Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015674.1 Corchorus olitorius cultivar O-4 contig15707, 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: 32558
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:925 original size:16 final size:16
Alignment explanation
Indices: 904--935 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
894 TCTTACTTAA
904 AAGTAACTAAAAAAGT
1 AAGTAACTAAAAAAGT
920 AAGTAACTAAAAAAGT
1 AAGTAACTAAAAAAGT
936 TTATGATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.19
Consensus pattern (16 bp):
AAGTAACTAAAAAAGT
Found at i:3298 original size:6 final size:6
Alignment explanation
Indices: 3287--3322 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
3277 AGACTTATAT
*
3287 AAGATA AAGATA AAGATA AAGACA AAGATA AAGATA
1 AAGATA AAGATA AAGATA AAGATA AAGATA AAGATA
3323 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.67, C:0.03, G:0.17, T:0.14
Consensus pattern (6 bp):
AAGATA
Found at i:3327 original size:2 final size:2
Alignment explanation
Indices: 3320--3360 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
3310 AAAGATAAAG
* *
3320 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT CT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
3361 GTAAAAGTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3451 original size:27 final size:27
Alignment explanation
Indices: 3416--3476 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3406 CTTATTTTTC
3416 AAAT-ATATTTCTAA-ATTGCCATTATT-
1 AAATAATATTT-TAATATT-CCATTATTA
3442 AAATAATATTTTAATTATTCCATTATTA
1 AAATAATATTTTAA-TATTCCATTATTA
3470 AAATAAT
1 AAATAAT
3477 GGAAATTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 7 0.23
27 14 0.45
28 10 0.32
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (27 bp):
AAATAATATTTTAATATTCCATTATTA
Found at i:6202 original size:43 final size:43
Alignment explanation
Indices: 6150--6232 Score: 107
Period size: 42 Copynumber: 1.9 Consensus size: 43
6140 CATACTATAG
*
6150 TATCAAAAAATTATAA-AGAGATTGACAAAATCTCATAGGAAAGT
1 TATCAAAAAATCATAAGA-AGATT-ACAAAATCTCATAGGAAAGT
* *
6194 TATC-AAAAATCATAGGAAGATTACAAAATTTCATAGGAA
1 TATCAAAAAATCATAAGAAGATTACAAAATCTCATAGGAA
6233 GGTTTATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 16 0.46
43 14 0.40
44 5 0.14
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (43 bp):
TATCAAAAAATCATAAGAAGATTACAAAATCTCATAGGAAAGT
Found at i:6208 original size:21 final size:22
Alignment explanation
Indices: 6168--6232 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
6158 AATTATAAAG
*
6168 AGATTGACAAAATCTCATAGGAA
1 AGATT-ACAAAATATCATAGGAA
6191 AG-TTATCAAAA-ATCATAGG-A
1 AGATTA-CAAAATATCATAGGAA
*
6211 AGATTACAAAATTTCATAGGAA
1 AGATTACAAAATATCATAGGAA
6233 GGTTTATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 8 0.22
21 18 0.50
22 8 0.22
23 2 0.06
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (22 bp):
AGATTACAAAATATCATAGGAA
Found at i:6233 original size:21 final size:22
Alignment explanation
Indices: 6175--6318 Score: 120
Period size: 21 Copynumber: 6.6 Consensus size: 22
