Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009399.1 Corchorus capsularis cultivar CVL-1 contig09420, 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: 31312
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:3727 original size:7 final size:7
Alignment explanation
Indices: 3715--3740 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3705 GTTCTTAAAC
3715 AAAAATT
1 AAAAATT
3722 AAAAATT
1 AAAAATT
3729 AAAAATT
1 AAAAATT
3736 AAAAA
1 AAAAA
3741 CGGAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAAATT
Found at i:10023 original size:26 final size:27
Alignment explanation
Indices: 9985--10058 Score: 98
Period size: 26 Copynumber: 2.8 Consensus size: 27
9975 AGGGTCACCT
9985 AGGGTCATTTTGGTCATTCTTACACT-A
1 AGGG-CATTTTGGTCATTCTTACACTCA
**
10012 AGGGCATTTTGGTCATTCGCACACTCA
1 AGGGCATTTTGGTCATTCTTACACTCA
*
10039 GGGGCATTTTGGTCA-TCTTA
1 AGGGCATTTTGGTCATTCTTA
10059 GTCCATTGCT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 22 0.54
27 19 0.46
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (27 bp):
AGGGCATTTTGGTCATTCTTACACTCA
Found at i:10279 original size:52 final size:52
Alignment explanation
Indices: 10217--10321 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
10207 ATTAGTAAGC
10217 TAGCATCAGCGCTTTAGATTTGATCCATGATTTATCCTAAGTATGTAGTCAT
1 TAGCATCAGCGCTTTAGATTTGATCCATGATTTATCCTAAGTATGTAGTCAT
10269 TAGCATCAGCGCTTTAGATTTGATCCATGATTTATCCTAAGTATGTAGTCAT
1 TAGCATCAGCGCTTTAGATTTGATCCATGATTTATCCTAAGTATGTAGTCAT
10321 T
1 T
10322 TGAAATCCAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (52 bp):
TAGCATCAGCGCTTTAGATTTGATCCATGATTTATCCTAAGTATGTAGTCAT
Found at i:14071 original size:27 final size:27
Alignment explanation
Indices: 14036--14110 Score: 132
Period size: 27 Copynumber: 2.8 Consensus size: 27
14026 AAATGGACTC
14036 AAAATGACCAAAATGCCCCTGAATGCA
1 AAAATGACCAAAATGCCCCTGAATGCA
* *
14063 AAAATGACCTAAATGCCCCTGAATGTA
1 AAAATGACCAAAATGCCCCTGAATGCA
14090 AAAATGACCAAAATGCCCCTG
1 AAAATGACCAAAATGCCCCTG
14111 GATGACCCTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.43, C:0.25, G:0.15, T:0.17
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGCA
Found at i:16154 original size:138 final size:138
Alignment explanation
Indices: 15906--16185 Score: 533
Period size: 138 Copynumber: 2.0 Consensus size: 138
15896 CAAGGGCAAA
* * *
15906 TACGTAATTTTAGTCATTCGAGGGTAAAATGGTCATTTATTCTTATTATAGGTTTCACAATGTAT
1 TACGTAATTTTACTCATTCGAGGGTAAAATGGTCATTTATGCTTATTATAGGTTTCACAACGTAT
15971 ATACGAATTTATTGGTGTGAGCAACATAGTCGAATTCTCTTAATTCCACCCTTAAGGGTAATTTC
66 ATACGAATTTATTGGTGTGAGCAACATAGTCGAATTCTCTTAATTCCACCCTTAAGGGTAATTTC
16036 GTAAATTT
131 GTAAATTT
16044 TACGTAATTTTACTCATTCGAGGGTAAAATGGTCATTTATGCTTATTATAGGTTTCACAACGTAT
1 TACGTAATTTTACTCATTCGAGGGTAAAATGGTCATTTATGCTTATTATAGGTTTCACAACGTAT
16109 ATACGAATTTATTGGTGTGAGCAACATAGTCGAATTCTCTTAATTCCACCCTTAAGGGTAATTTC
66 ATACGAATTTATTGGTGTGAGCAACATAGTCGAATTCTCTTAATTCCACCCTTAAGGGTAATTTC
16174 GTAAATTT
131 GTAAATTT
16182 TACG
1 TACG
16186 ACTAAGGGGG
Statistics
Matches: 139, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (138 bp):
TACGTAATTTTACTCATTCGAGGGTAAAATGGTCATTTATGCTTATTATAGGTTTCACAACGTAT
ATACGAATTTATTGGTGTGAGCAACATAGTCGAATTCTCTTAATTCCACCCTTAAGGGTAATTTC
GTAAATTT
Found at i:16745 original size:3 final size:3
Alignment explanation
Indices: 16737--16766 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
16727 AATATTTCTT
