 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGC
*
799 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
815 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1315 original size:18 final size:18
Alignment explanation
Indices: 1292--1336 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1282 GTCGATCAGA
*
1292 TGATAGCTCTGGGTGAGG
1 TGATAGCTCTGGGCGAGG
1310 TGATAGCTCTGGGCGAGG
1 TGATAGCTCTGGGCGAGG
*
1328 TGATGGCTC
1 TGATAGCTC
1337 CCGAAGTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATAGCTCTGGGCGAGG
Found at i:2670 original size:20 final size:20
Alignment explanation
Indices: 2645--2682 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2635 AATAGTTTCT
2645 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
2665 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
2683 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:3203 original size:20 final size:20
Alignment explanation
Indices: 3177--3249 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
3167 GATTATGTAT
*
3177 TATCGCGTTGCGAAAGTCAG
1 TATCGAGTTGCGAAAGTCAG
* *
3197 AATCGCGTTGCGAAAGTCAG
1 TATCGAGTTGCGAAAGTCAG
*
3217 TATCGAGTTGCGAAAGTAAG
1 TATCGAGTTGCGAAAGTCAG
3237 TATCGAGTTGCGA
1 TATCGAGTTGCGA
3250 TTTTGTATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (20 bp):
TATCGAGTTGCGAAAGTCAG
Found at i:3283 original size:20 final size:20
Alignment explanation
Indices: 3157--3291 Score: 98
Period size: 20 Copynumber: 6.7 Consensus size: 20
3147 CGCTTTGAAA
*
3157 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
3178 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
3198 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* *
3218 ATCG-AGTTGCGAAAGTAAGT
1 ATCGCA-TTGCGATAGTCAGT
* *
3238 ATCG-AGTTGCGATTTTGT-ATT
1 ATCGCA-TTGCGA--TAGTCAGT
3259 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
3279 ATCGCATTGCGAT
1 ATCGCATTGCGAT
3292 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
19 5 0.05
20 65 0.68
21 23 0.24
22 3 0.03
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:3294 original size:41 final size:41
Alignment explanation
Indices: 3157--3292 Score: 145
Period size: 41 Copynumber: 3.3 Consensus size: 41
3147 CGCTTTGAAA
* *
3157 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTCAGT
* * * *
3198 ATCGCGTTGCGA--AAGTCAGTATCG-AGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCA-TTGCGAAAGTCAGT
* *
3238 ATCG-AGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCA-TTGCGATTATGTATTATCGCATTGCGAAAGTCAGT
3279 ATCGCATTGCGATT
1 ATCGCATTGCGATT
3293 TTCCCAATTC
Statistics
Matches: 76, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
39 3 0.04
40 28 0.37
41 41 0.54
42 4 0.05
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTCAGT
Found at i:3309 original size:21 final size:21
Alignment explanation
Indices: 3280--3372 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
3270 ATAGTCAGTA
3280 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
3301 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
3321 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
3342 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
3362 TCGCATTGCGA
1 TCGCATTGCGA
3373 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:3310 original size:41 final size:41
Alignment explanation
Indices: 3280--3372 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
3270 ATAGTCAGTA
* *
3280 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* *
3321 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
3362 TCGCATTGCGA
1 TCGCATTGCGA
3373 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:6597 original size:128 final size:128
Alignment explanation
Indices: 6369--7202 Score: 1469
Period size: 128 Copynumber: 6.5 Consensus size: 128
6359 TTGGCACGCA
6369 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGAC
1 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGAC
*
6434 ACTACTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCC
66 ACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCC
*
6497 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGAGAC
1 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGAC
*
6562 ACTATTCATATCAGTACCTATTATTTCTCAAGGGACTTGAAGGCGCGTTCCC-GGGG-GCGCC
66 ACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCC
* *
