Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008560.1 Hibiscus syriacus cultivar Beakdansim tig00111467_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: 753118
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:742635 original size:21 final size:20
Alignment explanation
Indices: 742552--742705 Score: 71
Period size: 21 Copynumber: 7.7 Consensus size: 20
742542 AATGACCAAC
**
742552 AAATCGCAACGCGA-AAT-A
1 AAATCGCAACGCGATTTTCA
***
742570 AAATCGCAACGCGATCCCCA
1 AAATCGCAACGCGATTTTCA
* ** * *
742590 GAATCGCAAATC-AGTTTCC
1 AAATCGCAACGCGATTTTCA
*
742609 AAATCGCAACGCGATTCTTGA
1 AAATCGCAACGCGATT-TTCA
* * * *
742630 AAATCGCGATGCGATAGTACA
1 AAATCGCAACGCGAT-TTTCA
* **
742651 AATTCGCATTGCGATTTTCA
1 AAATCGCAACGCGATTTTCA
* * *
742671 ATAATCGCAACGCGAATATGA
1 A-AATCGCAACGCGATTTTCA
742692 AAATCGCAACGCGA
1 AAATCGCAACGCGA
742706 ACACATAAAT
Statistics
Matches: 97, Mismatches: 33, Indels: 10
0.69 0.24 0.07
Matches are distributed among these distances:
18 14 0.14
19 11 0.11
20 29 0.30
21 43 0.44
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGATTTTCA
Found at i:742698 original size:20 final size:20
Alignment explanation
Indices: 742673--742980 Score: 77
Period size: 20 Copynumber: 15.5 Consensus size: 20
742663 GATTTTCAAT
* *
742673 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
742693 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
742713 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
742733 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
742753 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
742773 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
742793 TATCGCAACGCGTATC-C--A
1 AATCGCAACGCG-AACACATA
** *
742811 AATCGCAACGATAATACATA
1 AATCGCAACGCGAACACATA
* *
742831 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
742851 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
742871 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
742891 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
742911 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
742931 AATCGCAACGATAATC-CGTA
1 AATCGCAACGCGAA-CACATA
* *
742951 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
742971 AATCGCAACG
1 AATCGCAACG
742981 ATAATCCGTA
Statistics
Matches: 241, Mismatches: 37, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
17 1 0.00
18 11 0.05
19 2 0.01
20 223 0.93
21 4 0.02
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:742718 original size:40 final size:40
Alignment explanation
Indices: 742673--743059 Score: 428
Period size: 40 Copynumber: 9.7 Consensus size: 40
742663 GATTTTCAAT
* ** * * *
742673 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAAC-CGTA
* *
742713 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
** * * *
742753 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
742793 TATCGCAACGCGTATCC--AAATCGCAACGA-TAATACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* *
742831 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
742871 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
742911 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
742951 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * *
742991 AATCGCAACGAGAATCTGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * * *
743031 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
743060 ACTGAAATTT
Statistics
Matches: 308, Mismatches: 33, Indels: 12
0.87 0.09 0.03
Matches are distributed among these distances:
37 2 0.01
38 29 0.09
39 2 0.01
40 271 0.88
41 4 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
Found at i:742987 original size:20 final size:19
Alignment explanation
Indices: 742711--743059 Score: 387
Period size: 20 Copynumber: 17.6 Consensus size: 19
742701 CGCGAACACA
742711 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
742731 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
**
742751 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACG-GTATCCG
*
742771 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
742791 TATATCGCAACGCGTATCC-
1 TAAATCGCAACG-GTATCCG
* * *
742810 -AAATCGCAACGATAATACA
1 TAAATCGCAACGGT-ATCCG
742829 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
742849 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
742869 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
742889 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
742909 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
742929 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
742949 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
742969 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
742989 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
743009 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
743029 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
743049 TAAATCACAAC
1 TAAATCGCAAC
743060 ACTGAAATTT
Statistics
Matches: 287, Mismatches: 32, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
17 1 0.00
18 13 0.05
19 2 0.01
20 269 0.94
21 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (19 bp):
TAAATCGCAACGGTATCCG
Found at i:743759 original size:24 final size:23
Alignment explanation
Indices: 743720--743765 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
743710 AAATTTGGTC
743720 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGA-TTTGATA
743744 TTGGTCAATA-CACGGATTTGAT
1 TTGGTCAATATC-CGGATTTGAT
743766 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (23 bp):
TTGGTCAATATCCGGATTTGATA
Found at i:746311 original size:19 final size:19
Alignment explanation
Indices: 746248--746490 Score: 324
Period size: 19 Copynumber: 13.7 Consensus size: 19
746238 AAATCCCAAC
746248 ATGAAAATCGCAATGCGGAA
1 ATGAAAATCGCAATGC-GAA
746268 ATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAA
*
746283 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
746301 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
746320 ATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAA
*
746335 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
746353 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
746372 ATG-AAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
*
746390 ATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
746409 ATG-AAATCGCAATGCG-A
1 ATGAAAATCGCAATGCGAA
746426 ATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAA
746443 A-G--AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
