Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006250.1 Hibiscus syriacus cultivar Beakdansim tig00014897_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: 70563
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:148 original size:21 final size:20
Alignment explanation
Indices: 102--149 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
92 ATCAACATTT
* *
102 TCAGAAGCAGAAGAAGAAGT
1 TCAGAAACAGAAGAAGAAGC
122 TACAGAAACAGAAGAAGACAGC
1 T-CAGAAACAGAAGAAGA-AGC
144 TCAGAA
1 TCAGAA
150 GGGACATGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 20 0.83
22 3 0.12
ACGTcount: A:0.52, C:0.15, G:0.25, T:0.08
Consensus pattern (20 bp):
TCAGAAACAGAAGAAGAAGC
Found at i:751 original size:51 final size:50
Alignment explanation
Indices: 682--816 Score: 157
Period size: 51 Copynumber: 2.7 Consensus size: 50
672 TTAGCAGTAA
* * *
682 AGCGCGCCTCATGCACCGCGCTATACGATGATTTGGCGCCACGTGGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGATTTGGCGCCACGT-AGGTAT
* * **
733 AGCGCGCCCCCTGTACCGCGCTATACGGTGAGCTGGCGCCACGTAGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGATTTGGCGCCACGTAGGTAT
* *
783 AGCGTG-CCCCTGCACCACGCTATAC-ATGTATTTG
1 AGCGCGCCCCCTGCACCGCGCTATACGATG-ATTTG
817 ATACGTGGGG
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
48 2 0.03
49 20 0.29
50 10 0.14
51 38 0.54
ACGTcount: A:0.18, C:0.32, G:0.29, T:0.21
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGCTATACGATGATTTGGCGCCACGTAGGTAT
Found at i:1209 original size:108 final size:110
Alignment explanation
Indices: 1067--1285 Score: 318
Period size: 108 Copynumber: 2.0 Consensus size: 110
1057 GATGGAAATC
* *
1067 ATATCTCTACACTTTACGATACGGTAACATTTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACGATACGGTAACATTTTTAACGGTTTAATTTAATTTAAATTATTAGTAA
* * * *
1132 TATTTAGTT-TTTTATTTAATGTATGATTATT-ATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAATTAAGAATTAA
** *
1175 ATATCTCGACACTTTGTTGATACGGTAACA-TTTTAACGGTTTAATTTAATTTAAATTATTATTA
1 ATATCTCGACACTTT-ACGATACGGTAACATTTTTAACGGTTTAATTTAATTTAAATTATTAGTA
1239 ATAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
65 ATAATTAGTTGATTCATTTAATGCATGATTATTA-ATTAAGAATTAA
1286 TTTTTGTAAT
Statistics
Matches: 98, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
108 55 0.56
109 31 0.32
111 12 0.12
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.47
Consensus pattern (110 bp):
ATATCTCGACACTTTACGATACGGTAACATTTTTAACGGTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAATTAAGAATTAA
Found at i:9662 original size:23 final size:23
Alignment explanation
Indices: 9606--9664 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 23
9596 ATGAATTAAA
9606 TTAAATGATATGATATGATATTAGT
1 TTAAA-GATATGATATGATATTA-T
*
9631 TTAAA-ATATGATGTGATATT-T
1 TTAAAGATATGATATGATATTAT
9652 TTAAGAGATATGA
1 TTAA-AGATATGA
9665 AATATCCATC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 5 0.16
22 1 0.03
23 20 0.65
25 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.42
Consensus pattern (23 bp):
TTAAAGATATGATATGATATTAT
Found at i:13573 original size:20 final size:20
Alignment explanation
Indices: 13548--13661 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
13538 AATTGGAAAA
*
13548 ATCGCAAAGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
13568 ATCGCAATGTGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
13588 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
13609 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
13629 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
13649 TTCGCAACGCGAT
1 ATCGCAACGCGAT
13662 TTACATAGCG
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 61 0.78
21 13 0.17
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:13654 original size:61 final size:61
Alignment explanation
Indices: 13545--13661 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
13535 GCGAATTGGA
* * * * *
13545 AAAATCGCAAAGCGATACTGACTATCGCAATGTGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAAAGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
13606 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAAAGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
13662 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAAAGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:14255 original size:19 final size:19
Alignment explanation
Indices: 14233--14344 Score: 126
Period size: 19 Copynumber: 6.1 Consensus size: 19
14223 GAAACCAAAA
*
14233 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
14252 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
14271 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
14285 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
14304 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
14323 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
14343 TC
1 TC
14345 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
14 10 0.13
16 2 0.03
