Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000037.1 Hibiscus syriacus cultivar Beakdansim tig00000058_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: 71886
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3252 original size:21 final size:21
Alignment explanation
Indices: 3228--3295 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
3218 TTCCCGTGCC
3228 TCAATCCCTAATTCCCCATTT
1 TCAATCCCTAATTCCCCATTT
* *
3249 TCAATCCC--A-T-CTCATGCCT
1 TCAATCCCTAATTCCCCAT--TT
3268 T-AATCCCTAATTCCCCATTT
1 TCAATCCCTAATTCCCCATTT
3288 TCAATCCC
1 TCAATCCC
3296 ATCTCGTGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
17 4 0.11
18 7 0.19
19 3 0.08
20 3 0.08
21 15 0.42
22 4 0.11
ACGTcount: A:0.24, C:0.40, G:0.01, T:0.35
Consensus pattern (21 bp):
TCAATCCCTAATTCCCCATTT
Found at i:3278 original size:39 final size:39
Alignment explanation
Indices: 3224--3316 Score: 168
Period size: 39 Copynumber: 2.4 Consensus size: 39
3214 CCCCTTCCCG
3224 TGCCTCAATCCCTAATTCCCCATTTTCAATCCCATCTCA
1 TGCCTCAATCCCTAATTCCCCATTTTCAATCCCATCTCA
* *
3263 TGCCTTAATCCCTAATTCCCCATTTTCAATCCCATCTCG
1 TGCCTCAATCCCTAATTCCCCATTTTCAATCCCATCTCA
3302 TGCCTCAATCCCTAA
1 TGCCTCAATCCCTAA
3317 CCCTTGACTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.23, C:0.40, G:0.04, T:0.33
Consensus pattern (39 bp):
TGCCTCAATCCCTAATTCCCCATTTTCAATCCCATCTCA
Found at i:3467 original size:2 final size:2
Alignment explanation
Indices: 3460--3489 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3450 TTATACATAC
3460 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
3490 TGCCGGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11016 original size:3 final size:3
Alignment explanation
Indices: 11008--11032 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10998 GTTCATGTAT
11008 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
11033 GCTTAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:11722 original size:3 final size:3
Alignment explanation
Indices: 11714--11745 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
11704 ATTTTTCAAT
11714 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
11746 TGATTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:13566 original size:20 final size:20
Alignment explanation
Indices: 13541--13595 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
13531 GGCCATCCGA
*
13541 CCGAGGCCATCTGAAAGCAT
1 CCGAGGCCATCCGAAAGCAT
*
13561 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAAAGCAT
13581 CCGAGGCCATCCGAA
1 CCGAGGCCATCCGAA
13596 CGAGCTATGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.35, G:0.27, T:0.11
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGCAT
Found at i:13616 original size:33 final size:33
Alignment explanation
Indices: 13572--13663 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
13562 CGAGGCCATC
* *
13572 CGAGAGCATCCGAGGCCATCCGAACGAGCTATG
1 CGAGGGCATCCGAGGCCAACCGAACGAGCTATG
* *
13605 CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCATCCGAGGCCAACCGAACGAGCTATG
* *
13638 CGAGGGAATCCGA-G-CAACCGAGCGAG
1 CGAGGGCATCCGAGGCCAACCGAACGAG
13664 GGTAGGTCGC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 12 0.22
32 1 0.02
33 41 0.76
ACGTcount: A:0.27, C:0.28, G:0.36, T:0.09
Consensus pattern (33 bp):
CGAGGGCATCCGAGGCCAACCGAACGAGCTATG
Found at i:13620 original size:10 final size:10
Alignment explanation
Indices: 13557--13651 Score: 64
Period size: 10 Copynumber: 8.9 Consensus size: 10
13547 CCATCTGAAA
13557 GCATCCGAGG
1 GCATCCGAGG
* *
13567 CCATCCGAGA
1 GCATCCGAGG
13577 GCATCCGAGG
1 GCATCCGAGG
* *
13587 CCATCCGAACGA
1 GCATCCG-A-GG
*
13599 GCTATGCGAGG
1 GC-ATCCGAGG
13610 GCATCCGAGG
1 GCATCCGAGG
*
13620 GCAACCGAGCG
1 GCATCCGAG-G
*
13631 AGCTATGCGAGG
1 -GC-ATCCGAGG
*
13643 GAATCCGAG
1 GCATCCGAG
13652 CAACCGAGCG
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
10 43 0.67
11 6 0.09
12 6 0.09
13 9 0.14
ACGTcount: A:0.25, C:0.29, G:0.35, T:0.11
Consensus pattern (10 bp):
GCATCCGAGG
Found at i:13748 original size:14 final size:14
Alignment explanation
Indices: 13729--13774 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
13719 CCTCGCATAG
13729 CTCGTTCGGATGGC
1 CTCGTTCGGATGGC
13743 CTCGTTCGGATGGC
1 CTCGTTCGGATGGC
*
13757 CTCGGTCGGATGGC
1 CTCGTTCGGATGGC
13771 CTCG
1 CTCG
13775 AATGCCCAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.07, C:0.30, G:0.37, T:0.26
Consensus pattern (14 bp):
CTCGTTCGGATGGC
Found at i:14392 original size:27 final size:26
Alignment explanation
Indices: 14352--14406 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
