Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001509.1 Hibiscus syriacus cultivar Beakdansim tig00002954_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: 81796
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:15834 original size:20 final size:20
Alignment explanation
Indices: 15805--15843 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
15795 ATTCCTCCAC
*
15805 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
15825 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
15844 TATGGTATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:25994 original size:18 final size:18
Alignment explanation
Indices: 25971--26024 Score: 90
Period size: 18 Copynumber: 2.9 Consensus size: 18
25961 TATATTTTCC
25971 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
25989 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
*
26007 AAAAATTGGTATACTTTT
1 AACAATTGGTAT-CTTTT
26025 GGTATCTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 29 0.85
19 5 0.15
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.48
Consensus pattern (18 bp):
AACAATTGGTATCTTTTT
Found at i:26305 original size:36 final size:36
Alignment explanation
Indices: 26247--26333 Score: 149
Period size: 36 Copynumber: 2.4 Consensus size: 36
26237 AAATGCAAAA
26247 GGGTACCGATA-CCCTTCAAATGGTATCCATACCCT
1 GGGTACCGATACCCCTTCAAATGGTATCCATACCCT
*
26282 GGGTACCGATACCCCTTCAAATGGTATCCATACCTT
1 GGGTACCGATACCCCTTCAAATGGTATCCATACCCT
*
26318 GGGTACTGATACCCCT
1 GGGTACCGATACCCCT
26334 GCCTGGGTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 11 0.22
36 38 0.78
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.26
Consensus pattern (36 bp):
GGGTACCGATACCCCTTCAAATGGTATCCATACCCT
Found at i:29159 original size:30 final size:30
Alignment explanation
Indices: 29118--29399 Score: 496
Period size: 30 Copynumber: 9.4 Consensus size: 30
29108 TCCGAAGGAC
*
29118 CTATTCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
29148 CTAACCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
29178 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
29208 CTATCCAGAGGTCATAAAGATCCTC-GTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
29237 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
29267 CTATCCAGA-GTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
29296 CTATCCAGAGGTCATAAAGATCCTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
29326 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
29356 CTATCCAGAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAG-AGGTCATAAAGATCCTCGGTAA
* *
29387 CTGTCCATAGGTC
1 CTATCCAGAGGTC
29400 CCGAAGACCT
Statistics
Matches: 242, Mismatches: 7, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
29 58 0.24
30 156 0.64
31 28 0.12
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:29275 original size:89 final size:89
Alignment explanation
Indices: 29118--29399 Score: 485
Period size: 89 Copynumber: 3.1 Consensus size: 89
29108 TCCGAAGGAC
* *
29118 CTATTCAGAGGTCATAAAGATCCTCGGTAACTAACCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCATAAAGATCCTC-GTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
