Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008280.1 Hibiscus syriacus cultivar Beakdansim tig00110940_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: 3557051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 17
Found at i:3520024 original size:33 final size:33
Alignment explanation
Indices: 3519967--3520065 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
3519957 ACGAGATAAT
*
3519967 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
3520001 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
3520034 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
3520066 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:3520059 original size:19 final size:19
Alignment explanation
Indices: 3519942--3520145 Score: 203
Period size: 19 Copynumber: 11.1 Consensus size: 19
3519932 TCTTTTGGTT
*
3519942 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
3519961 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
3519981 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
3519999 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
3520015 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
3520033 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3520048 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
3520068 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3520087 GAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGC
3520106 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3520125 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
3520144 GA
1 GA
3520146 TTTTGGTTTC
Statistics
Matches: 155, Mismatches: 17, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
14 19 0.12
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 79 0.51
20 45 0.29
21 2 0.01
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3520174 original size:19 final size:19
Alignment explanation
Indices: 3520141--3520207 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
3520131 AAAATCGCAA
**
3520141 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
3520160 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
3520179 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
3520199 TGCGATTTT
1 TGCGATTTT
3520208 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:3520773 original size:21 final size:20
Alignment explanation
Indices: 3520721--3520773 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
3520711 CGCTATGTAA
*
3520721 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
3520741 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
3520761 ATCTCGTTTGCGA
1 ATCGCG-TTGCGA
3520774 TTTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 24 0.80
21 6 0.20
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:3520810 original size:20 final size:20
Alignment explanation
Indices: 3520721--3520815 Score: 64
Period size: 20 Copynumber: 4.7 Consensus size: 20
3520711 CGCTATGTAA
* * *
3520721 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
3520741 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * ** * *
3520761 ATCTCGTTTGCGATTTTTTATT
1 ATCGC-ATTGCGA-TAGTAAGT
*
3520783 ACCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
3520803 ATCGCATTGCGAT
1 ATCGCATTGCGAT
3520816 TTTCCCAATT
Statistics
Matches: 57, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
20 39 0.68
21 12 0.21
22 6 0.11
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:3520833 original size:21 final size:21
Alignment explanation
Indices: 3520804--3520896 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
3520794 ATAGTAAGTA
3520804 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
3520825 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
3520845 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
3520866 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
3520886 TCGCATTGCGA
1 TCGCATTGCGA
3520897 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:3520834 original size:41 final size:41
Alignment explanation
Indices: 3520789--3520896 Score: 146
Period size: 41 Copynumber: 2.6 Consensus size: 41
3520779 TATTACCGCA
3520789 TTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAATTCGCG
1 TTGCGAT-GTAAGTATTCGCATTGCGATTTTCCCAATTCGCG
* **
3520830 TTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCGCG
1 TTGCGATGTAAGTATTCGCATTGCGATTTTCCCAATTCGCG
* **
3520871 TTGCGATTTACTTATTCGCATTGCGA
1 TTGCGATGTAAGTATTCGCATTGCGA
3520897 ATTGGGAAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
40 4 0.06
41 59 0.94
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (41 bp):
TTGCGATGTAAGTATTCGCATTGCGATTTTCCCAATTCGCG
Found at i:3528597 original size:17 final size:17
Alignment explanation
Indices: 3528575--3528608 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3528565 CATTTATATA
*
3528575 TTTAATCCTTCAATTAG
1 TTTAATCATTCAATTAG
*
3528592 TTTAATCATTTAATTAG
1 TTTAATCATTCAATTAG
3528609 ATAGTAACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.50
Consensus pattern (17 bp):
TTTAATCATTCAATTAG
Found at i:3528689 original size:2 final size:2
Alignment explanation
Indices: 3528682--3528709 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3528672 GTCAAATCTC
3528682 AT 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 AT
3528710 TAGTTAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3529615 original size:28 final size:27
Alignment explanation
Indices: 3529563--3529623 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
3529553 TTAAAAAAAA
*
3529563 AATTAGTCCTCAAACTTTCTAAAAATT
1 AATTAGTCCTCAAACTTGCTAAAAATT
* *
3529590 AATTAGGTCCTCAAACTTAGCCAAAAATC
1 AATTA-GTCCTCAAACTT-GCTAAAAATT
3529619 AATTA
1 AATTA
3529624 AGCACATCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 5 0.17
28 12 0.41
29 12 0.41
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.31
Consensus pattern (27 bp):
AATTAGTCCTCAAACTTGCTAAAAATT
Found at i:3530291 original size:22 final size:22
Alignment explanation
Indices: 3530266--3530313 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
3530256 ACTAGGGGCA
3530266 TATGAAATTT-TCCCGAATGACC
1 TATG-AATTTCTCCCGAATGACC
3530288 TATGAATTTCTCCCGAATGACC
1 TATGAATTTCTCCCGAATGACC
3530310 TATG
1 TATG
3530314 TAACCCTCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (22 bp):
TATGAATTTCTCCCGAATGACC
Found at i:3536639 original size:19 final size:19
Alignment explanation
Indices: 3536615--3536657 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
3536605 ATTTAAAGTA
*
3536615 GGTATTGGTACCCCCATAT
1 GGTATTGGTACCCCCATAG
*
3536634 GGTATTGGTACCCTCATAG
1 GGTATTGGTACCCCCATAG
3536653 GGTAT
1 GGTAT
3536658 CAGTACATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.33
Consensus pattern (19 bp):
GGTATTGGTACCCCCATAG
Found at i:3543514 original size:20 final size:20
Alignment explanation
Indices: 3543476--3543514 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3543466 CGATACCCTT
*
3543476 GCCCAAAAATCACTTTTTAA
1 GCCCAAAAATCACTCTTTAA
3543496 GCCCAAAAATTCA-TCTTTA
1 GCCCAAAAA-TCACTCTTTA
3543515 TCAGCTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (20 bp):
GCCCAAAAATCACTCTTTAA
Found at i:3545308 original size:13 final size:13
Alignment explanation
Indices: 3545292--3545316 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3545282 ATATAATTTA
3545292 AAATTTTTTAAAT
1 AAATTTTTTAAAT
3545305 AAATTTTTTAAA
1 AAATTTTTTAAA
3545317 AAGTTAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAATTTTTTAAAT
Found at i:3545465 original size:2 final size:2
Alignment explanation
Indices: 3545458--3545510 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3545448 ATCTAAAGTA
3545458 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
3545500 AT AT AT AT AT A
1 AT AT AT AT AT A
3545511 ATTTAAGCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3547185 original size:41 final size:41
Alignment explanation
Indices: 3547078--3547192 Score: 110
Period size: 41 Copynumber: 2.8 Consensus size: 41
3547068 CAAAATGATA
* * *
3547078 ACTTTAGCAGCGTTTTTATACAAACGCCGCAATAAGATTAGT
1 ACTTTAGCGGTGTTTTTA-ACAAACGCCGCAATAAGAGTAGT
* * * * *
3547120 -CTATAGTGGTGTTTTTCAATAAACGTCGCAA-CAGAGTAGT
1 ACTTTAGCGGTGTTTTT-AACAAACGCCGCAATAAGAGTAGT
3547160 ACTTTAGCGGTGTTTTTAGACAAACGCC-CAATA
1 ACTTTAGCGGTGTTTTTA-ACAAACGCCGCAATA
3547193 GGTTTCATAT
Statistics
Matches: 56, Mismatches: 13, Indels: 9