14342 ATTTTTTACA
*
14352 AATTATAAATTTATAATTAATCTTTT
1 AATTATAAAATTATAATTAATCTTTT
* *
14378 AATTCATAAAATTATAATTATTTTTTT
1 AATT-ATAAAATTATAATTAATCTTTT
14405 AA
1 AA
14407 AATATGAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (26 bp):
AATTATAAAATTATAATTAATCTTTT
Found at i:17193 original size:16 final size:16
Alignment explanation
Indices: 17172--17210 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
17162 ATTGAGCATT
17172 CAAATTCTATTTAATC
1 CAAATTCTATTTAATC
17188 CAAATTCTATTTAATC
1 CAAATTCTATTTAATC
17204 CAAATTC
1 CAAATTC
17211 ATATAACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (16 bp):
CAAATTCTATTTAATC
Found at i:20454 original size:3 final size:3
Alignment explanation
Indices: 20446--20491 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
20436 CATCCCTCAC
20446 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20492 TTTACCGTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:27866 original size:21 final size:21
Alignment explanation
Indices: 27840--27879 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
27830 GACTATCGCA
27840 TTGCGATTTTCCAAATTCGTG
1 TTGCGATTTTCCAAATTCGTG
*
27861 TTGCGATTTTCCTAATTCG
1 TTGCGATTTTCCAAATTCG
27880 CAATGCGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.45
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGTG
Found at i:27886 original size:21 final size:21
Alignment explanation
Indices: 27835--27907 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
27825 ATTCTGACTA
* *
27835 TCGCATTGCGATTTTCCAAAT
1 TCGCAATGCGATTTTCCTAAT
***
27856 TCGTGTTGCGATTTTCCTAAT
1 TCGCAATGCGATTTTCCTAAT
* * *
27877 TCGCAATGCGA-ATACCTAAA
1 TCGCAATGCGATTTTCCTAAT
27897 TCGCAATGCGA
1 TCGCAATGCGA
27908 ATTAGGAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 17 0.40
21 26 0.60
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCTAAT
Found at i:27900 original size:20 final size:20
Alignment explanation
Indices: 27877--28010 Score: 187
Period size: 20 Copynumber: 6.7 Consensus size: 20
27867 TTTTCCTAAT
*
27877 TCGCAATGCGAATACCTAAA
1 TCGCAATGCGAATACGTAAA
* *
27897 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
27918 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
27938 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
27958 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
27978 TCACAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
27998 TCGCAACGCGAAT
1 TCGCAATGCGAAT
28011 CTGACTATCG
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
20 84 0.84
21 16 0.16
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:28233 original size:22 final size:22
Alignment explanation
Indices: 28208--28273 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
28198 GGCGACATCT
*
28208 GTCCCCATCTTCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
28230 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
*
28252 GTCTCCATCTCC-AGCGAAATCA
1 GTCCCCATCTCCGA-CGAAATCA
28274 TTCACGGTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 1 0.03
22 38 0.97
ACGTcount: A:0.26, C:0.38, G:0.14, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:28650 original size:20 final size:20
Alignment explanation
Indices: 28625--28677 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
28615 TGATTTTCAT
28625 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
**
28645 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
28665 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
28678 TTAAAGTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:30594 original size:20 final size:20
Alignment explanation
Indices: 30569--30713 Score: 187
Period size: 20 Copynumber: 7.6 Consensus size: 20
30559 AGAATAGTTT
30569 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
30589 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
30609 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
30625 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
** *
30642 AAAATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
30662 ACTATCGCAATGTGAAAATG
1 ACTATCGCAATGCGAAAATG
30682 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
30702 ACTATCGCAATG
1 ACTATCGCAATG
30714 AAAAAATCGC
Statistics
Matches: 110, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
14 7 0.06
16 6 0.05
17 4 0.04
18 2 0.02
19 10 0.09
20 81 0.74
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:30720 original size:40 final size:39
Alignment explanation
Indices: 30569--30732 Score: 172
Period size: 40 Copynumber: 4.4 Consensus size: 39
30559 AGAATAGTTT
*
