Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006001.1 Hibiscus syriacus cultivar Beakdansim tig00014147_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: 57489
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:1717 original size:21 final size:21
Alignment explanation
Indices: 1693--1741 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1683 ACATGACAGA
*
1693 TGGACCGTCACATCAACACTG
1 TGGACCGCCACATCAACACTG
* * *
1714 TGGACTGCCACATTAACATTG
1 TGGACCGCCACATCAACACTG
*
1735 TGAACCG
1 TGGACCG
1742 GCACGCTACT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (21 bp):
TGGACCGCCACATCAACACTG
Found at i:2908 original size:3 final size:3
Alignment explanation
Indices: 2892--2933 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
2882 AAAATATATA
* *
2892 TAT TAT TAAA TAT TAT TAT TAT TA- TAA TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2934 ACAAATATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:2920 original size:17 final size:17
Alignment explanation
Indices: 2892--2934 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
2882 AAAATATATA
2892 TATTATTA-AATATTAT
1 TATTATTATAATATTAT
2908 TATTATTATAATATTAT
1 TATTATTATAATATTAT
2925 TATTATTATA
1 TATTATTATA
2935 CAAATATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTATTATAATATTAT
Found at i:2922 original size:14 final size:14
Alignment explanation
Indices: 2886--2930 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
2876 GATCTTAAAA
2886 TATATATATTATTA-
1 TATA-ATATTATTAT
* *
2900 AATATTATTATTAT
1 TATAATATTATTAT
2914 TATAATATTATTAT
1 TATAATATTATTAT
2928 TAT
1 TAT
2931 TATACAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 8 0.31
14 18 0.69
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATAATATTATTAT
Found at i:8661 original size:20 final size:20
Alignment explanation
Indices: 8557--8713 Score: 81
Period size: 20 Copynumber: 7.8 Consensus size: 20
8547 AAATGACCAA
** *
8557 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACGCGATTTT
* * *
8577 CAATTTCGCAACTC-AGTTTC
1 CAAATTCGCAACGCGA-TTTT
*
8597 CAAATTCGCAACGCGAATATGT
1 CAAATTCGCAACGCG-AT-TTT
* **
8619 -AAA-TCACATTGCGATTTT
1 CAAATTCGCAACGCGATTTT
8637 CCAAATTCGCAACGCGATTTT
1 -CAAATTCGCAACGCGATTTT
* *
8658 CAAAATCGCAACGCGAATATGT
1 CAAATTCGCAACGCG-AT-TTT
* *
8680 -AAA-TCGCAACGCGAATCT
1 CAAATTCGCAACGCGATTTT
**
8698 GTAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
8714 ATCTGTAATT
Statistics
Matches: 106, Mismatches: 20, Indels: 22
0.72 0.14 0.15
Matches are distributed among these distances:
18 4 0.04
19 6 0.06
20 71 0.67
21 21 0.20
22 4 0.04
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (20 bp):
CAAATTCGCAACGCGATTTT
Found at i:8714 original size:20 final size:20
Alignment explanation
Indices: 8640--8729 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
8630 CGATTTTCCA
* * **
8640 AATTCGCAACGCGATTTTCA
1 AATTCGCAACGCGAATCTGT
* *
8660 AAATCGCAACGCGAATATGT
1 AATTCGCAACGCGAATCTGT
*
8680 AAATCGCAACGCGAATCTGT
1 AATTCGCAACGCGAATCTGT
8700 AATTCGCAACGCGAATCTGT
1 AATTCGCAACGCGAATCTGT
8720 AATTCGCAAC
1 AATTCGCAAC
8730 ACAGAAGTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
AATTCGCAACGCGAATCTGT
Found at i:8744 original size:40 final size:38
Alignment explanation
Indices: 8657--8748 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 38
8647 AACGCGATTT
* *
8657 TCAAAATCGCAACGCGAATATGTAAATCGCAACGCGAA
1 TCAAATTCGCAACGCGAATATGTAAATCGCAACACGAA
* * *
8695 TCTGTAATTCGCAACGCGAATCTGTAATTCGCAACACAGAA
1 TC--AAATTCGCAACGCGAATATGTAAATCGCAACAC-GAA
8736 GTCAAATTCGCAA
1 -TCAAATTCGCAA
8749 AGTGCGTTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
38 2 0.05
40 37 0.84
41 3 0.07
42 2 0.05
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (38 bp):
TCAAATTCGCAACGCGAATATGTAAATCGCAACACGAA
Found at i:8928 original size:22 final size:22
