Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006837.1 Hibiscus syriacus cultivar Beakdansim tig00017376_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: 84328
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1732 original size:65 final size:66
Alignment explanation
Indices: 1614--1745 Score: 160
Period size: 65 Copynumber: 2.0 Consensus size: 66
1604 CTAAAAAATT
* * ** * *
1614 TTTTGTCTCTTTTGAGACAATTTCTTTTAAGAAAAATCTTTGAGTTTGTTTCTTTGGAAA-CAAA
1 TTTTATCTCTTTTGAGACAACTTCTTTTAAGAAAAATCACTGAGTTAGGTTCTTTGGAAACCAAA
1678 A
66 A
** *
1679 TTTTATCTCTTTTGAGACAACTTCTTTTGAAGAATTATCACTGAG-TAGGTTCTTTTGAAACCAA
1 TTTTATCTCTTTTGAGACAACTTCTTTT-AAGAAAAATCACTGAGTTAGGTTCTTTGGAAACCAA
1743 AA
65 AA
1745 T
1 T
1746 CCTTAGATGG
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
65 38 0.68
66 18 0.32
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.44
Consensus pattern (66 bp):
TTTTATCTCTTTTGAGACAACTTCTTTTAAGAAAAATCACTGAGTTAGGTTCTTTGGAAACCAAA
A
Found at i:1994 original size:128 final size:128
Alignment explanation
Indices: 1818--2127 Score: 331
Period size: 128 Copynumber: 2.4 Consensus size: 128
1808 GTAGGAACCG
* *
1818 TGTCAA-CCAGATAACCAGCCG-CTCTCATCACGTAGGAACCGTGTTATCACCTTTAGATTG-CC
1 TGTCAACCCAGATAACCAGCCGTC-CTCATCACGTAGGAACCGTGCTATCACCCTTAGA-TGCCC
* * **** ** *
1880 AGAAC-TCTTCATCACGTATGAGTTGTTTCATCAACTGACCAGATCTCCTCATTATGTAGGAGCT
64 AG-ACGTCCTCATCACGTAGGAACCATGCCATCAACCGACCAGATCTCCTCATTATGTAGGAGCT
1944 A
128 A
* ** *
1945 TGTCAACCCAGATAACCAGCCGTCCTTATCACGTAGGAGTCGTGCTATCACCCTTAGATGCCCTG
1 TGTCAACCCAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGCTATCACCCTTAGATGCCCAG
* * * * *
2010 TCGTCCTCATCAGGTAGGAACCATGCCATCACCCGACTAGATTTCCTCATTATGTAGGAGCTA
66 ACGTCCTCATCACGTAGGAACCATGCCATCAACCGACCAGATCTCCTCATTATGTAGGAGCTA
* * * * * *
2073 TGTCAACCTAGATAATCAGTCGTCCTCATCACTTAGGAACCGTGTTATCATCCTT
1 TGTCAACCCAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGCTATCACCCTT
2128 CCTAAAGATG
Statistics
Matches: 150, Mismatches: 29, Indels: 7
0.81 0.16 0.04
Matches are distributed among these distances:
127 9 0.06
128 140 0.93
129 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.28
Consensus pattern (128 bp):
TGTCAACCCAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGCTATCACCCTTAGATGCCCAG
ACGTCCTCATCACGTAGGAACCATGCCATCAACCGACCAGATCTCCTCATTATGTAGGAGCTA
Found at i:2216 original size:3 final size:3
Alignment explanation
Indices: 2208--2261 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
2198 GCTTTAAAAC
**
2208 TTA TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2256 TTA TTA
1 TTA TTA
2262 AAACAAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:3827 original size:16 final size:16
Alignment explanation
Indices: 3790--3828 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3780 GCAGACCAAC
3790 TTTTTGTCTTAAAAATG
1 TTTTT-TCTTAAAAATG
* *
3807 ATTTTTCTTAAAATTG
1 TTTTTTCTTAAAAATG
3823 TTTTTT
1 TTTTTT
3829 AAAATATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.62
Consensus pattern (16 bp):
TTTTTTCTTAAAAATG
Found at i:8002 original size:16 final size:16
Alignment explanation
Indices: 7981--8043 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
7971 TATCAAAGCG
7981 AAGAGAAAAGAAAACA
1 AAGAGAAAAGAAAACA
*
7997 AAGAGAAAAG-AAGCA
1 AAGAGAAAAGAAAACA
*
8012 AAGAAAGAAAA-AACAAAA
1 AAG--AGAAAAGAA-AACA
*
8030 AAGAGCAAAGAAAA
1 AAGAGAAAAGAAAA
8044 AAACAAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
15 7 0.18
16 17 0.45
17 9 0.24
18 5 0.13
ACGTcount: A:0.75, C:0.06, G:0.19, T:0.00
Consensus pattern (16 bp):
AAGAGAAAAGAAAACA