0.72 0.17 0.12
Matches are distributed among these distances:
40 11 0.20
41 44 0.79
42 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (41 bp):
ACTTTAGCGGTGTTTTTAACAAACGCCGCAATAAGAGTAGT
Found at i:3547609 original size:41 final size:40
Alignment explanation
Indices: 3547562--3547653 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 40
3547552 GTAACGCTTG
3547562 TTTACAAACGCCGCTATTGACACATACTTTAGTGGCATTT
1 TTTACAAACGCCGCTATTGACACATACTTTAGTGGCATTT
* * * * *
3547602 TTATACAAATGTCACTATAGA-ATTATACTTTAGTGGCATTT
1 TT-TACAAACGCCGCTATTGACA-CATACTTTAGTGGCATTT
3547643 TTT-CAAACGCC
1 TTTACAAACGCC
3547654 ACAACAGTCC
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
39 6 0.14
40 4 0.09
41 33 0.77
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (40 bp):
TTTACAAACGCCGCTATTGACACATACTTTAGTGGCATTT
Found at i:3547716 original size:42 final size:42
Alignment explanation
Indices: 3547664--3547775 Score: 143
Period size: 42 Copynumber: 2.7 Consensus size: 42
3547654 ACAACAGTCC
* *
3547664 TGTACCTTAGTGGCGTTTGTATAATAAAAGCCACAATAATCA
1 TGTAACTTAGTGGCGTTTTTATAATAAAAGCCACAATAATCA
* * * *
3547706 TGTAATTTAGTGGCATTTTTATAATAAACGCCACAATAGTCA
1 TGTAACTTAGTGGCGTTTTTATAATAAAAGCCACAATAATCA
* * *
3547748 TGTACCTTAATGGCGTTTTTATTATAAA
1 TGTAACTTAGTGGCGTTTTTATAATAAA
3547776 TGGCGCGATT
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (42 bp):
TGTAACTTAGTGGCGTTTTTATAATAAAAGCCACAATAATCA
Found at i:3551130 original size:132 final size:131
Alignment explanation
Indices: 3550746--3551149 Score: 471
Period size: 131 Copynumber: 3.1 Consensus size: 131
3550736 TATTCCACGG
* *
3550746 AGATTGAATCGAAATCGATTTGCTTCACTGTTCTTCAAGAAGACCAAATCTGAAAGAAGAAGAAT
1 AGATTGAATC-AAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAG-A-AAT
* * * ** *
3550811 TTGCTCCACT--T-TTT-AGGGCAGATCAGAATCGAGAAAACTTTGATCCACTTCACTATTCTTC
63 CTGCTCCACTACTCTTTAAGGG-AGATCAGACTCGAGAAAATTTTGATCCACTTCACTGCTCTTT
*
3550872 AGGAA
127 AGGGA
* * * **
3550877 ATATTAAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCCGAAAGAAG-CGTCT
1 AGATTGAATCA-AATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAATCT
*
3550941 GCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCACTGCTCTTTAGG
65 GCTCCACTACTCTTTAAGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCACTGCTCTTTAGG
3551006 GA
130 GA
* * * *
3551008 AGATTGAATCAAATGTGATTTGCTTCGCTGCTCTTCATGAAGA-AAAATCTGAGAAGAAGAAATC
1 AGATTGAATCAAAT-CGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGA-AAGAAGAAATC
* * * *
3551072 TGCTCCACTACTCTTTAAGGGAGACCAGACTCGACAAAGTTTTGATCCACTTCGCTGCT-TTTCA
64 TGCTCCACTACTCTTTAAGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCACTGCTCTTT-A
*
3551136 GAGA
128 GGGA
3551140 AGATTGAATC
1 AGATTGAATC
3551150 GAATATGTTT
Statistics
Matches: 234, Mismatches: 30, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
128 10 0.04
130 12 0.05
131 139 0.59
132 73 0.31
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (131 bp):
AGATTGAATCAAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAATCTG
CTCCACTACTCTTTAAGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCACTGCTCTTTAGGG
A
Found at i:3551960 original size:45 final size:45
Alignment explanation
Indices: 3551888--3552054 Score: 203
Period size: 45 Copynumber: 3.7 Consensus size: 45
3551878 TTGACTCTTA
* * * *
3551888 TTCGTGAGAAAG-TAAAATAGGACAACACTAAAAGATCAACTTCTC
1 TTCGTGAGAAAGTTAAGA-AGGACAACACTAAAATATCGACTCCTC
* * *
3551933 TTCGTGAGAAAGTTTAGAAGGATAACACTAAAATATTGACTCCTC
1 TTCGTGAGAAAGTTAAGAAGGACAACACTAAAATATCGACTCCTC
*
3551978 TTCGTGAGAAAGTCAAGAAGGACAACACTAAAATATCGACTCCTC
1 TTCGTGAGAAAGTTAAGAAGGACAACACTAAAATATCGACTCCTC
** *
3552023 TTCACGAGAAAGTCAAGTAAGG-CAACACTAAA
1 TTCGTGAGAAAGTTAAG-AAGGACAACACTAAA
3552055 TGATTTACTC
Statistics
Matches: 107, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
45 100 0.93
46 7 0.07
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (45 bp):
TTCGTGAGAAAGTTAAGAAGGACAACACTAAAATATCGACTCCTC
Found at i:3552070 original size:45 final size:45
Alignment explanation
Indices: 3551893--3552079 Score: 182
Period size: 45 Copynumber: 4.2 Consensus size: 45
3551883 TCTTATTCGT
* * ** * **