17 3 0.04
19 47 0.59
20 17 0.22
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:14303 original size:33 final size:33
Alignment explanation
Indices: 14255--14319 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
14245 TTTCATTTCG
**
14255 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
14288 CGTTGCGATAGTCATTTCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTC
14320 ATTATCTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:16499 original size:21 final size:21
Alignment explanation
Indices: 16475--16541 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
16465 TCATTCCTCG
16475 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
16496 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
16517 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
16538 AGAG
1 AGAG
16542 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:16499 original size:42 final size:42
Alignment explanation
Indices: 16423--16541 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
16413 GACTCGCCTG
* * * * * * *
16423 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
16465 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
16507 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
16542 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:17911 original size:13 final size:14
Alignment explanation
Indices: 17895--17929 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
17885 ATTGTTTAAT
17895 TGATTTGT-AAAGG
1 TGATTTGTAAAAGG
*
17908 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
17922 TGATTTGT
1 TGATTTGT
17930 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:17937 original size:13 final size:14
Alignment explanation
Indices: 17882--17930 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
17872 TGCTTATTTT
*
17882 TTGA-TTGTTTAA-
1 TTGATTTGTTAAAG
17894 TTGATTTG-TAAAG
1 TTGATTTGTTAAAG
* *
17907 GTGATTTGTAAAAG
1 TTGATTTGTTAAAG
17921 TTGATTTGTT
1 TTGATTTGTT
17931 TAATTGATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 7 0.24
13 10 0.34
14 12 0.41
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (14 bp):
TTGATTTGTTAAAG
Found at i:18079 original size:32 final size:33
Alignment explanation
Indices: 18035--18123 Score: 126
Period size: 32 Copynumber: 2.7 Consensus size: 33
18025 CAAAAGTACT
* *
18035 ATCGCAATGCGAAATGAAAATTGCAACGAGA-A
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
18067 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
18100 AACGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
18124 GTTGCGATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 29 0.57
33 22 0.43
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:18141 original size:19 final size:19
Alignment explanation
Indices: 18119--18269 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
18109 CGAAATTAAA
18119 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
18138 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
18153 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
18171 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
18185 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
18204 TTCGCATTGCGA--TT-A-
1 TTCGCGTTGCGATTTTCAT
*
18219 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
18237 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
18256 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
18270 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:18165 original size:33 final size:31
Alignment explanation
Indices: 18118--18249 Score: 183
Period size: 33 Copynumber: 4.1 Consensus size: 31
18108 GCGAAATTAA
*
18118 ATTCGCGTTGCGATTTTCATTTCGCATTGCG
1 ATTCTCGTTGCGATTTTCATTTCGCATTGCG
18149 ATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
1 ATT--CTCGTTGCGATTTTCATTTCGCATTGCG
**
18182 AAATTAGCGTTGCGATTTTCATTTCGCATTGCG
1 --ATTCTCGTTGCGATTTTCATTTCGCATTGCG
18215 ATTATCTCGTTGCGATTTTCATTTCGCATTGCG
1 A-T-TCTCGTTGCGATTTTCATTTCGCATTGCG
18248 AT
1 AT
18250 AGTAATTTCC
Statistics
Matches: 90, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
31 4 0.04
32 2 0.02
33 81 0.90
35 3 0.03
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (31 bp):
ATTCTCGTTGCGATTTTCATTTCGCATTGCG
Found at i:18196 original size:66 final size:66
Alignment explanation
Indices: 18116--18248 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
18106 ACGCGAAATT
* *
18116 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTACCTCGTTGCGATTTTCATTTCGCATTGC
18181 G
66 G
*
18182 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTACCTCGTTGCGATTTTCATTTCGCATTGC
18247 G
66 G
18248 A
1 A
18249 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTACCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:20550 original size:12 final size:12
Alignment explanation
Indices: 20533--20557 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20523 TCTTCGGGGA
20533 CTTTTTCTTCTT
1 CTTTTTCTTCTT