Found at i:8015 original size:15 final size:16
Alignment explanation
Indices: 7975--8015 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
7965 ATATCATATC
*
7975 AAAGCGAAGAGAAAAG
1 AAAGCAAAGAGAAAAG
*
7991 AAAACAAAGAGAAAAG
1 AAAGCAAAGAGAAAAG
8007 -AAGCAAAGA
1 AAAGCAAAGA
8016 AAGAAAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.68, C:0.07, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAGCAAAGAGAAAAG
Found at i:9149 original size:33 final size:33
Alignment explanation
Indices: 9095--9163 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
9085 AGGATCAGTG
*
9095 TTGAAGCAAGAAACAATGAACAATGGGGCATCT
1 TTGAAGCAAGAAACAATGAACAATGGGACATCT
** *
9128 TTGAAGCAATCAAC-ATCGAACATTGGGACATCT
1 TTGAAGCAAGAAACAAT-GAACAATGGGACATCT
9161 TTG
1 TTG
9164 GGGATTCAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.06
33 29 0.94
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (33 bp):
TTGAAGCAAGAAACAATGAACAATGGGACATCT
Found at i:9788 original size:133 final size:132
Alignment explanation
Indices: 9471--9848 Score: 409
Period size: 133 Copynumber: 2.8 Consensus size: 132
9461 ACGTAAAAAT
* *
9471 CGTGTCAT-CCCCGACCAGACCTCATCATCACA-TAAGAGCCGTGTCACCCTTAGATAATCAGAC
1 CGTGTCATCCCCCGACCAGACCTCCTCATCA-AGTAGGAGCCGTGTCACCCTT-GATAA-CAGAC
* ** * * *
9534 GTCCTCATCACGTAGGAACCATGTTATCTACCTTATTAATAAAGATGGCATGTCTTCCTCATTGC
63 GTCCTCATCACGTAGGAACCGTGTTATC-ACC--ATTCCTAAAGATGGCATGTCGTCCTCATCGA
9599 GTAAGAAC
125 GTAAGAAC
* * * * * *
9607 CGTGTCATCCCCCGACCAGACCTCCTCATCAAGTAGTAACCATTTCACCCTTGATAACCAGCCCT
1 CGTGTCATCCCCCGACCAGACCTCCTCATCAAGTAGGAGCCGTGTCACCCTTGATAA-CAGACGT
** * * *
9672 GTTCATCACGTAGGAACCGTGTTATCGCCATTCCTAAAGATGGCATGTCGTCTTCATCGAGTAGG
65 CCTCATCACGTAGGAACCGTGTTATCACCATTCCTAAAGATGGCATGTCGTCCTCATCGAGTAAG
9737 AAC
130 AAC
* * * ** *
9740 TGTGTCATCCCCCGACCAAACCTCCTCATCATGTAGGAGCCGTGTCACCCCAGATAACATGTCGT
1 CGTGTCATCCCCCGACCAGACCTCCTCATCAAGTAGGAGCCGTGTCACCCTTGATAACA-GACGT
* * * *
9805 CCTCATCGCGTGGGAACCGAGTTATCACCCTTCCTAAAGATGGC
65 CCTCATCACGTAGGAACCGTGTTATCACCATTCCTAAAGATGGC
9849 CAAGAACTCT
Statistics
Matches: 201, Mismatches: 38, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
132 2 0.01
133 120 0.60
135 2 0.01
136 42 0.21
137 35 0.17
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (132 bp):
CGTGTCATCCCCCGACCAGACCTCCTCATCAAGTAGGAGCCGTGTCACCCTTGATAACAGACGTC
CTCATCACGTAGGAACCGTGTTATCACCATTCCTAAAGATGGCATGTCGTCCTCATCGAGTAAGA
AC
Found at i:10134 original size:3 final size:3
Alignment explanation
Indices: 10122--10151 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
10112 TTTCTATTTA
10122 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
10152 ATACAATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:11642 original size:30 final size:30
Alignment explanation
Indices: 11561--11831 Score: 226
Period size: 30 Copynumber: 8.9 Consensus size: 30
11551 CAAATGTCTA
* *
11561 TTTTTATTATTTTAGTCCTTTAA-ATTCATG
1 TTTTTGTTATTTTAGTCCTTTAAGTTTC-TG
* * *
11591 TTTATATT-TTTTAGGTTCTTTAAGTTTCTG
1 TTTTTGTTATTTTA-GTCCTTTAAGTTTCTG
* *
11621 TATTTGTTATTTTAGTCCTTTAATTTTCTG
1 TTTTTGTTATTTTAGTCCTTTAAGTTTCTG
* * *
11651 TTTTAGCTATTTTAGTCCTTTAAGTTTATG
1 TTTTTGTTATTTTAGTCCTTTAAGTTTCTG
* *
11681 TTTTTTGTTCTTTTAGTCCTTTAAGTTTCTATTT
1 -TTTTTGTTATTTTAGTCCTTTAAGTTTC---TG
*
11715 TTTTTGTTATTTTAG-CACTTTAAGTTTCTA
1 TTTTTGTTATTTTAGTC-CTTTAAGTTTCTG
* * * *
11745 TTTTTGTTATTTTTG-CACTTTAACTTTTTA
1 TTTTTGTTATTTTAGTC-CTTTAAGTTTCTG
* * * *
11775 TTATTGTTATTTTAGTCCTTTGAGTTTATA
1 TTTTTGTTATTTTAGTCCTTTAAGTTTCTG
* *
11805 TTTTTGCTATTTTGGTCCTTTTAAGTT
1 TTTTTGTTATTTTAGTCC-TTTAAGTT
11832 CAAATACTTA