6165 AAGAGATTGA
*
6175 CAAAATCTCATAGGAA-AGTTAT
1 CAAAATTTCATAGGAAGA-TTAT
*
6197 CAAAA-ATCATAGGAAGATTA-
1 CAAAATTTCATAGGAAGATTAT
*
6217 CAAAATTTCATAGGAAGGTTTAT
1 CAAAATTTCATAGGAA-GATTAT
* * *
6240 TAAAATTTCATAGTTATG-TTAT
1 CAAAATTTCATAG-GAAGATTAT
* *
6262 CAAAGTTTCATATGG-AGTTTAT
1 CAAAATTTCATA-GGAAGATTAT
* *
6284 CACAATTTCATAGGTA-ATTAT
1 CAAAATTTCATAGGAAGATTAT
6305 CAAAATTTCATAGG
1 CAAAATTTCATAGG
6319 GTAATTGTAA
Statistics
Matches: 100, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
20 5 0.05
21 41 0.41
22 39 0.39
23 14 0.14
24 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGATTAT
Found at i:6282 original size:44 final size:44
Alignment explanation
Indices: 6175--6318 Score: 145
Period size: 44 Copynumber: 3.3 Consensus size: 44
6165 AAGAGATTGA
* * * *
6175 CAAAATCTCATAGGAAAG-TTATCAAAA-ATCATAGGAAGATTA-
1 CAAAATTTCATAGGAAGGTTTATCAAAATTTCATAGGTA-ATTAT
* * *
6217 CAAAATTTCATAGGAAGGTTTATTAAAATTTCATAGTTATGTTAT
1 CAAAATTTCATAGGAAGGTTTATCAAAATTTCATAGGTA-ATTAT
* *
6262 CAAAGTTTCATATGG-A-GTTTATCACAATTTCATAGGTAATTAT
1 CAAAATTTCATA-GGAAGGTTTATCAAAATTTCATAGGTAATTAT
6305 CAAAATTTCATAGG
1 CAAAATTTCATAGG
6319 GTAATTGTAA
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
42 18 0.21
43 23 0.27
44 29 0.35
45 12 0.14
46 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (44 bp):
CAAAATTTCATAGGAAGGTTTATCAAAATTTCATAGGTAATTAT
Found at i:6324 original size:22 final size:21
Alignment explanation
Indices: 6175--6324 Score: 101
Period size: 22 Copynumber: 6.9 Consensus size: 21
6165 AAGAGATTGA
* *
6175 CAAAATCTCATAGGAAAGTTAT
1 CAAAATTTCATAGGTAA-TTAT
* *
6197 CAAAA-ATCATAGGAAGATTA-
1 CAAAATTTCATAGGTA-ATTAT
6217 CAAAATTTCATAGG-AAGGTTTAT
1 CAAAATTTCATAGGTAA---TTAT
* * *
6240 TAAAATTTCATAGTTATGTTAT
1 CAAAATTTCATAGGTA-ATTAT
* *
6262 CAAAGTTTCATATGG-AGTTTAT
1 CAAAATTTCATA-GGTA-ATTAT
*
6284 CACAATTTCATAGGTAATTAT
1 CAAAATTTCATAGGTAATTAT
6305 CAAAATTTCATAGGGTAATT
1 CAAAATTTCATA-GGTAATT
6325 GTAATTATCA
Statistics
Matches: 103, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
19 1 0.01
20 6 0.06
21 36 0.35
22 46 0.45
23 13 0.13
24 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (21 bp):
CAAAATTTCATAGGTAATTAT
Found at i:9393 original size:36 final size:36
Alignment explanation
Indices: 9346--9415 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
9336 TTCAATAACC
* *
9346 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
9382 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
9416 CTAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:10305 original size:212 final size:203
Alignment explanation
Indices: 9927--10346 Score: 725
Period size: 207 Copynumber: 2.0 Consensus size: 203
9917 GCTTAATAAC
9927 TTTATCAATGGTGAATGTTATTAATTTTTTCAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
1 TTTATCAATGGTGAATGTTATTAATTTTTTCAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
*
9992 AAATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTT
66 AAATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTT
10057 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAAATTTTCAAAATTTATAAAAGATATTAAA
131 GATTTATTAAATTAAATTAGATCAATGTCAAAC-AAAA-TTTCAAAA-TTATAAAAGATATT-AA
10122 GATCCG-ATTTA
192 GATCCGAATTTA
10133 TTTATCAATGGTGAATGTTATTTAATTTTTTCAAGTCTAAGATTACTAACAAAGTTGTAGTGAAT
1 TTTATCAATGGTGAATGTTA-TTAATTTTTTCAAGTCTAAGATTACTAACAAAGTTGTAGTGAAT
*
10198 AAGATACAACAACATTACTATTATATATATAGAACTATACCAAAAAAAAAGTTAGTTGAACATTA
65 AAAATACAAC-ACATTACTATTATATATA-A-AACTATACC-AAAAAAAAG-TAGTTGAACATTA
10263 GTGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT
125 GTGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT
10328 AAGATCCGAATTTA
190 AAGATCCGAATTTA
10342 TTTAT
1 TTTAT
10347 TATTAAGAAA
Statistics
Matches: 205, Mismatches: 2, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
206 20 0.10
207 53 0.26
208 25 0.12
209 25 0.12
210 17 0.08
211 13 0.06
212 52 0.25
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (203 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTCAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
AAATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTT
GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATC
CGAATTTA
Found at i:10941 original size:37 final size:37
Alignment explanation
Indices: 10891--10965 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
10881 ATGTTGTTTG
10891 ACGACAAATTCTGGAAGACTTCAATGCATTTACACTT
1 ACGACAAATTCTGGAAGACTTCAATGCATTTACACTT
10928 ACGACAAATTCTGGAAGACTTCAATGCATTTACACTT
1 ACGACAAATTCTGGAAGACTTCAATGCATTTACACTT
10965 A
1 A
10966 TTCATCCTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.29
Consensus pattern (37 bp):
ACGACAAATTCTGGAAGACTTCAATGCATTTACACTT
Found at i:15892 original size:40 final size:40
Alignment explanation
Indices: 15837--15917 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
15827 TGCCCACTTG
15837 ACTTCTTTTCACCCTCATTTGTTGTTGCAATGGTTGAATC
1 ACTTCTTTTCACCCTCATTTGTTGTTGCAATGGTTGAATC
15877 ACTTCTTTTCACCCTCATTTGTTGTTGCAATGGTTGAATC
1 ACTTCTTTTCACCCTCATTTGTTGTTGCAATGGTTGAATC
15917 A
1 A
15918 GAGCTGGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (40 bp):
ACTTCTTTTCACCCTCATTTGTTGTTGCAATGGTTGAATC
Found at i:20562 original size:22 final size:22
Alignment explanation
Indices: 20533--20613 Score: 119
Period size: 22 Copynumber: 3.7 Consensus size: 22
20523 TGAATATTTT
*
20533 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAATTACCC
* *
20555 TATTAAATTTTGATAATTACGC
1 TATGAAATTTTGATAATTACCC
20577 TATGAAATTTTGATAATTA-CC
1 TATGAAATTTTGATAATTACCC
*
20598 TATGAAATTGTGATAA
1 TATGAAATTTTGATAA
20614 ACTCCATATG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 16 0.30
22 37 0.70
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAATTACCC
Found at i:20624 original size:43 final size:43
Alignment explanation
Indices: 20533--20627 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 43
20523 TGAATATTTT
* * *
20533 TATGAAATTTTGATAACTACCCTATTAAATTTTGATAATTACGC
1 TATGAAATTTTGATAACTACCCTATGAAATTGTGATAA-TACCC
*
20577 TATGAAATTTTGATAATTA-CCTATGAAATTGTGATAA-ACTCC
1 TATGAAATTTTGATAACTACCCTATGAAATTGTGATAATAC-CC