16737 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
16767 ATTTCTATTT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16775 original size:14 final size:14
Alignment explanation
Indices: 16738--16769 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
16728 ATATTTCTTT
16738 TATTATTATTATTA
1 TATTATTATTATTA
16752 TATTATTATTATTA
1 TATTATTATTATTA
16766 TATT
1 TATT
16770 TCTATTTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:16793 original size:6 final size:6
Alignment explanation
Indices: 16774--16811 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
16764 TATATTTCTA
*
16774 TTTCCT TTT-TT TTTCCT TTTCCT TTTCCT TTTCCT TTT
1 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTT
16812 ATTTTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTCCT
Found at i:16941 original size:18 final size:19
Alignment explanation
Indices: 16918--16954 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
16908 TTCTCTTCTT
16918 CTTTTCT-TTTTTTTTTTC
1 CTTTTCTCTTTTTTTTTTC
16936 CTTTTCTCCTTTTTTTTTT
1 CTTTTCT-CTTTTTTTTTT
16955 TTTTCCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
CTTTTCTCTTTTTTTTTTC
Found at i:16952 original size:25 final size:27
Alignment explanation
Indices: 16912--16973 Score: 94
Period size: 24 Copynumber: 2.4 Consensus size: 27
16902 CAGCCTTTCT
16912 CTTCTTCTTTTCTTTTTTTTTTTCCTT
1 CTTCTTCTTTTCTTTTTTTTTTTCCTT
*
16939 -TTC-TCCTTT-TTTTTTTTTTTCCTT
1 CTTCTTCTTTTCTTTTTTTTTTTCCTT
16963 CTTCTTCTTTT
1 CTTCTTCTTTT
16974 AATTCCAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 15 0.48
25 8 0.26
26 8 0.26
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (27 bp):
CTTCTTCTTTTCTTTTTTTTTTTCCTT
Found at i:16956 original size:16 final size:17
Alignment explanation
Indices: 16916--16973 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
16906 CTTTCTCTTC
**
16916 TTCTTTTCTTTTTTTTT
1 TTCTTTTCTCCTTTTTT
16933 TTCCTTTTCTCCTTTTTT
1 TT-CTTTTCTCCTTTTTT
* * *
16951 TT-TTTTTTCCTTCTTC
1 TTCTTTTCTCCTTTTTT
16967 TTCTTTT
1 TTCTTTT
16974 AATTCCAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 13 0.38
17 6 0.18
18 15 0.44
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTCTTTTCTCCTTTTTT
Found at i:23214 original size:3 final size:3
Alignment explanation
Indices: 23206--23238 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
23196 AATATTTCTT
23206 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
23239 ATTTCTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:23229 original size:14 final size:14
Alignment explanation
Indices: 23210--23241 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
23200 TTTCTTTTAT
23210 TATTATTATTATTA
1 TATTATTATTATTA
23224 TATTATTATTATTA
1 TATTATTATTATTA
23238 TATT
1 TATT
23242 TCTATTTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:23247 original size:14 final size:13
Alignment explanation
Indices: 23206--23247 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
23196 AATATTTCTT
*
23206 TTATTAT-TATTA
1 TTATTATATTTTA
23218 TTATTATATTATTA
1 TTATTATATT-TTA
23232 TTATTATATTTCTA
1 TTATTATATTT-TA
23246 TT
1 TT
23248 TCCCTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 7 0.27
13 2 0.08
14 17 0.65
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATTATATTTTA
Found at i:23362 original size:31 final size:31
Alignment explanation
Indices: 23322--23386 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
23312 TTGGGCCTGG
*