Statistics
Matches: 199, Mismatches: 32, Indels: 19
0.80 0.13 0.08
Matches are distributed among these distances:
29 5 0.03
30 127 0.64
31 40 0.20
32 1 0.01
33 25 0.13
34 1 0.01
ACGTcount: A:0.17, C:0.10, G:0.11, T:0.62
Consensus pattern (30 bp):
TTTTTGTTATTTTAGTCCTTTAAGTTTCTG
Found at i:11740 original size:124 final size:124
Alignment explanation
Indices: 11608--11831 Score: 294
Period size: 124 Copynumber: 1.8 Consensus size: 124
11598 TTTTTAGGTT
* *
11608 CTTTAAGTTTCTGTATTTGTTATTTTAGTC-CTTTAA-TTTTCTGTT-TTAGCTATTTTAGTCCT
1 CTTTAAGTTTCTATATTTGTTATTTTAG-CACTTTAACTTTT-TATTATT-GCTATTTTAGTCCT
* * *
11670 TTAAGTTTATGTTTTTTGTTCTTTTAGTCC-TTTAAGTTTCTATTTTTTTTGTTATTTTAGCA
63 TTAAGTTTAT-ATTTTTGCTATTTTAGTCCTTTTAAGTTTCTATTTTTTTTGTTATTTTAGCA
* * * *
11732 CTTTAAGTTTCTATTTTTGTTATTTTTGCACTTTAACTTTTTATTATTGTTATTTTAGTCCTTTG
1 CTTTAAGTTTCTATATTTGTTATTTTAGCACTTTAACTTTTTATTATTGCTATTTTAGTCCTTTA
*
11797 AGTTTATATTTTTGCTATTTTGGTCCTTTTAAGTT
66 AGTTTATATTTTTGCTATTTTAGTCCTTTTAAGTT
11832 CAAATACTTA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
123 16 0.19
124 64 0.74
125 6 0.07
ACGTcount: A:0.17, C:0.10, G:0.11, T:0.62
Consensus pattern (124 bp):
CTTTAAGTTTCTATATTTGTTATTTTAGCACTTTAACTTTTTATTATTGCTATTTTAGTCCTTTA
AGTTTATATTTTTGCTATTTTAGTCCTTTTAAGTTTCTATTTTTTTTGTTATTTTAGCA
Found at i:11951 original size:21 final size:22
Alignment explanation
Indices: 11909--11951 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
11899 TATGTATGTA
* *
11909 CATGTTGTAAATGTTATTATTT
1 CATGGTGTAAATATTATTATTT
11931 CATGGTGTAAATATT-TTATTT
1 CATGGTGTAAATATTATTATTT
11952 TTCATTTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (22 bp):
CATGGTGTAAATATTATTATTT
Found at i:13704 original size:25 final size:23
Alignment explanation
Indices: 13658--13706 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
13648 TATCATGTGC
*
13658 AAATGATTATTTTCTCTGATTTG
1 AAATGATTATTTTCTCTAATTTG
*
13681 AAATGAATTGTTTTGCTCTAATTTG
1 AAATG-ATTATTTT-CTCTAATTTG
13706 A
1 A
13707 CTACGAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.23
24 7 0.32
25 10 0.45
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (23 bp):
AAATGATTATTTTCTCTAATTTG
Found at i:13945 original size:36 final size:35
Alignment explanation
Indices: 13904--13974 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
13894 GAAGTCTCTG
*
13904 CAGGTTC-AACTTCGATGAAACTAGTAATTCCTTATA
1 CAGGTTCAAAC-T-GATCAAACTAGTAATTCCTTATA
* *
13940 CAGGTTCAAACTGATCAAGCTGGTAATTCCTTATA
1 CAGGTTCAAACTGATCAAACTAGTAATTCCTTATA
13975 GACCTAAGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 20 0.65
36 8 0.26
37 3 0.10
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (35 bp):
CAGGTTCAAACTGATCAAACTAGTAATTCCTTATA
Found at i:15553 original size:64 final size:64
Alignment explanation
Indices: 15483--15621 Score: 156
Period size: 63 Copynumber: 2.2 Consensus size: 64
15473 CATATTAATT
* ** * *
15483 TTTTTAAAAAGTACAAG-GGCTTCACCTGCCCTTTCACCTTAAAAAATTTAGATTAAATTATAAA
1 TTTTTAAAAAGTACAAGTAGCTTC-CAAGCCCTTTCACCTAAAAAAATTAAGATTAAATTATAAA
** * *
15547 TTTTT-AAAAGTACAAGTATTTTCCAAGCCGTTTCACCTAAAAAAATTAAGATTAAGTTATAAA
1 TTTTTAAAAAGTACAAGTAGCTTCCAAGCCCTTTCACCTAAAAAAATTAAGATTAAATTATAAA
* *
15610 TTTCTAGAAAGT
1 TTTTTAAAAAGT
15622 TAAAATATAA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 49 0.79
64 13 0.21
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.35
Consensus pattern (64 bp):
TTTTTAAAAAGTACAAGTAGCTTCCAAGCCCTTTCACCTAAAAAAATTAAGATTAAATTATAAA
Found at i:18930 original size:60 final size:60
Alignment explanation
Indices: 18843--18955 Score: 136