746459 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
746478 ATGAAAATCGCAA
1 ATGAAAATCGCAA
746491 CGAGATAATC
Statistics
Matches: 201, Mismatches: 4, Indels: 37
0.83 0.02 0.15
Matches are distributed among these distances:
14 28 0.14
15 2 0.01
16 12 0.06
17 10 0.05
18 43 0.21
19 93 0.46
20 13 0.06
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATGAAAATCGCAATGCGAA
Found at i:746528 original size:52 final size:52
Alignment explanation
Indices: 746248--746512 Score: 428
Period size: 52 Copynumber: 5.0 Consensus size: 52
746238 AAATCCCAAC
746248 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
746301 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
746353 ATGAAAATCGCAATGCGAAATG-AAATCGCAATGCGAAATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--G-AATCGCAATGCGAA
*
746409 ATG-AAATCGCAATGCG-AATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
746459 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
746511 AT
1 AT
746513 TATAAACGCA
Statistics
Matches: 201, Mismatches: 3, Indels: 17
0.91 0.01 0.08
Matches are distributed among these distances:
50 17 0.08
51 23 0.11
52 92 0.46
53 25 0.12
54 4 0.02
55 23 0.11
56 17 0.08
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:746609 original size:19 final size:19
Alignment explanation
Indices: 746519--746601 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
746509 AAATTATAAA
746519 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
746538 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
746558 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
746574 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
746591 CGCATTGCGAT
1 CGCATTGCGAT
746602 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:746728 original size:14 final size:14
Alignment explanation
Indices: 746709--746745 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
746699 CATCAATTAC
746709 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
746723 ACAAATCATCTTTT
1 ACAAATCAACTTTT
746737 ACAAATCAA
1 ACAAATCAA
746746 TTAACAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:748140 original size:22 final size:22
Alignment explanation
Indices: 748109--748173 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
748099 GTGAATCGGG
748109 CTCTTGAATGGTGGGAGGGGAC
1 CTCTTGAATGGTGGGAGGGGAC
* * ** *
748131 CTCTTCAATGATGACAGTGG-C
1 CTCTTGAATGGTGGGAGGGGAC
*
748152 CTCTTGAACGGTGGGAGGGGAC
1 CTCTTGAATGGTGGGAGGGGAC
748174 TCTCGAGGAA
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.20, C:0.18, G:0.38, T:0.23
Consensus pattern (22 bp):
CTCTTGAATGGTGGGAGGGGAC
Found at i:748176 original size:21 final size:21
Alignment explanation
Indices: 748109--748176 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
748099 GTGAATCGGG
748109 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
* * ** * *
748130 CCTCTTCAATGATGACAGTGGC
1 -CTCTTGAATGGTGGGAGGGGA
*
748152 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
748173 CTCT
1 CTCT
748177 CGAGGAATGA
Statistics
Matches: 33, Mismatches: 13, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.19, C:0.19, G:0.37, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGGA
Found at i:748640 original size:20 final size:19
Alignment explanation
Indices: 748615--748679 Score: 80
Period size: 18 Copynumber: 3.4 Consensus size: 19
748605 TAGTTTACTT
*
748615 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
*
748635 TCGCAACGCGAAAC-CAAA
1 TCGCAACGCGAAACTAAAA
748653 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
748672 TCGCAACG
1 TCGCAACG
748680 ACAGAATCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
18 16 0.40
19 11 0.28
20 13 0.32
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:748674 original size:19 final size:19
Alignment explanation
Indices: 748615--748746 Score: 101
Period size: 19 Copynumber: 7.6 Consensus size: 19
748605 TAGTTTACTT
* *
748615 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
748635 TCGCAACGCGAAA-CCAAA
1 TCGCAACGCGAAATGAAAA
748653 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
748672 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
748686 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
748705 TCGCAA--C-----GAAAA
1 TCGCAACGCGAAATGAAAA
748717 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
748736 TCGCAATGCGA
1 TCGCAACGCGA
748747 TTTTGGTTTC
Statistics
Matches: 91, Mismatches: 8, Indels: 27
0.72 0.06 0.21
Matches are distributed among these distances:
12 11 0.12
14 9 0.10
16 5 0.05
17 6 0.07
18 16 0.18
19 32 0.35
20 12 0.13
ACGTcount: A:0.45, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:748697 original size:33 final size:31
Alignment explanation
Indices: 748650--748741 Score: 157
Period size: 33 Copynumber: 2.9 Consensus size: 31
748640 ACGCGAAACC
748650 AAATCGCAACGCGAAATGAAAATCGCAACGA
1 AAATCGCAACGCGAAATGAAAATCGCAACGA
*
748681 CAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 -A-AATCGCAACGCGAAATGAAAATCGCAACGA
748714 AAATCGCAACGCGAAATGAAAATCGCAA
1 AAATCGCAACGCGAAATGAAAATCGCAA
748742 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
31 26 0.46
32 2 0.04
33 29 0.51
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.11
Consensus pattern (31 bp):
AAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:748717 original size:12 final size:12
Alignment explanation
Indices: 748700--748724 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
748690 AATGCGAAAT
748700 GAAAATCGCAAC
1 GAAAATCGCAAC
748712 GAAAATCGCAAC
1 GAAAATCGCAAC
748724 G
1 G
748725 CGAAATGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.24, G:0.20, T:0.08
Consensus pattern (12 bp):
GAAAATCGCAAC
Found at i:748764 original size:19 final size:19
Alignment explanation
Indices: 748742--748870 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
748732 AAAATCGCAA
748742 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
748761 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
748775 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
748794 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
748808 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
748827 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
748846 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
748866 TGCGA
1 TGCGA
748871 AAGTAACTAT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:748784 original size:33 final size:33