20619 ATATGAAAT
1 -TATGAAAT
20628 ATATATGTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
41 2 0.04
42 1 0.02
43 24 0.53
44 18 0.40
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (43 bp):
TATGAAATTTTGATAACTACCCTATGAAATTGTGATAATACCC
Found at i:20626 original size:22 final size:21
Alignment explanation
Indices: 20533--20627 Score: 93
Period size: 22 Copynumber: 4.4 Consensus size: 21
20523 TGAATATTTT
*
20533 TATGAAATTTTGATAACTACCC
1 TATGAAATTGTGATAACTA-CC
* * *
20555 TATTAAATTTTGATAATTACGC
1 TATGAAATTGTGATAACTAC-C
* *
20577 TATGAAATTTTGATAATTACC
1 TATGAAATTGTGATAACTACC
20598 TATGAAATTGTGATAAACT-CC
1 TATGAAATTGTGAT-AACTACC
20619 ATATGAAAT
1 -TATGAAAT
20628 ATATATGTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
21 17 0.26
22 48 0.74
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (21 bp):
TATGAAATTGTGATAACTACC
Found at i:20758 original size:156 final size:156
Alignment explanation
Indices: 20470--20769 Score: 478
Period size: 156 Copynumber: 1.9 Consensus size: 156
20460 TCCGATATAT
* *
20470 ATATATATATATTAACTTTTACATGCGTTGCACGTAGTCCAAAATGTTTCGATTGAATATTTTTA
1 ATATATATATATTAACTTTCACATGCGTTGCACGTAGCCCAAAATGTTTCGATTGAATATTTTTA
* * *
20535 TGAAATTTTGATAACTACCCTATTAAATTTTGATAATTACGCTATGAAATTTTGATAATTACCTA
66 TGAAATTTAGATAACTACCCTATTAAATTTTGATAATTACGCTATGAAATTGTGATAACTACCTA
20600 TGAAATTGTGATAAACTCCATATGAA
131 TGAAATTGTGATAAACTCCATATGAA
* * * *
20626 ATATATATGTTTTAACTTTCACGTGCGTTGCACGTTGCCCAAAATGTTTCGATTGAATATTTTTA
1 ATATATATATATTAACTTTCACATGCGTTGCACGTAGCCCAAAATGTTTCGATTGAATATTTTTA
20691 TGAAATTTAGATAACTACCCTATTAAATTTTGATAATTAC-CTATGAAATTGTGATAAACT-CCA
66 TGAAATTTAGATAACTACCCTATTAAATTTTGATAATTACGCTATGAAATTGTGAT-AACTACC-
*
20754 TATGAAATTTTGATAA
129 TATGAAATTGTGATAA
20770 CTTAACTATG
Statistics
Matches: 132, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
155 16 0.12
156 116 0.88
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (156 bp):
ATATATATATATTAACTTTCACATGCGTTGCACGTAGCCCAAAATGTTTCGATTGAATATTTTTA
TGAAATTTAGATAACTACCCTATTAAATTTTGATAATTACGCTATGAAATTGTGATAACTACCTA
TGAAATTGTGATAAACTCCATATGAA
Found at i:20762 original size:43 final size:42
Alignment explanation
Indices: 20689--20850 Score: 136
Period size: 43 Copynumber: 3.7 Consensus size: 42
20679 TGAATATTTT
* *
20689 TATGAAATTTAGAT-AACTACCCTATTAAATTTTGATAA-TTACC
1 TATGAAATTT-GATAAACT--CCTATGAAATTTTGATAACTTAAC
20732 TATGAAATTGTGATAAACTCCATATGAAATTTTGATAACTTAAC
1 TATGAAATT-TGATAAACTCC-TATGAAATTTTGATAACTTAAC
* *
20776 TATGAAATTTTAATAAACCTTCCTATGAAATTTTG-TAACATT-CC
1 TATGAAA-TTTGATAAA-C-TCCTATGAAATTTTGATAAC-TTAAC
**
20820 TATGATTTTTGAT-AACTCCCTATGAGAATTT
1 TATGAAATTTGATAAACT-CCTATGA-AATTT
20851 GTTAATCTCC
Statistics
Matches: 102, Mismatches: 7, Indels: 21
0.78 0.05 0.16
Matches are distributed among these distances:
40 1 0.01
41 8 0.08
42 9 0.09
43 32 0.31
44 32 0.31
45 17 0.17
46 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (42 bp):
TATGAAATTTGATAAACTCCTATGAAATTTTGATAACTTAAC
Found at i:20841 original size:20 final size:22