Period size: 60 Copynumber: 1.9 Consensus size: 60
18833 ATTTCACCCA
* * * ** *
18843 TAAACTATGAATCTCATTCTAATTTGGTCCTTAAAATTTTGAAAATTCTAATTCCATACC
1 TAAACTATGAACCTCATTCGAAATTGGTCCACAAAATTTTGAAAATTCCAATTCCATACC
* * * *
18903 TAAACTATGACCCTCTTTCGAAATTGGTCCACAATATTTTGAATATTCCAATT
1 TAAACTATGAACCTCATTCGAAATTGGTCCACAAAATTTTGAAAATTCCAATT
18956 TCATCCCCAA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 43 1.00
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (60 bp):
TAAACTATGAACCTCATTCGAAATTGGTCCACAAAATTTTGAAAATTCCAATTCCATACC
Found at i:19233 original size:60 final size:60
Alignment explanation
Indices: 19123--19257 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 60
19113 AATTTAGAAT
* * * * * *
19123 GTCATAGTTTGGGGATGAAATTGAAATGTTCAAAAGTATAAGGACTAATTTAGAATGATA
1 GTCATAGTTTAGGAATAAAATTGAAATGTTCAAAAGTATAAGGACCAATTTAAAATGAAA
* ** * * *
19183 GTCATAGTTTAGGAATAAAATTGAAATGTTTAATTGTTTAGGGACCAATTTAAAATTAAA
1 GTCATAGTTTAGGAATAAAATTGAAATGTTCAAAAGTATAAGGACCAATTTAAAATGAAA
*
19243 GTCATACTTTGAGGA
1 GTCATAGTTT-AGGA
19258 CATATGATAC
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
60 57 0.93
61 4 0.07
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (60 bp):
GTCATAGTTTAGGAATAAAATTGAAATGTTCAAAAGTATAAGGACCAATTTAAAATGAAA
Found at i:21387 original size:18 final size:19
Alignment explanation
Indices: 21364--21405 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
21354 TAGTAATTCT
*
21364 ATTCCC-TAGTAATCTTAC
1 ATTCCCATAATAATCTTAC
21382 ATTCCCATTAATAATCTTAC
1 ATTCCCA-TAATAATCTTAC
21402 ATTC
1 ATTC
21406 TGTGAACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.31, C:0.26, G:0.02, T:0.40
Consensus pattern (19 bp):
ATTCCCATAATAATCTTAC
Found at i:23311 original size:30 final size:30
Alignment explanation
Indices: 23275--23332 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
23265 GCATGTATAA
*
23275 AAAAATCGTTGTGTAGTT-CTGATGACTTTT
1 AAAAATCGTTGTGTA-TTCCTAATGACTTTT
23305 AAAAATCGTTGTGTATTCCTAATGACTT
1 AAAAATCGTTGTGTATTCCTAATGACTT
23333 CCACATGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.41
Consensus pattern (30 bp):
AAAAATCGTTGTGTATTCCTAATGACTTTT
Found at i:23704 original size:2 final size:2
Alignment explanation
Indices: 23697--23802 Score: 73
Period size: 2 Copynumber: 56.5 Consensus size: 2
23687 TAAAAATAAT
*
23697 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
23737 TT TA -A TT TA AA T- TA -A AA AA TA TA TA TA -A TA TT 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
* * *
23775 TT TA -A TT TA AA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23803 CTGGCCCGAT
Statistics
Matches: 80, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
1 7 0.09
2 73 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29793 original size:7 final size:7
Alignment explanation
Indices: 29781--29843 Score: 51
Period size: 7 Copynumber: 9.1 Consensus size: 7
29771 AAATAACCTA
29781 AAAATAT
1 AAAATAT
29788 AAAATAT
1 AAAATAT
29795 -AAA-AT
1 AAAATAT
29800 AAAATAT
1 AAAATAT
*
29807 ATAATAT
1 AAAATAT
* *
29814 ATAATCT
1 AAAATAT
*
29821 ATAATAGT
1 AAAATA-T
29829 AATAATA-
1 AA-AATAT
29836 AAAATAT
1 AAAATAT
29843 A
1 A
29844 TATAAGTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
5 2 0.04
6 10 0.21
7 29 0.62
8 2 0.04
9 4 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (7 bp):
AAAATAT
Found at i:29810 original size:21 final size:21
Alignment explanation
Indices: 29761--29817 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
29751 GAAAACCAAT
* **
29761 AAATAAATAAAA-ATAACCTA
1 AAATATATAAAATATAAAATA
29781 AAA-ATATAAAATATAAAATA
1 AAATATATAAAATATAAAATA