29183 CAGAGGTCATAAAGATCCTCGGTAA
65 CAGAGGTCATAAAGATCCTCGGTAA
29208 CTATCCAGAGGTCATAAAGATCCTCGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATCC
1 CTATCCAGAGGTCATAAAGATCCTCGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATCC
29273 AGA-GTCATAAAGATCCTCGGTAA
66 AGAGGTCATAAAGATCCTCGGTAA
*
29296 CTATCCAGAGGTCATAAAGATCCTTGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCATAAAGATCC-TCGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
29361 CAGAAGGTCATAAAGATCCTCGGTAA
65 CAG-AGGTCATAAAGATCCTCGGTAA
* *
29387 CTGTCCATAGGTC
1 CTATCCAGAGGTC
29400 CCGAAGACCT
Statistics
Matches: 184, Mismatches: 5, Indels: 5
0.95 0.03 0.03
Matches are distributed among these distances:
88 43 0.23
89 85 0.46
90 25 0.14
91 31 0.17
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (89 bp):
CTATCCAGAGGTCATAAAGATCCTCGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATCC
AGAGGTCATAAAGATCCTCGGTAA
Found at i:32206 original size:158 final size:150
Alignment explanation
Indices: 31910--32215 Score: 531
Period size: 158 Copynumber: 2.0 Consensus size: 150
31900 CTGTACAATA
*
31910 AAGATACCTCTATTCTCTGGATCCTCATTATCTTCACTGAGATTTATATACTCTAGCCGTAGAGC
1 AAGATACCTCTATTCTCTGGATCCTCATTATCTTCACTGAGAATTATATACTCTAGCCGTAGAGC
31975 GCATTTCCTGTTGAGTAGAAAATTCTGTCTGACTTCTTTCTCTACCTCTACCCCGTCCTCTCTGG
66 GCATTTCCTGTTGAGTAGAAAATTCTGTCTGACTTCTTTCTCTACCTCTACCCCGTCCTCTCTGG
32040 GATATCGAAGCAGATCGCAG
131 GATATCGAAGCAGATCGCAG
32060 AAGATACCTGCTATTATCTCTGGATCCTCATTATCTTCACTGATATTGAGATTATATACTCTAGC
1 AAGATACCT-CTA-T-TCTCTGGATCCTCATTATCTTCACTG--A--GA-ATTATATACTCTAGC
32125 CGTAGAGCGCATTTCCTGTTGAGTAGAAAATTCTGTCTGACTTCTTTCTCTACCTCTACCCCGTC
58 CGTAGAGCGCATTTCCTGTTGAGTAGAAAATTCTGTCTGACTTCTTTCTCTACCTCTACCCCGTC
32190 CTCTCTGGGATATCGAAGCAGATCGC
123 CTCTCTGGGATATCGAAGCAGATCGC
32216 TCCGACTGCA
Statistics
Matches: 147, Mismatches: 1, Indels: 8
0.94 0.01 0.05
Matches are distributed among these distances:
150 9 0.06
151 3 0.02
152 1 0.01
153 26 0.18
155 1 0.01
157 2 0.01
158 105 0.71
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (150 bp):
AAGATACCTCTATTCTCTGGATCCTCATTATCTTCACTGAGAATTATATACTCTAGCCGTAGAGC
GCATTTCCTGTTGAGTAGAAAATTCTGTCTGACTTCTTTCTCTACCTCTACCCCGTCCTCTCTGG
GATATCGAAGCAGATCGCAG
Found at i:34066 original size:29 final size:30
Alignment explanation
Indices: 34016--34145 Score: 203
Period size: 29 Copynumber: 4.4 Consensus size: 30
34006 TTCGAAGGAC
* *
34016 CTATTCAGAGGTCATATAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
34046 CTATCCA-AGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
34075 CTATCCAGAGGTCATAAAGATCCTC-GTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
34104 CTATCCAGAGGTCAT-AAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
34133 CTGTCCATAGGTC
1 CTATCCAGAGGTC
34146 CCGAAGACCT
Statistics
Matches: 94, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
28 9 0.10
29 62 0.66
30 23 0.24
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:35108 original size:21 final size:21
Alignment explanation
Indices: 35084--35126 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
35074 TCATATTCGT