23322 GGCCATGCCTTGCCAAGGCGCGCCTGCTCTA
1 GGCCATGCCTTGCCAAGGAGCGCCTGCTCTA
* *
23353 GGCCCTGCCTTGCCAAGTAGCGCCTGCTCTA
1 GGCCATGCCTTGCCAAGGAGCGCCTGCTCTA
23384 GGC
1 GGC
23387 GCTGGGCCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.12, C:0.38, G:0.29, T:0.20
Consensus pattern (31 bp):
GGCCATGCCTTGCCAAGGAGCGCCTGCTCTA
Found at i:23449 original size:19 final size:20
Alignment explanation
Indices: 23425--23468 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
23415 TCTTCTTGTT
*
23425 TCTTTTTTTTTCCTT-TT-C
1 TCTTTTTTTTTTCTTCTTCC
23443 TCTTTTTTTTTTCTTCTTCC
1 TCTTTTTTTTTTCTTCTTCC
23463 TCTTTT
1 TCTTTT
23469 AATTCGAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.61
19 2 0.09
20 7 0.30
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (20 bp):
TCTTTTTTTTTTCTTCTTCC
Found at i:24849 original size:30 final size:29
Alignment explanation
Indices: 24784--24850 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 29
24774 CAAGGAAGCA
24784 AATTCAAGGACAAATCAAGAAGAGCAAAAG
1 AATTCAAGGACAAATCAAGAAGAGC-AAAG
*
24814 GATTCAAGGAAGCAAAGTCAAGAA-AGC-AAG
1 AATTCAAGG-A-CAAA-TCAAGAAGAGCAAAG
24844 AATTCAA
1 AATTCAA
24851 AATAACAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
30 17 0.53
31 1 0.03
32 7 0.22
33 7 0.22
ACGTcount: A:0.54, C:0.13, G:0.21, T:0.12
Consensus pattern (29 bp):
AATTCAAGGACAAATCAAGAAGAGCAAAG
Found at i:26362 original size:19 final size:18
Alignment explanation
Indices: 26329--26364 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
26319 TTGAAATAAT
26329 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
26347 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
26365 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:26883 original size:68 final size:68
Alignment explanation
Indices: 26738--27152 Score: 543
Period size: 69 Copynumber: 6.1 Consensus size: 68
26728 CTTCGACTTC
* * * * * ** *
26738 TCCATAAGTCAAACTCGTTTCCATACGAGGT-TGTTCAAGCTTTGGTTCCATCCAAGCATTTAGG
1 TCCACAAGCCAAACTCGTTTCCATACGA-GTCAGTT-TAGCCTTGGTTCCATCCAAGCA-ACAGA
26802 GGCTTT
63 GGCTTT
* * *
26808 TCCACAAGCCAAAGTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGTAGCATG-GG
1 TCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAACA-GAGG
26872 CTTT
65 CTTT
* *
26876 TCCACAAGCCAATCTCGTTTCAATACGAGTCAGTTTAGCC-TGGTTCCATCCAAGCAACAGAGGC
1 TCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAACAGAGGC
26940 TTT
66 TTT
*
26943 TCCACGAGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAACAGAGGC
1 TCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAACAGAGGC
*
27008 CTT
66 TTT
* *
27011 TCCACAAGCCAAACTCGTTTCCATACGAGAT-AGTTCAAGCATTGGTTCCATCCAAGCAACAGAG
1 TCCACAAGCCAAACTCGTTTCCATACGAG-TCAGTT-TAGCCTTGGTTCCATCCAAGCAACAGAG
27075 GCTTT
64 GCTTT
* **
27080 TCCACAAGCCAAACTCGTTTCCATACGAGCCAGTTTAAGTATTGGTTCCATCCAAGCAACATG-G
1 TCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTT-AGCCTTGGTTCCATCCAAGCAACA-GAG
27144 GCTTT
64 GCTTT
27149 TCCA
1 TCCA
27153 TAAGTCAAGT
Statistics
Matches: 311, Mismatches: 25, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
66 1 0.00
67 60 0.19
68 102 0.33
69 119 0.38
70 29 0.09
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (68 bp):
TCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAACAGAGGC
TTT
Found at i:26961 original size:135 final size:137
Alignment explanation
Indices: 26738--27152 Score: 568
Period size: 135 Copynumber: 3.0 Consensus size: 137
26728 CTTCGACTTC