20545 CTTTTTCTTCTT
1 CTTTTTCTTCTT
20557 C
1 C
20558 AGAATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:20766 original size:24 final size:24
Alignment explanation
Indices: 20732--20778 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
20722 CTAAAACATC
*
20732 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAT
*
20756 ATCAAAGTCCGGGTATTGACCAA
1 ATCAAAATCCGGGTATTGACCAA
20779 GATTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAT
Found at i:21867 original size:20 final size:20
Alignment explanation
Indices: 21842--21899 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
21832 ATTCATTTGA
21842 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
21862 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
21882 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
21900 CGCAATGCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:21942 original size:14 final size:16
Alignment explanation
Indices: 21922--21995 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
21912 TGAAAATCGC
21922 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
21937 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
21954 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
21973 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
21989 -TTGCGAT
1 ATTGCGAT
21996 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:21959 original size:19 final size:19
Alignment explanation
Indices: 21918--21985 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
21908 AAAATGAAAA
21918 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
21934 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
21951 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
21970 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
21986 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:22121 original size:14 final size:14
Alignment explanation
Indices: 22102--22138 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
22092 CATCAATTAA
22102 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
22116 ACAAATCATCTTTT
1 ACAAATCAACATTT
22130 ACAAATCAA
1 ACAAATCAA
22139 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:24039 original size:20 final size:19
Alignment explanation
Indices: 24004--24059 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
23994 GAAACTTAAA
24004 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
24023 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
*
24043 ATCGCAATGCGAAATGA
1 ATCGCAACGCGAAATGA
24060 AAATTGCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:24082 original size:14 final size:14
Alignment explanation
Indices: 24059--24116 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
24049 ATGCGAAATG
*
24059 AAAATTGCAACGAC
1 AAAATCGCAACGAC
*
24073 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
24089 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
24105 AAAATCGCAACG
1 AAAATCGCAACG
24117 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:24106 original size:32 final size:33
Alignment explanation
Indices: 24043--24121 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
24033 GGAAATGGCT
* *
24043 ATCGCAATGCGAAATGAAAATTGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
24076 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
24108 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
24122 CACAAATTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:24167 original size:14 final size:14
Alignment explanation
Indices: 24144--24207 Score: 76
Period size: 14 Copynumber: 4.4 Consensus size: 14
24134 TGCGATTTTC
24144 ATTTTG-CGTTGCG
1 ATTTTGTCGTTGCG
24157 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
*
24171 ATTTCATTTCGCATTGCG
1 ATTT--TGTCG--TTGCG
24189 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
24203 ATTTT
1 ATTTT
24208 CATTTCGCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 6 0.14
14 21 0.48
16 8 0.18
18 9 0.20
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (14 bp):
ATTTTGTCGTTGCG
Found at i:24214 original size:33 final size:33
Alignment explanation
Indices: 24133--24223 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
24123 ACAAATTGCA
* *
24133 TTGCGATTTTCATTTTGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
24166 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
24198 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
24224 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:24230 original size:19 final size:19
Alignment explanation
Indices: 24208--24251 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
24198 TTGCGATTTT
24208 CATTTCGCA-TTGCGATAGC
1 CATTTC-CACTTGCGATAGC
*
24227 CATTTCCACGTTGCGATAGT
1 CATTTCCAC-TTGCGATAGC
24247 CATTT
1 CATTT
24252 TCGTGTTGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 14 0.64
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (19 bp):
CATTTCCACTTGCGATAGC