30569 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATG-GAAAATG
*
30609 ACTATCGCAA--CG-AGA-GA--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATG-GAAAATG
** *
30642 AAAATCGCAACGCGAAAATGACTATCGCAATGTGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATG-GAAAATG
30682 ACTATCGCAATGCGAAAATGACTATCGCAAT-GAAAA--
1 ACTATCGCAATGCGAAAATGACTATCGCAATGGAAAATG
30718 A--ATCGCAATGCGAAA
1 ACTATCGCAATGCGAAA
30733 TGAAAATCGC
Statistics
Matches: 108, Mismatches: 9, Indels: 20
0.79 0.07 0.15
Matches are distributed among these distances:
33 13 0.12
34 24 0.22
35 2 0.02
36 5 0.05
37 4 0.04
38 7 0.06
39 10 0.09
40 43 0.40
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (39 bp):
ACTATCGCAATGCGAAAATGACTATCGCAATGGAAAATG
Found at i:30728 original size:93 final size:93
Alignment explanation
Indices: 30569--30743 Score: 305
Period size: 93 Copynumber: 1.9 Consensus size: 93
30559 AGAATAGTTT
* *
30569 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAAT
1 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAAAATCGCAAT
30634 GCGAAATGAAAATCGCAACGCGAAAATG
66 GCGAAATGAAAATCGCAACGCGAAAATG
* * *
30662 ACTATCGCAATGTGAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGAAAAAATCGCAAT
1 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAAAATCGCAAT
30727 GCGAAATGAAAATCGCA
66 GCGAAATGAAAATCGCA
30744 TTGCGATTCT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (93 bp):
ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAAAATCGCAAT
GCGAAATGAAAATCGCAACGCGAAAATG
Found at i:30738 original size:20 final size:19
Alignment explanation
Indices: 30625--30749 Score: 107
Period size: 20 Copynumber: 6.7 Consensus size: 19
30615 GCAACGAGAG
30625 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
30644 AATCGCAACGCGAAAATGAC
1 AATCGCAATGCG-AAATGAA
* * *
30664 TATCGCAATGTGAAAATGAC
1 AATCGCAATGCG-AAATGAA
* *
30684 TATCGCAATGCGAAAATGAC
1 AATCGCAATGCG-AAATGAA
*
30704 TATCGCAAT--G-AA--AA
1 AATCGCAATGCGAAATGAA
30718 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
30737 AATCGCATTGCGA
1 AATCGCAATGCGA
30750 TTCTCTCGTT
Statistics
Matches: 91, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
14 9 0.10
16 3 0.03
17 2 0.02
18 1 0.01
19 25 0.27
20 51 0.56
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.18
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:30743 original size:73 final size:73
Alignment explanation
Indices: 30572--30732 Score: 209
Period size: 73 Copynumber: 2.2 Consensus size: 73
30562 ATAGTTTACT
*
30572 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAATGCG
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAAAATCGCAATGCG
30637 AAATGAAA
66 AAATGAAA
* * * * * *
30645 ATCGCAACGCGAAAATGACTATCGCAATGTGAAAATGACTATCGCAATGCGAAAAT-GACTAT-C
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAAAATCG-CAATGC
*
30708 GCAATGAAAAA
65 GAAATG--AAA
30719 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
30733 TGAAAATCGC
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
72 7 0.09
73 53 0.70
74 16 0.21
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (73 bp):
ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAAAATCGCAATGCG
AAATGAAA
Found at i:31359 original size:21 final size:21
Alignment explanation
Indices: 31268--31372 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
31258 GACTCACCTG
*
31268 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
31290 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
31310 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
31331 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
31352 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
31373 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:31365 original size:42 final size:42
Alignment explanation
Indices: 31265--31375 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
31255 CCCGACTCAC
* * * *
31265 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
31307 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
31349 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
31376 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:32824 original size:36 final size:36
Alignment explanation
Indices: 32777--32861 Score: 170
Period size: 36 Copynumber: 2.4 Consensus size: 36
32767 AAATGTTGAT
32777 TTGTTTAATTGATGTGTACATAATTATTATTTTTGC
1 TTGTTTAATTGATGTGTACATAATTATTATTTTTGC
32813 TTGTTTAATTGATGTGTACATAATTATTATTTTTGC
1 TTGTTTAATTGATGTGTACATAATTATTATTTTTGC
32849 TTGTTTAATTGAT
1 TTGTTTAATTGAT
32862 TGAAATGTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.56
Consensus pattern (36 bp):