Alignment explanation
Indices: 8903--8950 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
8893 CGGCGACATT
8903 CGTCCCCATCTCCGACGAAATC
1 CGTCCCCATCTCCGACGAAATC
* *
8925 CGTCCCCATCTCCGGCGAAATT
1 CGTCCCCATCTCCGACGAAATC
8947 CGTC
1 CGTC
8951 TATCTCCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.44, G:0.17, T:0.21
Consensus pattern (22 bp):
CGTCCCCATCTCCGACGAAATC
Found at i:9392 original size:19 final size:19
Alignment explanation
Indices: 9368--9406 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
9358 AATATGTAAA
*
9368 TCGCATTGCGATTTTCATT
1 TCGCATTGCAATTTTCATT
9387 TCGCATTGCAATTTTCATT
1 TCGCATTGCAATTTTCATT
9406 T
1 T
9407 TCAGAAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.49
Consensus pattern (19 bp):
TCGCATTGCAATTTTCATT
Found at i:11163 original size:21 final size:23
Alignment explanation
Indices: 11139--11235 Score: 66
Period size: 21 Copynumber: 4.6 Consensus size: 23
11129 TGGTGCATGG
11139 CGTGATGAGGTA-CGGT-CTTTA
1 CGTGATGAGGTAGCGGTACTTTA
* *
11160 CGTGGTGAGGTAGAGGT--TTTA
1 CGTGATGAGGTAGCGGTACTTTA
* ** *
11181 CGTGATGA--CAATGGTGCTTTA
1 CGTGATGAGGTAGCGGTACTTTA
* *
11202 CGTGGTGAGGTATC--TACTTTA
1 CGTGATGAGGTAGCGGTACTTTA
11223 CGTGATGAGGTAG
1 CGTGATGAGGTAG
11236 TCGCTCTATG
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
19 4 0.07
21 50 0.86
22 3 0.05
23 1 0.02
ACGTcount: A:0.21, C:0.11, G:0.35, T:0.33
Consensus pattern (23 bp):
CGTGATGAGGTAGCGGTACTTTA
Found at i:11211 original size:63 final size:63
Alignment explanation
Indices: 11114--11235 Score: 158
Period size: 63 Copynumber: 1.9 Consensus size: 63
11104 AGGTCGGTAC
* *
11114 TTTACGTGAAGACAATGGTGCATGGCGTGATGAGGTA-CGGT-CTTTACGTGGTGAGGTAGAGGT
1 TTTACGTGAAGACAATGGTGCATGACGTGATGAGGTATC--TACTTTACGTGATGAGGTAGAGGT
* * * *
11177 TTTACGTGATGACAATGGTGCTTTACGTGGTGAGGTATCTACTTTACGTGATGAGGTAG
1 TTTACGTGAAGACAATGGTGCATGACGTGATGAGGTATCTACTTTACGTGATGAGGTAG
11236 TCGCTCTATG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
62 1 0.02
63 49 0.96
64 1 0.02
ACGTcount: A:0.22, C:0.11, G:0.34, T:0.32
Consensus pattern (63 bp):
TTTACGTGAAGACAATGGTGCATGACGTGATGAGGTATCTACTTTACGTGATGAGGTAGAGGT
Found at i:11557 original size:21 final size:21
Alignment explanation
Indices: 11514--11563 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
11504 CCTGTCATCA
* * *
11514 TTCAAGAGGCCTCTCCTATCG
1 TTCAAGAGGCCCCTCCCACCG
11535 TTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCCCCTCCCACCG
*
11556 TTCGAGAG
1 TTCAAGAG
11564 CCCGATTCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.36, G:0.22, T:0.22
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCCACCG
Found at i:12933 original size:13 final size:14
Alignment explanation
Indices: 12908--12940 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
12898 AAATTGATGT
12908 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
12922 ATTTGT-AAAGTTG
1 ATTTGTAAAAGTTG
12935 ATTTGT
1 ATTTGT
12941 TTAATTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:13001 original size:14 final size:14
Alignment explanation
Indices: 12982--13021 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
12972 GCTTGTTTAA
12982 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
12996 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
13010 TTGATGTGTAAA
1 TTGATTTGTAAA
13022 TAATTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:13031 original size:65 final size:64
Alignment explanation
Indices: 12919--13064 Score: 213
Period size: 65 Copynumber: 2.3 Consensus size: 64
12909 TTTGTAAAAG
**
12919 TTGATTTGT-AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAA
1 TTGATTTGTAAAAGTTGATTTGTAAAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAA
* * ** *
12982 TTGATTTGTAAAAGTTGATTTGTAAAAGTTGATGTGTAAATAATTATTATTTTTTGTTTGTTTAA