*
29801 AAATATATAATATATAA
1 AAATATATAAAATATAA
29818 TCTATAATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 7 0.23
20 12 0.39
21 12 0.39
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATATATAAAATATAAAATA
Found at i:29826 original size:21 final size:21
Alignment explanation
Indices: 29779--29817 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29769 AAAAATAACC
*
29779 TAAAA-ATATAAAATATAAAA
1 TAAAATATATAATATATAAAA
29799 TAAAATATATAATATATAA
1 TAAAATATATAATATATAA
29818 TCTATAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAATATATAATATATAAAA
Found at i:31646 original size:106 final size:106
Alignment explanation
Indices: 31478--31933 Score: 644
Period size: 106 Copynumber: 4.3 Consensus size: 106
31468 GTATTGTTCC
* * * * *
31478 GAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTATTGACAA
* * * * *** *
31543 TCAGCCGCCCCTTCG-CTGTGAAGTTGAGCTTGTGCTGTCTC
66 CCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCATTGTCTG
* * * * * * * *
31584 AAGTCTAATGTCCTTCGCTATGAAGTTGAAATTGGATCCGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTATTGACAA
*
31649 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
* *
31690 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTATTGACAA
31755 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
* *
31796 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTATTGACAA
31861 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
**
31902 GAGTCTGATATCCTTCGCTGTGAAGTTGAAAT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
31934 CGTGGATGTT
Statistics
Matches: 313, Mismatches: 36, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
106 312 1.00
107 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
Found at i:43345 original size:7 final size:7
Alignment explanation
Indices: 43333--43395 Score: 51
Period size: 7 Copynumber: 9.1 Consensus size: 7
43323 AAATAACCTA
43333 AAAATAT
1 AAAATAT
43340 AAAATAT
1 AAAATAT
43347 -AAA-AT
1 AAAATAT
43352 AAAATAT
1 AAAATAT
*
43359 ATAATAT
1 AAAATAT
* *
43366 ATAATCT
1 AAAATAT
*
43373 ATAATAGT
1 AAAATA-T
43381 AATAATA-
1 AA-AATAT
43388 AAAATAT
1 AAAATAT
43395 A
1 A
43396 TATAAGTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
5 2 0.04
6 10 0.21
7 29 0.62
8 2 0.04
9 4 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (7 bp):
AAAATAT
Found at i:43362 original size:21 final size:21
Alignment explanation
Indices: 43313--43369 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
43303 GAAAACCAAT
* **
43313 AAATAAATAAAA-ATAACCTA
1 AAATATATAAAATATAAAATA
43333 AAA-ATATAAAATATAAAATA
1 AAATATATAAAATATAAAATA
*
43353 AAATATATAATATATAA
1 AAATATATAAAATATAA
43370 TCTATAATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 7 0.23
20 12 0.39
21 12 0.39
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATATATAAAATATAAAATA
Found at i:43378 original size:21 final size:21
Alignment explanation
Indices: 43331--43369 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43321 AAAAATAACC
*
43331 TAAAA-ATATAAAATATAAAA
1 TAAAATATATAATATATAAAA
43351 TAAAATATATAATATATAA
1 TAAAATATATAATATATAA
43370 TCTATAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAATATATAATATATAAAA
Found at i:44562 original size:27 final size:26
Alignment explanation
Indices: 44511--44563 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
44501 AAAAATGTAA
44511 ATAAATATATATAATATAATTTATAAT
1 ATAAATATATATAATATAA-TTATAAT
44538 ATAAATATATATATTATATAA-TATAA
1 ATAAATATATATA--ATATAATTATAA
44564 GGACGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 18 0.75