3551893 GAGAAAGT-AAAATAGGACAACACTAAAAGATCAACTTCTCTTCGT
1 GAGAAAGTCAAGA-AGGACAACACTAAAATATTGACTCCTCTTCAC
** * **
3551938 GAGAAAGTTTAGAAGGATAACACTAAAATATTGACTCCTCTTCGT
1 GAGAAAGTCAAGAAGGACAACACTAAAATATTGACTCCTCTTCAC
*
3551983 GAGAAAGTCAAGAAGGACAACACTAAAATATCGACTCCTCTTCAC
1 GAGAAAGTCAAGAAGGACAACACTAAAATATTGACTCCTCTTCAC
* *
3552028 GAGAAAGTCAAGTAAGG-CAACACT-AAATGATTTACTCATCTTCAC
1 GAGAAAGTCAAG-AAGGACAACACTAAAAT-ATTGACTCCTCTTCAC
*
3552073 AAGAAAG
1 GAGAAAG
3552080 CCAAAAATTA
Statistics
Matches: 122, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
44 4 0.03
45 112 0.92
46 6 0.05
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (45 bp):
GAGAAAGTCAAGAAGGACAACACTAAAATATTGACTCCTCTTCAC
Found at i:3552356 original size:42 final size:41
Alignment explanation
Indices: 3552270--3552377 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 41
3552260 GACTTGACTT
* * *
3552270 CTCTTCATAAGGAAGTCAAGAATAA-TAGAAAGAATGACTT
1 CTCTTCACAAGGAAGTCAAGAATAACTAGAAAGAATGAATC
* * *
3552310 CTCTTCACAAGGAAGTTAAGAATAACTTTGAAAGATTGAATC
1 CTCTTCACAAGGAAGTCAAGAATAAC-TAGAAAGAATGAATC
* * *
3552352 CTCTTCGCGAGGGAGTCAAGAATAAC
1 CTCTTCACAAGGAAGTCAAGAATAAC
3552378 AAATATCGAC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 23 0.41
42 33 0.59
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (41 bp):
CTCTTCACAAGGAAGTCAAGAATAACTAGAAAGAATGAATC
Found at i:3552455 original size:38 final size:38
Alignment explanation
Indices: 3552263--3552551 Score: 249
Period size: 38 Copynumber: 7.3 Consensus size: 38
3552253 AAAGATTGAC
** *
3552263 TTGACTTCTCTTCATAAGGAAGTCAAGAATAATAGAAAGA
1 TTGACTTCTCTTCACGAGGAAGTCAAGAAT-A-ACAAAGA
* * *
3552303 ATGACTTCTCTTCACAAGGAAGTTAAGAATAACTTTGAAAGA
1 TTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAAGA
* * * * *
3552345 TTGAATCCTCTTCGCGAGGGAGTCAAGAATAACAAATA
1 TTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGA
* * *
3552383 TCGACTTGACT-TCTCATGAGAAAGTCAAGAATAACAAAGA
1 TTGACTT--CTCT-TCACGAGGAAGTCAAGAATAACAAAGA
*
3552423 TCGACTTCTCTTCACGAGGAAGTCAAGAATAACATTAAAAGA
1 TTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAAGA
* * *
3552465 -TGACTCCTCTTCACGAGGGAGTCAAGAATAACAAACA
1 TTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGA
* * * *
3552502 TTGACTTCTTTTTATGAGGAAGTTAAGAATAACAAAGA
1 TTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGA
3552540 TTGACTTCTCTT
1 TTGACTTCTCTT
3552552 AATGGGAGTT
Statistics
Matches: 202, Mismatches: 34, Indels: 28
0.77 0.13 0.11
Matches are distributed among these distances:
37 4 0.02
38 72 0.36
39 3 0.01
40 58 0.29
41 29 0.14
42 36 0.18
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.27
Consensus pattern (38 bp):
TTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGA
Found at i:3552588 original size:119 final size:118
Alignment explanation
Indices: 3552225--3552553 Score: 338
Period size: 119 Copynumber: 2.7 Consensus size: 118
3552215 AAATATTGAT
* * * * * * *
3552225 TCCTTTTCATGAGGGAGCCAAGAATAACAAAGATTGACTTGACTTCTCTTCATAAGGAAGTCAAG
1 TCCTCTTCACGAGGGAGTCAAGAATAACAAACATCGACTT-AC-T-TC-TCATGAGAAAGTCAAG
* * * * * * * *
3552290 AATAATAGAAAGAAT-GACTTCTCTTCACAAGGAAGTTAAGAATAACTTTGAAAGATTGAA
62 AAT-A-ACAAAG-ATCGACTTCTCTTAACGAGGAAGTCAAGAATAACATT-AAAAAATGAC
* *
3552350 TCCTCTTCGCGAGGGAGTCAAGAATAACAAATATCGACTTGACTTCTCATGAGAAAGTCAAGAAT
1 TCCTCTTCACGAGGGAGTCAAGAATAACAAACATCGACTT-ACTTCTCATGAGAAAGTCAAGAAT
* *
3552415 AACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAACATTAAAAGATGAC
65 AACAAAGATCGACTTCTCTTAACGAGGAAGTCAAGAATAACATTAAAAAATGAC
* * * * *
3552469 TCCTCTTCACGAGGGAGTCAAGAATAACAAACATTGACTT-CTTTTTATGAGGAAGTTAAGAATA
1 TCCTCTTCACGAGGGAGTCAAGAATAACAAACATCGACTTACTTCTCATGAGAAAGTCAAGAATA
*
3552533 ACAAAGATTGACTTCTCTTAA
66 ACAAAGATCGACTTCTCTTAA
3552554 TGGGAGTTAA
Statistics
Matches: 178, Mismatches: 25, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
117 39 0.22
119 45 0.25
120 36 0.20
121 1 0.01
122 17 0.10
123 2 0.01
124 1 0.01
125 37 0.21
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (118 bp):
TCCTCTTCACGAGGGAGTCAAGAATAACAAACATCGACTTACTTCTCATGAGAAAGTCAAGAATA
ACAAAGATCGACTTCTCTTAACGAGGAAGTCAAGAATAACATTAAAAAATGAC
Done.