TTGTTTAATTGATGTGTACATAATTATTATTTTTGC
Found at i:32979 original size:33 final size:34
Alignment explanation
Indices: 32922--33050 Score: 199
Period size: 33 Copynumber: 3.9 Consensus size: 34
32912 AAAATAGACT
* ** *
32922 ATCGCAACGCGAAAATGACTATCGCAATGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
32956 ATCGCAATGCG-AAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
32989 ATCGCAATGCG-AAATGAAAATTGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
33022 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
33051 CGAAACTAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
33 62 0.70
34 26 0.30
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:33046 original size:20 final size:19
Alignment explanation
Indices: 32955--33055 Score: 87
Period size: 19 Copynumber: 5.8 Consensus size: 19
32945 GCAATGAGAG
32955 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
32974 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
32988 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
33007 AATTGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
33021 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
33041 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
33056 CTAAATTCGC
Statistics
Matches: 64, Mismatches: 7, Indels: 22
0.69 0.08 0.24
Matches are distributed among these distances:
14 19 0.30
15 2 0.03
16 4 0.06
17 4 0.06
18 1 0.02
19 21 0.33
20 13 0.20
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:33128 original size:33 final size:33
Alignment explanation
Indices: 33065--33160 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
33055 ACTAAATTCG
* *
33065 CGTTGCGATTTTCATTTTCACATTGTGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
33099 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
** *
33132 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
33161 AGTCAAATGA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 31 0.56
34 24 0.44
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:36400 original size:20 final size:20
Alignment explanation
Indices: 36375--36421 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
36365 AAATTCAGTA
36375 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
36395 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
36415 TTGCGAT
1 TTGCGAT
36422 TTACGTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:36438 original size:20 final size:20
Alignment explanation
Indices: 36415--36496 Score: 155
Period size: 20 Copynumber: 4.1 Consensus size: 20
36405 CAGAATCTCG
36415 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
36435 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
36455 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
36475 TTGCGATTTACGTATTCACA
1 TTGCGATTTACGTATTCGCA
36495 TT
1 TT
36497 ACGAATTAGA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:36524 original size:21 final size:21
Alignment explanation
Indices: 36498--36542 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
36488 ATTCACATTA
36498 CGAATTAGAAAAATCGCAACG
1 CGAATTAGAAAAATCGCAACG
* * *
36519 CGAATTTGGAAAATCGCAATG
1 CGAATTAGAAAAATCGCAACG
36540 CGA
1 CGA
36543 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (21 bp):
CGAATTAGAAAAATCGCAACG
Found at i:37610 original size:15 final size:16
Alignment explanation
Indices: 37590--37622 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
37580 ATTAATTTTC
*
37590 TTTTAAAA-AATGTTT
1 TTTTAAAATAATCTTT
37605 TTTTAAAATAATCTTT
1 TTTTAAAATAATCTTT
37621 TT
1 TT
37623 ACTTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (16 bp):
TTTTAAAATAATCTTT
Found at i:46617 original size:15 final size:15
Alignment explanation
Indices: 46599--46630 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
46589 CCCCCTTACT
46599 TTAACAATACTCCTC
1 TTAACAATACTCCTC
*
46614 TTAACACTACTCCTC
1 TTAACAATACTCCTC
46629 TT
1 TT
46631 TAAAACGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAACAATACTCCTC
Found at i:48234 original size:34 final size:32
Alignment explanation
Indices: 48172--48241 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
48162 ACCTTACAAC
* *
48172 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
48204 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
48238 TCCC
1 TCCC
48242 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):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:48550 original size:21 final size:21
Alignment explanation
Indices: 48524--48565 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
48514 CCAGAATGGG
*
48524 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