* *
35084 TTGAGGGGGAATCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
* *
35105 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
35126 T
1 T
35127 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGAACCGATTCCCC
Found at i:43030 original size:24 final size:24
Alignment explanation
Indices: 42977--43030 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
42967 TACACAAAAA
*
42977 TATTGTTTTAAATAATGATAATAAT
1 TATT-TTTTAAATAATAATAATAAT
* * *
43002 AATTTTTTAATTAATAATAATTAT
1 TATTTTTTAAATAATAATAATAAT
43026 TATTT
1 TATTT
43031 CAAATAAATG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
TATTTTTTAAATAATAATAATAAT
Found at i:45698 original size:11 final size:11
Alignment explanation
Indices: 45684--45730 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
45674 TTAGTATTTA
*
45684 TTATTAATTTG
1 TTATTAGTTTG
*
45695 TTA-TGGTTTG
1 TTATTAGTTTG
* *
45705 TTATCAGCTTG
1 TTATTAGTTTG
45716 TTATTAGTTTG
1 TTATTAGTTTG
45727 TTAT
1 TTAT
45731 GGTGTGTTGC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
10 8 0.29
11 20 0.71
ACGTcount: A:0.19, C:0.04, G:0.17, T:0.60
Consensus pattern (11 bp):
TTATTAGTTTG
Found at i:47538 original size:36 final size:36
Alignment explanation
Indices: 47064--47524 Score: 654
Period size: 36 Copynumber: 12.8 Consensus size: 36
47054 GGTAAAGTTA
*
47064 GCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAA
1 GCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAG
*
47100 GCATCGACACTTCCGATTCAAGTCGAACGGAAGGAG
1 GCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAG
* *
47136 GCATCGGCAATTCCAATTCAAGTCGAACGGAAGGAG
1 GCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAG
* * *
47172 GCATCAGCACTTTCGATTCAAGTCGAACGGAAGAAG
1 GCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAG
*
47208 GCATCGGCACTTCCGATTCAAGTCGAACGAAAGGAG
1 GCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAG
* *
47244 GGATCGACACTTCCGATTCAAGTCGAACGGAAGGAG
1 GCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAG
**
47280 GCATCGGCACTTCCGATTCAAG-CTGAACGGAATAAG
1 GCATCGGCACTTCCGATTCAAGTC-GAACGGAAGGAG
* *
47316 GCATCGGCACTTCCAATTCAAGTCGAATGGAAGGAG
1 GCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAG
* *
47352 GCATCGACACTTCCGATTCAAGTCGAACGGAATGAG
1 GCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAG
* * *
47388 GCATCAGCACTTCCGATTCAAATCGAACGGAATGAG
1 GCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAG
* * * *
47424 GCATCAGCATTTCAGATTCAAATCGAACGGAAGGAG
1 GCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAG
* * * *
47460 GCATCGACACTTCCGATTCAAATCAAACGGAAGGAA
1 GCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAG
*
47496 GCATCGCCACTTCCGATTCAAGTCGAACG
1 GCATCGGCACTTCCGATTCAAGTCGAACG
47525 AAAAGATGTA
Statistics
Matches: 379, Mismatches: 44, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
35 1 0.00
36 377 0.99
37 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (36 bp):
GCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAG
Found at i:47640 original size:11 final size:11
Alignment explanation
Indices: 47624--47717 Score: 120
Period size: 11 Copynumber: 8.7 Consensus size: 11