1 TTGATTTGTAAAAGTTGATTTGTAAAA-TTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAA
13047 TTGATTTGTAAAAGTTGA
1 TTGATTTGTAAAAGTTGA
13065 GGTTGTTTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
63 9 0.12
64 15 0.20
65 50 0.68
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.50
Consensus pattern (64 bp):
TTGATTTGTAAAAGTTGATTTGTAAAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAA
Found at i:13187 original size:20 final size:20
Alignment explanation
Indices: 13127--13188 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
13117 AAGGTAGAAT
*
13127 TTCGCAACGCGAAAGTCAAA
1 TTCGCAATGCGAAAGTCAAA
** * *
13147 TTCGCGTTGTGATAGTCAAA
1 TTCGCAATGCGAAAGTCAAA
*
13167 TTCGCAATGCGAAAGTTAAA
1 TTCGCAATGCGAAAGTCAAA
13187 TT
1 TT
13189 TGGGTTGTGA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (20 bp):
TTCGCAATGCGAAAGTCAAA
Found at i:13459 original size:18 final size:18
Alignment explanation
Indices: 13436--13472 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
13426 AAGCCGGTTG
*
13436 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
13454 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
13472 T
1 T
13473 CTTTTACTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.03, G:0.24, T:0.57
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:15764 original size:24 final size:24
Alignment explanation
Indices: 15730--15783 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
15720 CTGAAACATC
15730 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
15754 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
15778 ATCAAA
1 ATCAAA
15784 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:15797 original size:24 final size:24
Alignment explanation
Indices: 15730--15797 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
15720 CTGAAACATC
* * *
15730 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
15754 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
15778 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
15798 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:16732 original size:20 final size:20
Alignment explanation
Indices: 16688--16836 Score: 87
Period size: 20 Copynumber: 7.5 Consensus size: 20
16678 CAAAACATTT
*
16688 GTGTTGCGAAACTAAAA--C
1 GTGTTGCGAAATTAAAATTC
*
16706 ATGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
*
16726 GTGTTGCGAATTTGAAAA-TC
1 GTGTTGCGAAATT-AAAATTC
* **
16746 GAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAATTAAAATTC
** *
16766 ACGTTGCGAATTTAAAAATT-
1 GTGTTGCGAAATT-AAAATTC
*
16786 GAGTTGC-AAATTTAAAAATT-
1 GTGTTGCGAAA-TT-AAAATTC
* *
16806 GAGTTGC-AAATTTGAAATTC
1 GTGTTGCGAAA-TTAAAATTC
16826 AGTGTTGCGAA
1 -GTGTTGCGAA
16837 TTTGGAAATC
Statistics
Matches: 104, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
18 15 0.14
19 11 0.11
20 60 0.58
21 16 0.15
22 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (20 bp):
GTGTTGCGAAATTAAAATTC
Found at i:16763 original size:40 final size:40
Alignment explanation
Indices: 16708--16792 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
16698 ACTAAAACAT
** ** *
16708 GTTGCGAAATTAAAATTCGTGTTGCGAATTTGAAAATCGA
1 GTTGCGAAAACAAAATTCACGTTGCGAATTTAAAAATCGA
*
16748 GTTGCGAAAACAAAATTCACGTTGCGAATTTAAAAATTGA
1 GTTGCGAAAACAAAATTCACGTTGCGAATTTAAAAATCGA
16788 GTTGC
1 GTTGC
16793 AAATTTAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (40 bp):
GTTGCGAAAACAAAATTCACGTTGCGAATTTAAAAATCGA
Found at i:16781 original size:60 final size:62
Alignment explanation
Indices: 16708--16867 Score: 159
Period size: 60 Copynumber: 2.6 Consensus size: 62
16698 ACTAAAACAT
* *
16708 GTTGCGAAATT-AAAATTCGTGTTGCGAATTTGAAAATCGAGTTGCGAAA-ACAAAATTCA-C
1 GTTGCGAATTTAAAAATTCGAGTTGCGAATTTGAAAATCGAGTTGC-AAATACAAAATTCAGC
* * * *** *
16768 GTTGCGAATTTAAAAATT-GAGTTGCAAATTTAAAAATTGAGTTGCAAATTTGAAATTCAGT