29 6 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATAAATATATATAATATAATTATAAT
Found at i:51821 original size:24 final size:24
Alignment explanation
Indices: 51794--51845 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
51784 CGTTCATTTA
* *
51794 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGATTATGTT
* **
51818 CGTTTATGTTCGTTCGATTATGTT
1 CGTTCATGAACGTTCGATTATGTT
51842 CGTT
1 CGTT
51846 TATGTTCATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.15, G:0.25, T:0.48
Consensus pattern (24 bp):
CGTTCATGAACGTTCGATTATGTT
Found at i:51832 original size:14 final size:14
Alignment explanation
Indices: 51815--51845 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
51805 GTTCGGTTAT
*
51815 GTTCGTTTATGTTC
1 GTTCGATTATGTTC
51829 GTTCGATTATGTTC
1 GTTCGATTATGTTC
51843 GTT
1 GTT
51846 TATGTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.55
Consensus pattern (14 bp):
GTTCGATTATGTTC
Found at i:51846 original size:24 final size:24
Alignment explanation
Indices: 51804--51865 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
51794 CGTTCGTGAA
*
51804 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
51828 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
*
51852 CATTC-ATTTATGTT
1 CGTTCGA-TTATGTT
51866 TAACACAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.13, C:0.13, G:0.19, T:0.55
Consensus pattern (24 bp):
CGTTCGATTATGTTCGTTTATGTT
Found at i:52604 original size:10 final size:10
Alignment explanation
Indices: 52589--52663 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
52579 GGGTCTCCAA
52589 CGTTTATGTT
1 CGTTTATGTT
52599 CGTTTATGTT
1 CGTTTATGTT
52609 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
52620 ATGTTCGTGTT
1 -CGTTTATGTT
52631 CGTTTATGTT
1 CGTTTATGTT
52641 CG----TGTT
1 CGTTTATGTT
52647 CGTTTATGTT
1 CGTTTATGTT
52657 CGTTTAT
1 CGTTTAT
52664 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:52620 original size:16 final size:16
Alignment explanation
Indices: 52595--52659 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
52585 CCAACGTTTA
52595 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
52611 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
52627 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
52643 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
52659 T
1 T
52660 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:52750 original size:16 final size:16
Alignment explanation
Indices: 52729--52761 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
52719 AAAAATATTT
52729 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
52745 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
52761 T
1 T
52762 TTATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:64356 original size:14 final size:13
Alignment explanation
Indices: 64337--64366 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
64327 AATTTAGTAG
64337 AAAATATAATAAAT
1 AAAATATAAT-AAT
64351 AAAATATAATAAT
1 AAAATATAATAAT
64364 AAA
1 AAA
64367 TCAAACTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAATATAATAAT
Found at i:64398 original size:19 final size:22
Alignment explanation
Indices: 64353--64399 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
64343 TAATAAATAA
64353 AATATAATAATAAATCAAACTT
1 AATATAATAATAAATCAAACTT
* *
64375 TATATAATAA-AACTC-AA-TT
1 AATATAATAATAAATCAAACTT
64394 AATATA
1 AATATA
64400 TTAGAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 7 0.32
20 2 0.09
21 4 0.18
22 9 0.41
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (22 bp):
AATATAATAATAAATCAAACTT
Found at i:70458 original size:29 final size:29