47614 TTAGTTAGTA
47624 TTTGTTATTAG
1 TTTGTTATTAG
*
47635 TTTGTTATCAG
1 TTTGTTATTAG
*
47646 TTTGTTA-TGG
1 TTTGTTATTAG
*
47656 TTTGTTATCAG
1 TTTGTTATTAG
*
47667 CTTGTTATTAG
1 TTTGTTATTAG
*
47678 TTTGTTA-TGG
1 TTTGTTATTAG
47688 TTTGTTATTAG
1 TTTGTTATTAG
*
47699 CTTGTTATTAG
1 TTTGTTATTAG
47710 TTTGTTAT
1 TTTGTTAT
47718 GGTGTGTTGC
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
10 17 0.25
11 52 0.75
ACGTcount: A:0.16, C:0.04, G:0.20, T:0.60
Consensus pattern (11 bp):
TTTGTTATTAG
Found at i:47658 original size:21 final size:22
Alignment explanation
Indices: 47624--47717 Score: 129
Period size: 21 Copynumber: 4.4 Consensus size: 22
47614 TTAGTTAGTA
47624 TTTGTTATTAGTTTGTTATCAG
1 TTTGTTATTAGTTTGTTATCAG
*
47646 TTTGTTA-TGGTTTGTTATCAG
1 TTTGTTATTAGTTTGTTATCAG
* *
47667 CTTGTTATTAGTTTGTTAT-GG
1 TTTGTTATTAGTTTGTTATCAG
* *
47688 TTTGTTATTAGCTTGTTATTAG
1 TTTGTTATTAGTTTGTTATCAG
47710 TTTGTTAT
1 TTTGTTAT
47718 GGTGTGTTGC
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
21 37 0.59
22 26 0.41
ACGTcount: A:0.16, C:0.04, G:0.20, T:0.60
Consensus pattern (22 bp):
TTTGTTATTAGTTTGTTATCAG
Found at i:47672 original size:32 final size:32
Alignment explanation
Indices: 47624--47725 Score: 168
Period size: 32 Copynumber: 3.2 Consensus size: 32
47614 TTAGTTAGTA
* *
47624 TTTGTTATTAGTTTGTTATCAGTTTGTTATGG
1 TTTGTTATTAGCTTGTTATTAGTTTGTTATGG
*
47656 TTTGTTATCAGCTTGTTATTAGTTTGTTATGG
1 TTTGTTATTAGCTTGTTATTAGTTTGTTATGG
47688 TTTGTTATTAGCTTGTTATTAGTTTGTTATGG
1 TTTGTTATTAGCTTGTTATTAGTTTGTTATGG
*
47720 TGTGTT
1 TTTGTT
47726 GCTTACTTAG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.15, C:0.04, G:0.23, T:0.59
Consensus pattern (32 bp):
TTTGTTATTAGCTTGTTATTAGTTTGTTATGG
Found at i:49008 original size:11 final size:11
Alignment explanation
Indices: 48987--49039 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
48977 CAAATAACGA
48987 AAAATAATAAAT
1 AAAA-AATAAAT
48999 AAAAAATAAAAT
1 AAAAAAT-AAAT
* *
49011 AAAAAAGAATT
1 AAAAAATAAAT
49022 AAAAAAATAAA-
1 -AAAAAATAAAT
49033 AAAAAAT
1 AAAAAAT
49040 TATTATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 7 0.20
11 6 0.17
12 22 0.63
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:50848 original size:3 final size:3
Alignment explanation
Indices: 50842--50896 Score: 58
Period size: 3 Copynumber: 17.7 Consensus size: 3
50832 ATAGTAGTAG
*
50842 TAA TAA TAA TAA TAA TAA -AT TAA TAA TAAA TAA TAA TAA GTTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA --TAA TAA
*
50889 TAA AAA TA
1 TAA TAA TA
50897 GAACCCGGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 1 0.02
3 37 0.84
4 3 0.07
5 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:50855 original size:21 final size:19
Alignment explanation
Indices: 50840--50896 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
50830 AAATAGTAGT
50840 AGTAATAATAATAATAATAA
1 AGTAATAATAATAATAAT-A
*
50860 ATTAATAATAAATAATAATA
1 AGTAATAAT-AATAATAATA
*
50880 AGTTAATAATAAAAATA
1 AG-TAATAATAATAATA
50897 GAACCCGGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (19 bp):
AGTAATAATAATAATAATA