Alignment explanation
Indices: 20818--20876 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 22
20808 TTGTAACATT
20818 CCTATGA-TTTTTGATAA-CTC
1 CCTATGAGTTTTTGATAATCTC
** *
20838 CCTATGAGAATTTGTTAATCTC
1 CCTATGAGTTTTTGATAATCTC
* *
20860 CCTATAATTTTTTGATA
1 CCTATGAGTTTTTGATA
20877 CTATAGTATG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 7 0.24
21 7 0.24
22 15 0.52
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (22 bp):
CCTATGAGTTTTTGATAATCTC
Found at i:20851 original size:21 final size:21
Alignment explanation
Indices: 20689--20864 Score: 142
Period size: 22 Copynumber: 8.1 Consensus size: 21
20679 TGAATATTTT
*
20689 TATGAAATTTAGATAACTACCC
1 TATGAAATTTTGATAACT-CCC
* * *
20711 TATTAAATTTTGATAATTACC
1 TATGAAATTTTGATAACTCCC
* *
20732 TATGAAATTGTGATAAACTCCA
1 TATGAAATTTTGAT-AACTCCC
**
20754 TATGAAATTTTGATAACTTAAC
1 TATGAAATTTTGATAAC-TCCC
* *
20776 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AA-CTCCC
*
20799 TATGAAATTTTG-TAACATTCC
1 TATGAAATTTTGATAAC-TCCC
*
20820 TATG-ATTTTTGATAACTCCC
1 TATGAAATTTTGATAACTCCC
*
20840 TATGAGAA-TTTGTTAATCTCCC
1 TATGA-AATTTTGATAA-CTCCC
20862 TAT
1 TAT
20865 AATTTTTTGA
Statistics
Matches: 124, Mismatches: 21, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
20 14 0.11
21 38 0.31
22 56 0.45
23 15 0.12
24 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (21 bp):
TATGAAATTTTGATAACTCCC
Found at i:23825 original size:45 final size:45
Alignment explanation
Indices: 23774--23862 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
23764 AATCTAATCC
23774 GGTTTAGCTCTTATAGTATGATTATACGTTTAAAAATTCAACTCT
1 GGTTTAGCTCTTATAGTATGATTATACGTTTAAAAATTCAACTCT
*
23819 GGTTTAGTTCTTATAGTATGATTATACGTTTAAAAATTCAACTC
1 GGTTTAGCTCTTATAGTATGATTATACGTTTAAAAATTCAACTC
23863 CTTTGAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.43
Consensus pattern (45 bp):
GGTTTAGCTCTTATAGTATGATTATACGTTTAAAAATTCAACTCT
Found at i:26175 original size:29 final size:29
Alignment explanation
Indices: 26108--26178 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
26098 GAAGATCCTA
26108 GCGTTCGTCGTTCCTGTAGTAAAGTCCAGG
1 GCGTTCGT-GTTCCTGTAGTAAAGTCCAGG
* ** * *
26138 ACGAACGTGTTCC-GATGGTAATGTCCAGG
1 GCGTTCGTGTTCCTG-TAGTAAAGTCCAGG
26167 GCGTTCGTGTTC
1 GCGTTCGTGTTC
26179 ATTTGGCAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
28 1 0.03
29 26 0.81
30 5 0.16
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.30
Consensus pattern (29 bp):
GCGTTCGTGTTCCTGTAGTAAAGTCCAGG
Found at i:26189 original size:29 final size:31
Alignment explanation
Indices: 26157--26223 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 31
26147 TTCCGATGGT
* *
26157 AATGTCCAGGG-CGTTCGT-GTTCATTTGGC
1 AATGTCCAGGGACGTTCGTCGTTCATGTGCC
*
26186 AATGT-CTGGGACGTTCGTCGTTCATGTGCC
1 AATGTCCAGGGACGTTCGTCGTTCATGTGCC
26216 AATGTCCA
1 AATGTCCA
26224 AGACGAAGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 4 0.13
29 12 0.39
30 14 0.45
31 1 0.03
ACGTcount: A:0.16, C:0.22, G:0.28, T:0.33
Consensus pattern (31 bp):
AATGTCCAGGGACGTTCGTCGTTCATGTGCC
Done.