* * * * * ** ** *
26738 TCCATAAGTCAAACTCGTTTCCATACGAGGTTGTTCAAGCTTTGGTTCCATCCAAGCATTTAGGG
1 TCCACAAGCCAAACTCGTTTCAATACGAGATAGTTCAAGCACTGGTTCCATCCAAGCA-ACAGAG
* * *
26803 GCTTTTCCACAAGCCAAAGTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGTAGCA
65 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAACA
26868 TGGGCTTT
130 TGGGCTTT
* *
26876 TCCACAAGCCAATCTCGTTTCAATACGAG-TCAGTT-TAGC-CTGGTTCCATCCAAGCAACAGAG
1 TCCACAAGCCAAACTCGTTTCAATACGAGAT-AGTTCAAGCACTGGTTCCATCCAAGCAACAGAG
*
26938 GCTTTTCCACGAGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAACA
65 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAACA
*
27003 -GAGGCCTT
130 TG-GGCTTT
* *
27011 TCCACAAGCCAAACTCGTTTCCATACGAGATAGTTCAAGCATTGGTTCCATCCAAGCAACAGAGG
1 TCCACAAGCCAAACTCGTTTCAATACGAGATAGTTCAAGCACTGGTTCCATCCAAGCAACAGAGG
* **
27076 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGCCAGTTTAAGTATTGGTTCCATCCAAGCAACA
66 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTT-AGCCTTGGTTCCATCCAAGCAACA
27141 TGGGCTTT
130 TGGGCTTT
27149 TCCA
1 TCCA
27153 TAAGTCAAGT
Statistics
Matches: 246, Mismatches: 24, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
134 1 0.00
135 100 0.41
136 20 0.08
137 65 0.26
138 59 0.24
139 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (137 bp):
TCCACAAGCCAAACTCGTTTCAATACGAGATAGTTCAAGCACTGGTTCCATCCAAGCAACAGAGG
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAACAT
GGGCTTT
Found at i:27428 original size:48 final size:47
Alignment explanation
Indices: 27271--27509 Score: 313
Period size: 47 Copynumber: 5.0 Consensus size: 47
27261 ATCCAGGCAA
*
27271 TCTTTTCTCGCTTCCACGCGAGTTTTCAGTTTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTTAGTTTAGTGACCAAAGATGG
* *
27318 TCTTTTCTCGCTTCTACGCGAGCTTTTTCAATTTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAG-TTTTT-AGTTTAGTGACCAAAGATGG
27367 TCTTTTCTCGCTTCCACGCGAGTTTTTAGTTTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTTAGTTTAGTGACCAAAGATGG
* * *
27414 TCTTTCTCTCGCTTCCACGCGAG--TCTACGATTTAGTGACCAAAGTTAG
1 TCTTT-TCTCGCTTCCACGCGAGTTTTTA-G-TTTAGTGACCAAAGATGG
** * * *
27462 TC-TTTCTCGCTTCCACGCGAGTTTACAATTCAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTTAGTTTAGTGACCAAAGATGG
27508 TC
1 TC
27510 AACGAGTTTT
Statistics
Matches: 172, Mismatches: 13, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
46 38 0.22
47 48 0.28
48 46 0.27
49 40 0.23
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (47 bp):
TCTTTTCTCGCTTCCACGCGAGTTTTTAGTTTAGTGACCAAAGATGG
Found at i:27604 original size:15 final size:15
Alignment explanation
Indices: 27586--27625 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
27576 ACAAAAAGCT
27586 AAAAAAAAAGAAGGA
1 AAAAAAAAAGAAGGA
*
27601 AAAAAATAAGAAGGA
1 AAAAAAAAAGAAGGA
27616 AAAAGAAAAA
1 AAAA-AAAAA
27626 AACATGCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAGAAGGA
Found at i:28379 original size:28 final size:28
Alignment explanation
Indices: 28348--28423 Score: 143
Period size: 28 Copynumber: 2.7 Consensus size: 28
28338 AGGGTCACCT
28348 AGGGGCATTTTGGTCATTTTAGCATTCA
1 AGGGGCATTTTGGTCATTTTAGCATTCA
*
28376 AGGGGCATTTTGGTCATTTTTGCATTCA
1 AGGGGCATTTTGGTCATTTTAGCATTCA
28404 AGGGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
28424 GAGTCAATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.18, C:0.13, G:0.26, T:0.42
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTAGCATTCA
Done.