Found at i:51442 original size:139 final size:139
Alignment explanation
Indices: 51216--51474 Score: 385
Period size: 139 Copynumber: 1.9 Consensus size: 139
51206 ACGATTCCTA
* * *
51216 CGTGATGAGGAAATCTGGTTATCTAATGTTGACACTGCTCCTACGTGATGAGGAGATCAGGTCGG
1 CGTGATGAGGAAATCTGGTTATCTAAGGATGACACTGCACCTACGTGATGAGGAGATCAGGTCGG
*
51281 TAGATGACATTATTCCTACGTGATGAGGAAGTCTAACCATCTTTAGGGATAATTTAAAAACAACA
66 TAGATGACATTATTCCTACGTGATGAGGAAGTCCAACCATCTTTAGGGATAATTTAAAAACAACA
51346 CTGTTCTTG
131 CTGTTCTTG
* ****
51355 CGTGATGAGGAAGTCTGGTTATCTAAGGATGGTGTTGCACCTACGTGATGAGGAGAT-ATGGTCG
1 CGTGATGAGGAAATCTGGTTATCTAAGGATGACACTGCACCTACGTGATGAGGAGATCA-GGTCG
* * * *
51419 GTGGATGACATTGTTTCTACGTGATGAGGATGTCCAACCATCTTTAGGGATAATTT
65 GTAGATGACATTATTCCTACGTGATGAGGAAGTCCAACCATCTTTAGGGATAATTT
51475 GTTTCAAGAG
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
138 1 0.01
139 105 0.99
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (139 bp):
CGTGATGAGGAAATCTGGTTATCTAAGGATGACACTGCACCTACGTGATGAGGAGATCAGGTCGG
TAGATGACATTATTCCTACGTGATGAGGAAGTCCAACCATCTTTAGGGATAATTTAAAAACAACA
CTGTTCTTG
Found at i:51596 original size:37 final size:37
Alignment explanation
Indices: 51540--51769 Score: 233
Period size: 37 Copynumber: 6.4 Consensus size: 37
51530 CAATTGTTTA
* * *
51540 TGTTTTAAGTGAAACTGTCTTAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
* *
51577 TGTTTCAAGAGAAATTGTCTCAAGTGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
** ** ***
51614 TGTTTCAA-AGGAAACAATCTC-A-ATTG--TTTA--T
1 TGTTTCAAGA-GAAACTGTCTCAAGAGAGACAAAACTT
* *
51645 T-TTTCAAGAGAAACTTTCTCAAGAGAGATAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
*
51681 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
* *
51718 TGTTTCAAGAGAAACTTTCTCAAGCGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
*
51755 TGTTTCAAGGGAAAC
1 TGTTTCAAGAGAAAC
51770 AATCTCAGTT
Statistics
Matches: 158, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
30 15 0.09
31 4 0.03
32 2 0.01
33 1 0.01
34 1 0.01
35 1 0.01
36 4 0.03
37 130 0.82
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
Found at i:51691 original size:20 final size:19
Alignment explanation
Indices: 51668--51768 Score: 56
Period size: 20 Copynumber: 5.4 Consensus size: 19
51658 CTTTCTCAAG
51668 AGAGATAAAACTTTGTTTCA
1 AGAGA-AAAACTTTGTTTCA
*
51688 AGAG--AAAC--TGTCTCA
1 AGAGAAAAACTTTGTTTCA
51703 AGCGAGACAAAACTTTGTTTCA
1 A--GAGA-AAAACTTTGTTTCA
*
51725 AGAG--AAAC-TT-TCTCA
1 AGAGAAAAACTTTGTTTCA
51740 AGCGAGACAAAACTTTGTTTCA
1 A--GAGA-AAAACTTTGTTTCA
*
51762 AGGGAAA
1 AGAGAAA
51769 CAATCTCAGT
Statistics
Matches: 62, Mismatches: 5, Indels: 29
0.65 0.05 0.30
Matches are distributed among these distances:
15 12 0.19
16 2 0.03
17 14 0.23
19 2 0.03
20 18 0.29
21 2 0.03
22 12 0.19
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (19 bp):
AGAGAAAAACTTTGTTTCA
Found at i:51726 original size:22 final size:22
Alignment explanation
Indices: 51700--51763 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
51690 AGAAACTGTC
51700 TCAAGCGAGACAAAACTTTGTT
1 TCAAGCGAGACAAAACTTTGTT
*
51722 TCAA--GAG---AAAC-TT-TC
1 TCAAGCGAGACAAAACTTTGTT