6623 TTCAATTA-TTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTCATGTCCCTCGGGGAC
1 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGAC
*
6687 ACTATTCATATCATTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCC
66 ACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCC
*
6750 TTCCATTATTTTGTTAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGAC
1 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGAC
* * *
6815 ACTATTCATATCAGTGCCTATTATTTCTCAGGGGACTTGAAGGCACGTTCCCGGGGGTGCGCC
66 ACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCC
* *
6878 TTCCATTATTTTGTCAGAGAATATATTATCATTTCCCTATTATGTCACTCATGTCCCTCGGGGAC
1 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGAC
* * * *
6943 ACTAAAT-ATATCAATACCTATTATTTCTCAAGGGACTTGAAGGCGCGTTCCCGGGGGGGCGCC
66 ACT-ATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCC
*
7006 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGTAC
1 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGAC
7071 ACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCC
66 ACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCC
*
7134 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGAGGAC
1 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGAC
7199 ACTA
66 ACTA
7203 GATGGATTGT
Statistics
Matches: 668, Mismatches: 33, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
125 104 0.16
126 16 0.02
127 18 0.03
128 528 0.79
129 2 0.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (128 bp):
TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGAC
ACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCC
Found at i:7606 original size:28 final size:28
Alignment explanation
Indices: 7564--7667 Score: 93
Period size: 28 Copynumber: 3.5 Consensus size: 28
7554 ATTAAGTTGA
* *
7564 AATTTA-ATGTTAAATTTCGAATACTAT
1 AATTTATATTTTAAATTTCGAATAATAT
7591 AATTTATATTTTAAATTTCGAATAATATT
1 AATTTATATTTTAAATTTCGAATAATA-T
* * *
7620 ATTTTTATTTTTATTTTAACTTTTGAATAATAT
1 A-----ATTTATATTTTAAATTTCGAATAATAT
*
7653 AATTTGTATTTTAAA
1 AATTTATATTTTAAA
7668 AACATTTATC
Statistics
Matches: 63, Mismatches: 7, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
27 6 0.10
28 30 0.48
29 2 0.03
33 2 0.03
34 23 0.37
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.54
Consensus pattern (28 bp):
AATTTATATTTTAAATTTCGAATAATAT
Found at i:7635 original size:34 final size:34
Alignment explanation
Indices: 7592--7664 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
7582 GAATACTATA
* * *
7592 ATTTATATTTTAAATTTCGAATAATATTATTTTT
1 ATTTTTATTTTAAATTTCGAATAATATAATTTGT
* *
7626 ATTTTTATTTTAACTTTTGAATAATATAATTTGT
1 ATTTTTATTTTAAATTTCGAATAATATAATTTGT
7660 ATTTT
1 ATTTT
7665 AAAAACATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (34 bp):
ATTTTTATTTTAAATTTCGAATAATATAATTTGT
Found at i:8253 original size:21 final size:21
Alignment explanation
Indices: 8186--8258 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
8176 TATGGTATAA
*
8186 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
8207 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* *
8228 AACCCTGAGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
8249 AACCCTGCGG
1 AACCCTGCGG
8259 AGATGACATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.22, C:0.26, G:0.34, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:13259 original size:76 final size:77
Alignment explanation
Indices: 13132--13275 Score: 209
Period size: 76 Copynumber: 1.9 Consensus size: 77
13122 ATCATAACCC
* * * *
13132 ATACATAGATAAAAGGAAAAGGATGAAATTAATTTCACATTACAACAACAAACCTACATCGTAAC
1 ATACATAGATAAAAGAAAAAGAATGAAATCAATTTCACATTACAACAACAAACCTACATCATAAC
13197 CACTTATGAAAT
66 CACTTATGAAAT
* * * *
13209 ATACATAGAT-AATGAAAAAGAATGGAATCAATTTCACATTCCAACAACAAACCTACATTATAAC
1 ATACATAGATAAAAGAAAAAGAATGAAATCAATTTCACATTACAACAACAAACCTACATCATAAC
13273 CAC
66 CAC
13276 ATACTTCATA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
76 49 0.83
77 10 0.17
ACGTcount: A:0.49, C:0.19, G:0.09, T:0.23
Consensus pattern (77 bp):
ATACATAGATAAAAGAAAAAGAATGAAATCAATTTCACATTACAACAACAAACCTACATCATAAC
CACTTATGAAAT
Found at i:14477 original size:19 final size:21
Alignment explanation
Indices: 14439--14477 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
14429 AATTTATATG
*
14439 ATTTGATTTATAGTTTAATAA