1 GTTGCGAATTTAAAAATTCGAGTTGCGAATTTGAAAATCGAGTTGCAAATACAAAATTCAGC
** * *
16829 GTTGCGAATTTGGAAA-TCGCGTTGCGAATTTGGAAATCG
1 GTTGCGAATTTAAAAATTCGAGTTGCGAATTTGAAAATCG
16868 CGTTATGAAT
Statistics
Matches: 80, Mismatches: 16, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
59 3 0.04
60 41 0.51
61 36 0.45
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.32
Consensus pattern (62 bp):
GTTGCGAATTTAAAAATTCGAGTTGCGAATTTGAAAATCGAGTTGCAAATACAAAATTCAGC
Found at i:16812 original size:40 final size:39
Alignment explanation
Indices: 16708--16836 Score: 100
Period size: 40 Copynumber: 3.2 Consensus size: 39
16698 ACTAAAACAT
** * *
16708 GTTGCGAAATTAAAATTCGTGTTGCGAATTTGAAAATCGA
1 GTTGCGAAAACAAAATT-GAGTTGCGAATTTAAAAATCGA
* *
16748 GTTGCGAAAACAAAATTCACGTTGCGAATTTAAAAATTGA
1 GTTGCGAAAACAAAATTGA-GTTGCGAATTTAAAAATCGA
* * * *
16788 GTTGC-AAATTTA-AAAATTGAGTTGCAAATTTGAAATTCAGT
1 GTTGCGAAA---ACAAAATTGAGTTGCGAATTTAAAAATC-GA
16829 GTTGCGAA
1 GTTGCGAA
16837 TTTGGAAATC
Statistics
Matches: 71, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
39 3 0.04
40 52 0.73
41 13 0.18
42 3 0.04
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (39 bp):
GTTGCGAAAACAAAATTGAGTTGCGAATTTAAAAATCGA
Found at i:16854 original size:20 final size:20
Alignment explanation
Indices: 16829--16884 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
16819 GAAATTCAGT
16829 GTTGCGAATTTGGAAATCGC
1 GTTGCGAATTTGGAAATCGC
16849 GTTGCGAATTTGGAAATCGC
1 GTTGCGAATTTGGAAATCGC
**
16869 GTTATGAATTTGGAAA
1 GTTGCGAATTTGGAAA
16885 CTGAGTTGCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTTGGAAATCGC
Found at i:17251 original size:31 final size:31
Alignment explanation
Indices: 17198--17263 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
17188 CAGTAAATAT
*
17198 AAGATTTAGTCATTTTCATTTTTATTTAATC
1 AAGATTTAGTCATTGTCATTTTTATTTAATC
* * * *
17229 AAGATTTGGTTATTGTCGTTTTTATTTAATT
1 AAGATTTAGTCATTGTCATTTTTATTTAATC
17260 AAGA
1 AAGA
17264 CATGGTCAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (31 bp):
AAGATTTAGTCATTGTCATTTTTATTTAATC
Found at i:20289 original size:183 final size:184
Alignment explanation
Indices: 20082--20467 Score: 611
Period size: 183 Copynumber: 2.1 Consensus size: 184
20072 ATTAAATTTT
* **
20082 AAATTTTAAATATATTATATATAACATATGGGCTCAA-CCCAAATGATTAAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCT-AAGCCCAAACCATTAAAAACCCAATTAATA
* *
20146 ATTTAAGATCTAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAA-AATTATATAAATTT
65 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAACAATTATATAAAATT
*
20210 TTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTT-AATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
*
20265 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTAAAAACCCAATTAATAA
** *
20330 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAACTTTTATCTAAAATTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAACAATTATATAAAATTT
*
20395 TTATTTTATAATTATTTATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
*
20449 AAATATTTAAT-T-TTATATA
1 AAATATTAAATATATTATATA
20468 AATTAGAAAA
Statistics
Matches: 188, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
182 9 0.05
183 113 0.60
184 66 0.35
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTAAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAACAATTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:21871 original size:2 final size:2
Alignment explanation
Indices: 21864--21914 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
21854 GTTATCAAGT
21864 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21906 T- TA TA TA TA
1 TA TA TA TA TA
21915 AAATAAAATC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29061 original size:12 final size:12
Alignment explanation