51737 TCAAGCGAGACAAAACTTTGTT
1 TCAAGCGAGACAAAACTTTGTT
51759 TCAAG
1 TCAAG
51764 GGAAACAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
15 5 0.15
16 2 0.06
17 7 0.21
20 7 0.21
21 2 0.06
22 10 0.30
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (22 bp):
TCAAGCGAGACAAAACTTTGTT
Found at i:51734 original size:17 final size:17
Alignment explanation
Indices: 51675--51735 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
51665 AAGAGAGATA
51675 AAACTTTGTTTCAAGAG
1 AAACTTTGTTTCAAGAG
*
51692 AAAC--TGTCTCAAGCGAG
1 AAACTTTGTTTCAA--GAG
51709 ACAAAACTTTGTTTCAAGAG
1 ---AAACTTTGTTTCAAGAG
51729 AAACTTT
1 AAACTTT
51736 CTCAAGCGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
15 7 0.20
17 14 0.40
20 7 0.20
22 7 0.20
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (17 bp):
AAACTTTGTTTCAAGAG
Found at i:51740 original size:104 final size:104
Alignment explanation
Indices: 51472--51732 Score: 402
Period size: 104 Copynumber: 2.5 Consensus size: 104
51462 TTAGGGATAA
* * *
51472 TTTGTTTCAAGAGAAACTTTCTCAAGCTAGACAAAA-TTTGTTTCAAGGGAAACAATCTCAATTG
1 TTTGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAATTG
* *
51536 TTTATGTTTTAAGTGAAACTGTCTTAAGAGAGACAAAAC
66 TTTATGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAAC
* *
51575 TTTGTTTCAAGAGAAATTGTCTCAAGTGAGACAAAACTTTGTTTCAA-AGGAAACAATCTCAATT
1 TTTGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGA-GAAACAATCTCAATT
* *
51639 GTTTAT-TTTTCAAGAGAAACTTTCTCAAGAGAGATAAAAC
65 GTTTATGTTTT-AAGAGAAACTGTCTCAAGAGAGACAAAAC
51679 TTTGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAAC
1 TTTGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAAC
51733 TTTCTCAAGC
Statistics
Matches: 143, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
103 36 0.25
104 106 0.74
105 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (104 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAATTG
TTTATGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAAC
Found at i:51826 original size:141 final size:136
Alignment explanation
Indices: 51507--51826 Score: 328
Period size: 141 Copynumber: 2.3 Consensus size: 136
51497 GCTAGACAAA
* * * * * * *
51507 ATTTGTTTCAAGGGAAACAATCTC-AATTGTTTATGTTTTAAGTGAAACTGTCTTAAGAGAGACA
1 ATTTGTTTCAAGAGAAACAATTTCAAAATATTT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACA
*
51571 AAACTTTGTTTCAAGAGAAATTGTCTCAAGTGAGACAAAACTTTGTTTCAAAGGAAACAATCTCA
65 AAACTTTGTTTCAAGAGAAATTGTCTCAAGCGAGACAAAACTTTGTTTCAAAGGAAACAATCTCA
51636 ATTGTTT
130 ATTGTTT
* *
51643 A-TT-TTTCAAGAGAAAC-TTTCTCAAGAGAGATAAAACTTTGTTTCAAGAGAAACTGTCTCAAG
1 ATTTGTTTCAAGAGAAACAATT-TC-A-A-A-AT---ATTTTGTTTCAAGAGAAACTGTCTCAAG
* *
51705 CGAGACAAAACTTTGTTTCAAGAGAAACTT-TCTCAAGCGAGACAAAACTTTGTTTCAAGGGAAA
58 AGAGACAAAACTTTGTTTCAAGAGAAA-TTGTCTCAAGCGAGACAAAACTTTGTTTCAAAGGAAA
*
51769 CAATCTCAGTTGTTTAT
122 CAATCTCAATTG-TT-T
*
51786 CAATTTTGTTTCAAGTGAAACAATTTCAAAAT-TTTGTGTTT
1 --A-TTTGTTTCAAGAGAAACAATTTCAAAATATTT-TGTTT
51827 TGAGGAAAAA
Statistics
Matches: 149, Mismatches: 16, Indels: 33
0.75 0.08 0.17
Matches are distributed among these distances:
133 1 0.01
134 14 0.09
135 2 0.01
136 1 0.01