Alignment explanation
Indices: 748742--748833 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
748732 AAAATCGCAA
748742 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
748775 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
748808 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
748834 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:749092 original size:91 final size:93
Alignment explanation
Indices: 748912--749285 Score: 674
Period size: 91 Copynumber: 4.1 Consensus size: 93
748902 TTGAATGGAT
748912 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTG-T-AAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
748974 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
749002 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
749065 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
749093 AAATTTACTTTCAACCAAAAGACAAAAACAAAGAC-AATA-TA-TTCACAGTGTTAAAGAATACA
1 AAATTTACTTTCAACCAAAAGAC-AAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACA
749155 CAGTTTAGCAGAATTGGCAGCAACCGAAC
65 CAGTTTAGCAGAATTGGCAGCAACCGAAC
749184 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
749249 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
749277 AAATTTACT
1 AAATTTACT
749286 AAGCATCTAA
Statistics
Matches: 276, Mismatches: 1, Indels: 11
0.96 0.00 0.04
Matches are distributed among these distances:
89 12 0.04
90 50 0.18
91 138 0.50
92 8 0.03
93 68 0.25
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:751004 original size:33 final size:33
Alignment explanation
Indices: 750959--751072 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
750949 TCTTTTGGTT
750959 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
750992 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
751025 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
751057 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
751073 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 31 0.41
33 45 0.59
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:751005 original size:19 final size:18
Alignment explanation
Indices: 750966--751077 Score: 95
Period size: 14 Copynumber: 6.8 Consensus size: 18
750956 GTTGAAATGA
750966 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
750981 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
750998 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
751014 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
751031 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
*
751046 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
751063 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
751078 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 24
0.74 0.04 0.22
Matches are distributed among these distances:
14 24 0.30
15 1 0.01
16 18 0.23
17 8 0.10
18 8 0.10
19 20 0.25
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:751108 original size:14 final size:14
Alignment explanation
Indices: 751089--751143 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
751079 TTTGGTTTCG
751089 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
751103 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
751122 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
751136 CGTTGCGA
1 CGTTGCGA
751144 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:751121 original size:33 final size:33
Alignment explanation
Indices: 751073--751143 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
751063 AAAATCGCAA
**
751073 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
751106 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
751139 TGCGA
1 TGCGA
751144 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:751151 original size:33 final size:33
Alignment explanation
Indices: 751084--751165 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
751074 GCGATTTTGG
***
751084 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
751117 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
751150 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
751166 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:751170 original size:20 final size:20
Alignment explanation
Indices: 751096--751184 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
751086 TCGCGTTGCG
751096 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
751116 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
751129 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
751149 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
751169 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
751185 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:751303 original size:33 final size:33
Alignment explanation
Indices: 751261--751331 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
751251 AATACTAACT
*
751261 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* * *
751294 TGAAAATCGCAACGACCGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
751327 TGAAA
1 TGAAA
751332 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:751559 original size:22 final size:22
Alignment explanation
Indices: 751507--751561 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
751497 TGGTTGTGAG
**
751507 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
751529 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
751551 GGATTTCTTCG
1 GGATTTCTTCG
751562 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:751731 original size:20 final size:20
Alignment explanation
Indices: 751706--751897 Score: 201
Period size: 20 Copynumber: 9.6 Consensus size: 20
751696 CTTTAAATAT
751706 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
751726 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
751748 -TCTTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
751767 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
751787 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
751807 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
751827 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
751847 CGCGTTGCGA-TTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
751866 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
751886 CGCGTTGCGATT
1 CGCGTTGCGATT
751898 ATTGAAAATC
Statistics
Matches: 142, Mismatches: 24, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
19 17 0.12
20 110 0.77
21 13 0.09
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Done.