Found at i:24770 original size:18 final size:18
Alignment explanation
Indices: 24744--24788 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
24734 GTCGATCAGA
*
24744 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
24762 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
24780 TGATGGCTC
1 TGATGGCTC
24789 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:26133 original size:20 final size:20
Alignment explanation
Indices: 26108--26160 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
26098 AATAGTTTCT
26108 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
26128 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
26148 GAAACT-AAAATCG
1 GAAAATGAAAATCG
26161 TGTTGCGATT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.49, C:0.21, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:26422 original size:22 final size:22
Alignment explanation
Indices: 26395--26438 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
26385 GATGGAGATA
26395 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
26417 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
26439 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:26652 original size:20 final size:20
Alignment explanation
Indices: 26626--26698 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
26616 GATTATGTAT
26626 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
26646 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
26666 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
26686 TATCTCGTTGCGA
1 TATCGCGTTGCGA
26699 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:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:26729 original size:41 final size:41
Alignment explanation
Indices: 26612--26729 Score: 141
Period size: 40 Copynumber: 2.9 Consensus size: 41
26602 GAAAATCGCA
* *
26612 TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCG
1 TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCTCG
* * *
26653 TTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGTATCTCG
1 TTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGTATCTCG
* * *
26693 TTGCGATTTTGTATTATCGCATTGCGATAGTCAGTAT
1 TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTAT
26730 TGCATTGCGA
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
39 3 0.05
40 31 0.49
41 27 0.43
42 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (41 bp):
TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCTCG
Found at i:26743 original size:41 final size:41
Alignment explanation
Indices: 26609--26741 Score: 137
Period size: 41 Copynumber: 3.3 Consensus size: 41
26599 TTTGAAAATC
* *
26609 GCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATC
1 GCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATT
* * * *
26650 GCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGTATCT
1 GCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGTAT-T
* * * *
26691 -CGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGTATT
1 GCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATT
26731 GCATTGCGATT
1 GCATTGCGATT
26742 TTCCCAATTC
Statistics
Matches: 74, Mismatches: 13, Indels: 10
0.76 0.13 0.10
Matches are distributed among these distances:
39 3 0.04
40 31 0.42
41 38 0.51
42 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.34
Consensus pattern (41 bp):
GCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATT
Found at i:26759 original size:41 final size:41
Alignment explanation
Indices: 26733--26821 Score: 124
Period size: 41 Copynumber: 2.2 Consensus size: 41
26723 TCAGTATTGC
* *
26733 ATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCGA
1 ATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTATTCGA
* * * *
26774 ATTGCGATTTTCCCAATTCACGTTGCGATTTACTTATTCGC
1 ATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTATTCGA
26815 ATTGCGA
1 ATTGCGA
26822 ATTGGGAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.40
Consensus pattern (41 bp):
ATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTATTCGA
Found at i:26760 original size:21 final size:21
Alignment explanation
Indices: 26734--26804 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
26724 CAGTATTGCA
26734 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
* ** **
26755 TTGCGA-TTTACTTATTCGAA
1 TTGCGATTTTCCCAATTCGCG
*
26775 TTGCGATTTTCCCAATTCACG
1 TTGCGATTTTCCCAATTCGCG
26796 TTGCGATTT
1 TTGCGATTT
26805 ACTTATTCGC
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 15 0.39
21 23 0.61
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.42
Consensus pattern (21 bp):
TTGCGATTTTCCCAATTCGCG
Found at i:26778 original size:20 final size:20
Alignment explanation
Indices: 26755--26821 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
26745 CCAATTCGCG
26755 TTGCGATTTACTTATTCGAA
1 TTGCGATTTACTTATTCGAA
* ** *
26775 TTGCGATTTTCCCAATTC-ACG
1 TTGCGA-TTTACTTATTCGA-A
*