137 1 0.01
138 1 0.01
139 1 0.01
140 2 0.01
141 95 0.64
142 6 0.04
143 1 0.01
144 2 0.01
145 2 0.01
146 1 0.01
147 3 0.02
148 14 0.09
149 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (136 bp):
ATTTGTTTCAAGAGAAACAATTTCAAAATATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
AACTTTGTTTCAAGAGAAATTGTCTCAAGCGAGACAAAACTTTGTTTCAAAGGAAACAATCTCAA
TTGTTT
Found at i:57492 original size:23 final size:23
Alignment explanation
Indices: 57434--57497 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
57424 CGAGGGTTCT
* * **
57434 ATGTGGTCCTTCAGGACAAAATT
1 ATGTGGTCTTTCGGGACAAAACA
57457 ATGTGGTCTTTCGGGACAAAACA
1 ATGTGGTCTTTCGGGACAAAACA
57480 ATGTGGT-TATTCGGGACA
1 ATGTGGTCT-TTCGGGACA
57498 TTTATGTGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (23 bp):
ATGTGGTCTTTCGGGACAAAACA
Found at i:58631 original size:60 final size:61
Alignment explanation
Indices: 58559--58741 Score: 198
Period size: 60 Copynumber: 3.0 Consensus size: 61
58549 CATTACAAAT
** *
58559 CCTCAAACTATGACCTTCATTTTAAATTGGTCCATAAACTTTTAAACATTCCAATTTTATC
1 CCTCAAACTATGACCTTCATTTTAAATTTATCCATAAACTTTTAAACATTCTAATTTTATC
* * * * * *
58620 CCT-AAACTATGA-ATATCATTCTAGATTTATCC-TCAAGCTTTTGAATATTCTAATTTTAT-
1 CCTCAAACTATGACCT-TCATTTTAAATTTATCCAT-AAACTTTTAAACATTCTAATTTTATC
*
58679 CCTCAAACTATGACTCTT-ATTTTAAATTTATCCATAAACTTTTAAATC-TTCTAATTTCATC
1 CCTCAAACTATGAC-CTTCATTTTAAATTTATCCATAAACTTTTAAA-CATTCTAATTTTATC
58740 CC
1 CC
58742 AAATCCATCC
Statistics
Matches: 98, Mismatches: 16, Indels: 16
0.75 0.12 0.12
Matches are distributed among these distances:
59 5 0.05
60 85 0.87
61 7 0.07
62 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.42
Consensus pattern (61 bp):
CCTCAAACTATGACCTTCATTTTAAATTTATCCATAAACTTTTAAACATTCTAATTTTATC
Found at i:72941 original size:32 final size:32
Alignment explanation
Indices: 72903--72967 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
72893 GCTTCCCATT
72903 AAATGTGTTAATTATTAACTTCTAAAAATTAA
1 AAATGTGTTAATTATTAACTTCTAAAAATTAA
* *
72935 AAATGTGTTAATTATTAATTTTTAAAAATTAA
1 AAATGTGTTAATTATTAACTTCTAAAAATTAA
72967 A
1 A
72968 TTTTTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (32 bp):
AAATGTGTTAATTATTAACTTCTAAAAATTAA
Found at i:80936 original size:96 final size:94
Alignment explanation
Indices: 80756--80947 Score: 215
Period size: 96 Copynumber: 2.0 Consensus size: 94
80746 AGTGATACCA
* * * * * *
80756 ATTTATTTGAAAAAAATAAAAAATTAAAATAAAATGATAACATAATTTGAAGAATAATTACCACT
1 ATTTATTTGAAAAAAATAAAAAATAAAAATAAAATAATAAAACAATTTCAAGAATAAATACCAC-
* *
80821 TAATTTTAAAATATTAAAAAGTCAAACTCCT
65 AAATTTTAAAATATTAAAAAATC-AACTCCT
* * * **
80852 ATTTCTTTGAAAATAATAAAAAATAAAAATAAAGTAATAAAACAATTTCAAGAATAAATATGA-A
1 ATTTATTTGAAAAAAATAAAAAATAAAAATAAAATAATAAAACAATTTCAAGAATAAATACCACA
*
80916 AATTTTGAAATATTAAAAAAAATCAACTCCT
66 AATTTTAAAATATT--AAAAAATCAACTCCT
80947 A
1 A
80948 AAGGGTTTAT
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
94 13 0.16
95 8 0.10
96 59 0.74
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (94 bp):
ATTTATTTGAAAAAAATAAAAAATAAAAATAAAATAATAAAACAATTTCAAGAATAAATACCACA
AATTTTAAAATATTAAAAAATCAACTCCT
Done.