Indices: 29040--29068 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29030 CAGTTCTATC
29040 ATAT-TAAAATA
1 ATATATAAAATA
29051 ATATATAAAATA
1 ATATATAAAATA
29063 ATATAT
1 ATATAT
29069 GAGCAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATATAAAATA
Found at i:36631 original size:9 final size:9
Alignment explanation
Indices: 36619--36657 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
36609 TTTTTATTTT
36619 TTTTTGTAA
1 TTTTTGTAA
36628 TTTTTGTAA
1 TTTTTGTAA
36637 -TTTTGTAA
1 TTTTTGTAA
36645 TTTTTGTAA
1 TTTTTGTAA
36654 TTTT
1 TTTT
36658 CAATTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 8 0.28
9 21 0.72
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (9 bp):
TTTTTGTAA
Found at i:36640 original size:17 final size:17
Alignment explanation
Indices: 36620--36657 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
36610 TTTTATTTTT
36620 TTTTGTAATTTTTGTAA
1 TTTTGTAATTTTTGTAA
36637 TTTTGTAATTTTTGTAA
1 TTTTGTAATTTTTGTAA
36654 TTTT
1 TTTT
36658 CAATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (17 bp):
TTTTGTAATTTTTGTAA
Found at i:36666 original size:17 final size:17
Alignment explanation
Indices: 36620--36665 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
36610 TTTTATTTTT
*
36620 TTTTGTAATTTTTGTAA
1 TTTTGCAATTTTTGTAA
*
36637 TTTTGTAATTTTTGTAA
1 TTTTGCAATTTTTGTAA
36654 TTTT-CAATTTTT
1 TTTTGCAATTTTT
36666 TTGTACTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.22, C:0.02, G:0.09, T:0.67
Consensus pattern (17 bp):
TTTTGCAATTTTTGTAA
Found at i:36881 original size:11 final size:11
Alignment explanation
Indices: 36865--36921 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
36855 GAAAATGACT
36865 AAGAAAGGATG
1 AAGAAAGGATG
*
36876 AAGAAAGGAAG
1 AAGAAAGGATG
* *
36887 AAGAAAGTATA
1 AAGAAAGGATG
**
36898 AAGAAATCATG
1 AAGAAAGGATG
*
36909 AAGAAATGATG
1 AAGAAAGGATG
36920 AA
1 AA
36922 TAAGGTTGCT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 38 1.00
ACGTcount: A:0.60, C:0.02, G:0.26, T:0.12
Consensus pattern (11 bp):
AAGAAAGGATG
Found at i:39424 original size:21 final size:21
Alignment explanation
Indices: 39388--39434 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
39378 TAAATATTCA
39388 AAAAAGTAAATATAAAATACT
1 AAAAAGTAAATATAAAATACT
* *
39409 AAAAA-TAAATATTAAATTATT
1 AAAAAGTAAATA-TAAAATACT
39430 AAAAA
1 AAAAA
39435 AATTTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAAAGTAAATATAAAATACT
Found at i:39715 original size:2 final size:2
Alignment explanation
Indices: 39708--39775 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
39698 TAGAAATTAT
39708 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39750 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
39776 GACATTAAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39926 original size:25 final size:25
Alignment explanation
Indices: 39898--39955 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
39888 TAGATTAACT
39898 GAGATTTATAAAATTTAAATTAATC
1 GAGATTTATAAAATTTAAATTAATC
* * * *
39923 GAGAGTTATAAATTTTAGATTAGTC
1 GAGATTTATAAAATTTAAATTAATC
*
39948 GAAATTTA
1 GAGATTTA
39956 CTATGTTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (25 bp):
GAGATTTATAAAATTTAAATTAATC
Found at i:45026 original size:23 final size:23
Alignment explanation
Indices: 44963--45052 Score: 80
Period size: 23 Copynumber: 4.0 Consensus size: 23
44953 CACAGCTCGT
*
44963 AATTTGCA-CAGAAGTGCCACAT-
1 AATTTGCACCA-AAATGCCACATA
*
44985 AATTTTC-CC-AAATGACCACATA
1 AATTTGCACCAAAATG-CCACATA
45007 AATTTGCACCAAAATGCCACATA
1 AATTTGCACCAAAATGCCACATA
** * *
45030 GGTTTGCACCGAAGTGCCACATA
1 AATTTGCACCAAAATGCCACATA
45053 CTTGTCCTGA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
20 4 0.07
21 6 0.11
22 13 0.23
23 28 0.50
24 5 0.09
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (23 bp):
AATTTGCACCAAAATGCCACATA
Done.