Alignment explanation
Indices: 70424--70502 Score: 122
Period size: 29 Copynumber: 2.7 Consensus size: 29
70414 CGGTGATCGG
* * *
70424 TATATTTATCGATTTAATACCGGTCAGAT
1 TATATTTCTCGATCTAATACCGATCAGAT
*
70453 TATATTTCTCGATCTAACACCGATCAGAT
1 TATATTTCTCGATCTAATACCGATCAGAT
70482 TATATTTCTCGATCTAATACC
1 TATATTTCTCGATCTAATACC
70503 CGTAGCAGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.39
Consensus pattern (29 bp):
TATATTTCTCGATCTAATACCGATCAGAT
Found at i:71121 original size:111 final size:111
Alignment explanation
Indices: 70927--71259 Score: 585
Period size: 111 Copynumber: 3.0 Consensus size: 111
70917 TAAAAATCAT
* *
70927 ATATCTCTACACTTTGCTGATATGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
70992 TATTTAGTTGATTTATTTAATACATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
71038 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTGAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
71103 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
71149 ATATCTCGACACTTTGCTGATACGGTAAAATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
71214 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAAAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
71260 TTTTTGTAAT
Statistics
Matches: 212, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 212 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:76147 original size:19 final size:19
Alignment explanation
Indices: 76123--76161 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
76113 TCGAATGCAT
76123 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
76142 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
76161 T
1 T
76162 GAATATTTTC
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:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:76284 original size:64 final size:65
Alignment explanation
Indices: 76109--76271 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
76099 GAATTAATTG
* * * *
76109 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* * **
76174 AACATCGAATGCATTTGATGCATCGATGCACAATCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
76237 A
65 A
*
76238 AACATTGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
76272 TGGTGCACCG
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 36 0.42
65 50 0.58
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:78336 original size:14 final size:14
Alignment explanation
Indices: 78314--78351 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
78304 AAATCAAACT
*
78314 AGAAGAATTTGAAA
1 AGAAAAATTTGAAA
78328 AGAAAAATTTGAAA
1 AGAAAAATTTGAAA
78342 AGAAAAATTT
1 AGAAAAATTT
78352 AGATTTGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.24
Consensus pattern (14 bp):
AGAAAAATTTGAAA
Found at i:83767 original size:64 final size:60
Alignment explanation
Indices: 83634--83788 Score: 197
Period size: 64 Copynumber: 2.5 Consensus size: 60
83624 GAATTAATTG
* * **
83634 AACATC-AATGCATTCCATGCACCGATGCACTCTCATGCATCGATGCACTTGAATTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACTCTCATGCATCGATGCACAGGAATTTTCA
* *
83693 AACATCGAATGCATTTGATGCATCGATGCACAATC-CATGCATCGATGCACCAGGCTATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCAC--TCTCATGCATCGATGCA-CAGG--AATTTTCA
83757 AACATCGAATGCATTTCATGCATCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACT
83789 TGGTGCACCG
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
59 6 0.07
60 21 0.25
61 14 0.17
62 5 0.06
64 37 0.45
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (60 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTCATGCATCGATGCACAGGAATTTTCA
Done.