1 ATTTGATTTATAGCTTAATAA
14460 ATTTGATTTA-A-CTTAATA
1 ATTTGATTTATAGCTTAATA
14478 TAAAATAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (21 bp):
ATTTGATTTATAGCTTAATAA
Found at i:14726 original size:22 final size:20
Alignment explanation
Indices: 14689--14732 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
14679 TAAAATTACA
*
14689 AAAAAATAATCCAAATCCCT
1 AAAAAATAACCCAAATCCCT
14709 AAAAAATCAACCCAAAATCCCT
1 AAAAAAT-AACCC-AAATCCCT
14731 AA
1 AA
14733 CCATAACCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 4 0.19
22 10 0.48
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAAAATAACCCAAATCCCT
Found at i:17548 original size:77 final size:79
Alignment explanation
Indices: 17458--17615 Score: 284
Period size: 78 Copynumber: 2.0 Consensus size: 79
17448 GGGAGTGATT
*
17458 ATAGTTTACTCATT-AAAAAACTAAGGGTTTTGTAAAGGTTACTATTGAGCCTAG-AAAAATAAA
1 ATAGTTTACTCATTAAAAAAACTAAGGGTTTTGTAAAGGTTACTATTGAGCCTAGAAAAAAGAAA
17521 GAACAAATTAGTGA
66 GAACAAATTAGTGA
*
17535 ATAGTTTAGTCATTAAAAAAACTAAGGGTTTTGTAAAGGTTACTATTGAGCCTAGAAAAAAGAAA
1 ATAGTTTACTCATTAAAAAAACTAAGGGTTTTGTAAAGGTTACTATTGAGCCTAGAAAAAAGAAA
17600 GAACAAATTAGTGA
66 GAACAAATTAGTGA
17614 AT
1 AT
17616 TTGTTAGAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
77 13 0.17
78 40 0.52
79 24 0.31
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (79 bp):
ATAGTTTACTCATTAAAAAAACTAAGGGTTTTGTAAAGGTTACTATTGAGCCTAGAAAAAAGAAA
GAACAAATTAGTGA
Found at i:19065 original size:20 final size:20
Alignment explanation
Indices: 19031--19128 Score: 65
Period size: 20 Copynumber: 4.8 Consensus size: 20
19021 AATGATTTTC
*
19031 TTTTG-AAAGCAAAATTAGA
1 TTTTGAAAAACAAAATTAGA
* *
19050 TTTTGAAAAACAAAATGAAA
1 TTTTGAAAAACAAAATTAGA
* * *
19070 TTTTGAAAAA-TAATTTCGA
1 TTTTGAAAAACAAAATTAGA
* *
19089 GCTTTCAAAAACCAAAATTGAAGA
1 -TTTTGAAAAA-CAAAATT--AGA
*
19113 TTTTGAAAAAGAAAAT
1 TTTTGAAAAACAAAAT
19129 CTTTAATTGA
Statistics
Matches: 57, Mismatches: 16, Indels: 9
0.70 0.20 0.11
Matches are distributed among these distances:
19 9 0.16
20 29 0.51
22 9 0.16
23 8 0.14
24 2 0.04
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (20 bp):
TTTTGAAAAACAAAATTAGA
Found at i:20632 original size:21 final size:22
Alignment explanation
Indices: 20594--20634 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
20584 TTAAATATTA
*
20594 TAAAGGTAGTATCAATACTCAT
1 TAAAGGTAATATCAATACTCAT
*
20616 TAAAGG-AATATCGATACTC
1 TAAAGGTAATATCAATACTC
20635 CCTGTTTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (22 bp):
TAAAGGTAATATCAATACTCAT
Found at i:22439 original size:13 final size:13
Alignment explanation
Indices: 22421--22447 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22411 ATGTTAGGAC
22421 TTAGGCCCTTATT
1 TTAGGCCCTTATT
22434 TTAGGCCCTTATT
1 TTAGGCCCTTATT
22447 T
1 T
22448 GAGTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (13 bp):
TTAGGCCCTTATT
Found at i:23985 original size:30 final size:30
Alignment explanation
Indices: 23949--24015 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
23939 AGTGTACCGG
*
23949 CGGTTCAAACCGGTTTTA-CTGGTTTTCAGC
1 CGGTTCAAACCGGTTTTATC-GATTTTCAGC
** *
23979 CGGTTCACCCCGGTTTTATCGATTTTTAGC
1 CGGTTCAAACCGGTTTTATCGATTTTCAGC
24009 CGGTTCA
1 CGGTTCA
24016 TTGTTAGTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.15, C:0.25, G:0.22, T:0.37
Consensus pattern (30 bp):
CGGTTCAAACCGGTTTTATCGATTTTCAGC
Found at i:25022 original size:29 final size:29
Alignment explanation
Indices: 24985--25041 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
24975 GTCCTAACAC
* *
24985 ATAGGTCGCCATGCCCTCCGGGCGACCTT
1 ATAGATCGCCATGCCCTCCGGACGACCTT
*
25014 ATAGATCGCCATGCTCTCCGGACGACCT
1 ATAGATCGCCATGCCCTCCGGACGACCT
25042 ACCCTTGCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.18, C:0.37, G:0.25, T:0.21
Consensus pattern (29 bp):
ATAGATCGCCATGCCCTCCGGACGACCTT
Found at i:25217 original size:29 final size:29
Alignment explanation
Indices: 25184--25241 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
25174 GTAATCTCTC
25184 GTAGGTCG-CCAGGAAGACATGGCGACCTA
1 GTAGGTCGTCC-GGAAGACATGGCGACCTA
* *
25213 GTAGGTCGTCCGGAAGGCATGGTGACCTA
1 GTAGGTCGTCCGGAAGACATGGCGACCTA
25242 CGACAAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.24, C:0.22, G:0.36, T:0.17
Consensus pattern (29 bp):
GTAGGTCGTCCGGAAGACATGGCGACCTA
Done.