48545 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
48566 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:48698 original size:15 final size:15
Alignment explanation
Indices: 48678--48733 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
48668 AACCATGCAG
48678 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
**
48693 GGGGAATCAATACCC
1 GGGGAATCTGTACCC
*
48708 TTGGGGGAATCTGTTCCC
1 ---GGGGAATCTGTACCC
48726 GGGGAATC
1 GGGGAATC
48734 GATACCCCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
15 21 0.64
18 12 0.36
ACGTcount: A:0.21, C:0.23, G:0.34, T:0.21
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:48716 original size:33 final size:35
Alignment explanation
Indices: 48677--48761 Score: 120
Period size: 33 Copynumber: 2.5 Consensus size: 35
48667 AAACCATGCA
*
48677 GGGGGAATCTGTACCCGGGGAATCAATA-CCCT-T
1 GGGGGAATCTGTACCCGGGGAATCAATACCCCTGG
* *
48710 GGGGGAATCTGTTCCCGGGGAATCGATACCCCCTGG
1 GGGGGAATCTGTACCCGGGGAATCAATA-CCCCTGG
48746 GGGGGAATCTGTACCC
1 GGGGGAATCTGTACCC
48762 CCTGGACAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
33 26 0.58
35 4 0.09
36 15 0.33
ACGTcount: A:0.20, C:0.26, G:0.34, T:0.20
Consensus pattern (35 bp):
GGGGGAATCTGTACCCGGGGAATCAATACCCCTGG
Found at i:48750 original size:21 final size:21
Alignment explanation
Indices: 48726--48766 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
48716 ATCTGTTCCC
48726 GGGGAATC-GATACCCCCTGGG
1 GGGGAATCTG-TACCCCCTGGG
48747 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
48767 ACAATCTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.17, C:0.29, G:0.37, T:0.17
Consensus pattern (21 bp):
GGGGAATCTGTACCCCCTGGG
Found at i:51784 original size:34 final size:32
Alignment explanation
Indices: 51731--51800 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
51721 CCTTACAAAC
* *
51731 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
*
51763 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
51797 TCCC
1 TCCC
51801 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:52110 original size:21 final size:21
Alignment explanation
Indices: 52084--52124 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
52074 CAGAATGGGG
*
52084 GGAATCGGTACCCCTTCATAT
1 GGAATCGATACCCCTTCATAT
52105 GGAATCGATACCCCTTCATA
1 GGAATCGATACCCCTTCATA
52125 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (21 bp):
GGAATCGATACCCCTTCATAT
Found at i:52276 original size:33 final size:35
Alignment explanation
Indices: 52236--52314 Score: 117
Period size: 33 Copynumber: 2.3 Consensus size: 35
52226 CAAACCATGC
52236 AGGGGGAATCTGTACCCGGGGAATCAATACC-CCT
1 AGGGGGAATCTGTACCCGGGGAATCAATACCTCCT
** *
52270 -GGGGGAATCTGTTTCCGGGGAATCGATACCTCCT
1 AGGGGGAATCTGTACCCGGGGAATCAATACCTCCT
52304 AGGGGGAATCT
1 AGGGGGAATCT
52315 ATTCCCCCTG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
33 27 0.68
34 3 0.08
35 10 0.25
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.22
Consensus pattern (35 bp):
AGGGGGAATCTGTACCCGGGGAATCAATACCTCCT
Found at i:52344 original size:20 final size:20
Alignment explanation
Indices: 52286--52345 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
52276 ATCTGTTTCC
* *
52286 GGGGAATC-GATACCTCCTAG
1 GGGGAATCTG-TACCCCCTGG
* *
52306 GGGGAATCTATTCCCCCTGG
1 GGGGAATCTGTACCCCCTGG
52326 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
52346 ACAATCTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.18, C:0.28, G:0.32, T:0.22
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTGG
Found at i:53145 original size:21 final size:20
Alignment explanation
Indices: 53122--53160 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53112 AACCCCCCCG
*
53122 GGGGGGTATCGATTCCCCTA
1 GGGGGGAATCGATTCCCCTA
*
53142 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
53161 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.26, G:0.38, T:0.23
Consensus pattern (20 bp):
GGGGGGAATCGATTCCCCTA
Found at i:63920 original size:60 final size:60
Alignment explanation
Indices: 63845--63962 Score: 182
Period size: 60 Copynumber: 2.0 Consensus size: 60
63835 CTAAATTAGA
*
63845 TCTTCTGTTCCCAGTATCCACTTCTCCCTCCAACGAACCATCATCAGGCTCCTTCCTATT
1 TCTTCTGTTCCCAGTATCCACTTCTCCCTCCAACCAACCATCATCAGGCTCCTTCCTATT
* * * * *
63905 TCTTCTGTTCTCAGTATCCGCTTCTCCCTCCAACCCACCTTCATCGGGCTCCTTCCTA
1 TCTTCTGTTCCCAGTATCCACTTCTCCCTCCAACCAACCATCATCAGGCTCCTTCCTA
63963 GTCTTTGAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.15, C:0.42, G:0.09, T:0.34
Consensus pattern (60 bp):
TCTTCTGTTCCCAGTATCCACTTCTCCCTCCAACCAACCATCATCAGGCTCCTTCCTATT
Done.