26796 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGAA
26816 TTGCGA
1 TTGCGA
26822 ATTGGGAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
20 21 0.60
21 14 0.40
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (20 bp):
TTGCGATTTACTTATTCGAA
Found at i:28442 original size:23 final size:21
Alignment explanation
Indices: 28399--28457 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
28389 CGAAATAATA
* **
28399 TATTTATTAAAAATATTATTTT
1 TATTTAATAAAAATAAGA-TTT
28421 TATTTAATAAAAATAGAGATTT
1 TATTTAATAAAAATA-AGATTT
* *
28443 AATTGAATAAAAATA
1 TATTTAATAAAAATA
28458 TATATAGAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
TATTTAATAAAAATAAGATTT
Found at i:34392 original size:31 final size:30
Alignment explanation
Indices: 34294--34392 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 30
34284 ATTTTTAAAG
* *
34294 TTACAAAAT-AGTCATCAAATTTATCTAAATG
1 TTACAAAATGA-TCATTAAATTTATC-AAATT
* * *
34325 ATACAAAATGATCATTATATTTTATCGAATT
1 TTACAAAATGATCATTA-AATTTATCAAATT
*
34356 ATTACAAATTGATCATTAAATTTATCAAAATT
1 -TTACAAAATGATCATTAAATTTATC-AAATT
34388 TTACA
1 TTACA
34393 CTTACTATAG
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
31 28 0.51
32 27 0.49
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.39
Consensus pattern (30 bp):
TTACAAAATGATCATTAAATTTATCAAATT
Found at i:35604 original size:111 final size:111
Alignment explanation
Indices: 35410--35742 Score: 549
Period size: 111 Copynumber: 3.0 Consensus size: 111
35400 TGGAAATCAT
* *
35410 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAGTTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
35475 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
35521 ATATCTCGACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
35586 TAATTAGTTAATTTATTTAATGCATGATTATTATATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* * * **
35632 ATATTTCGACACTTTACTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTTTTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
35697 TAATTTGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
35743 TTTTTGTAAT
Statistics
Matches: 206, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 206 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:36331 original size:14 final size:14
Alignment explanation
Indices: 36314--36341 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36304 GTTGGGGCTC
36314 GGCAGTTTTAGCTT
1 GGCAGTTTTAGCTT
36328 GGCAGTTTTAGCTT
1 GGCAGTTTTAGCTT
36342 TGCTGTACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (14 bp):
GGCAGTTTTAGCTT
Found at i:37639 original size:21 final size:21
Alignment explanation
Indices: 37613--37652 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
37603 ACCTGCTCAG
37613 GACGACGACGAT-GACGATGGT
1 GACGACGACG-TCGACGATGGT
37634 GACGACGACGTCGACGATG
1 GACGACGACGTCGACGATG
37653 ACAACGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.28, C:0.23, G:0.38, T:0.12
Consensus pattern (21 bp):
GACGACGACGTCGACGATGGT
Found at i:37831 original size:50 final size:46
Alignment explanation
Indices: 37746--37838 Score: 123
Period size: 50 Copynumber: 1.9 Consensus size: 46
37736 AGGCATCGAT
* * *
37746 ATTTTTTTTTATTATATTTGTATTTACTTTATTTTGTTTAATTGTA
1 ATTTTTTTTTATTATATTTATACTTACTTTATTTTGTTAAATTGTA
37792 ATTTTTTTATTATTTATCATTTAATACTTACTTTATTTTGTTAAATT
1 ATTTTTTT-TTA-TTAT-ATTT-ATACTTACTTTATTTTGTTAAATT
37839 TGTTGGACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 8 0.20
47 3 0.08
48 4 0.10
49 4 0.10
50 21 0.52
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (46 bp):
ATTTTTTTTTATTATATTTATACTTACTTTATTTTGTTAAATTGTA
Found at i:37868 original size:54 final size:50
Alignment explanation
Indices: 37769--37870 Score: 125
Period size: 54 Copynumber: 2.0 Consensus size: 50
37759 ATATTTGTAT
* *
37769 TTACTTTATTTTGTTTAATTGTAATTTTTTTATTATTTATCATTTAATAC
1 TTACTTTATTTTGTTAAATTGTAATTTTTTTAATATTTATCATTTAATAC
*
37819 TTACTTTATTTTGTTAAATTTGTTGGACTTTTTTTAATATATT-TCATTTAAT
1 TTACTTTATTTTGTTAAA-TTG-T--AATTTTTTTAATAT-TTATCATTTAAT
37871 TTTGTTTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
50 17 0.39
51 3 0.07
52 1 0.02
54 21 0.48
55 2 0.05
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.63
Consensus pattern (50 bp):
TTACTTTATTTTGTTAAATTGTAATTTTTTTAATATTTATCATTTAATAC
Found at i:60328 original size:20 final size:20
Alignment explanation
Indices: 60299--60341 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
60289 ATTCCACCAC
*
60299 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
60319 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
60339 ATG
1 ATG
60342 GGCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:67512 original size:2 final size:2
Alignment explanation
Indices: 67505--67530 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
67495 TGATAAAATA
67505 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
67531 GAAGATATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.