Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017097.1 Corchorus olitorius cultivar O-4 contig17130, 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: 22347
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:4341 original size:39 final size:40
Alignment explanation
Indices: 4283--4363 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
4273 TTTAATTCTG
*
4283 ATGTAATATAAATAATAACTAAAATACTTATATTAATTAA
1 ATGTAATATAAATAATAACTAAAATACTTACATTAATTAA
* *
4323 ATGTAATAT-TATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATAAATAATAACTAAAATACTTACATTAATTAA
4362 AT
1 AT
4364 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 29 0.76
40 9 0.24
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATAAATAATAACTAAAATACTTACATTAATTAA
Found at i:4358 original size:21 final size:20
Alignment explanation
Indices: 4295--4358 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 20
4285 GTAATATAAA
*
4295 TAATAACTAAAATACTTATAT
1 TAATAACTGAAATACTTA-AT
* *
4316 TAATTAAATGTAATA-TT-A-
1 TAA-TAACTGAAATACTTAAT
4334 TAATAACTGAAATACTTACAT
1 TAATAACTGAAATACTTA-AT
4355 TAAT
1 TAAT
4359 TAAATTCTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 9 0.27
18 5 0.15
19 1 0.03
20 1 0.03
21 9 0.27
22 8 0.24
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (20 bp):
TAATAACTGAAATACTTAAT
Found at i:4390 original size:25 final size:25
Alignment explanation
Indices: 4354--4425 Score: 137
Period size: 25 Copynumber: 2.9 Consensus size: 25
4344 AATACTTACA
4354 TTAATT-AAATTCTTAGGTATTTTT
1 TTAATTCAAATTCTTAGGTATTTTT
4378 TTAATTCAAATTCTTAGGTATTTTT
1 TTAATTCAAATTCTTAGGTATTTTT
4403 TTAATTCAAATTCTTAGGTATTT
1 TTAATTCAAATTCTTAGGTATTT
4426 GTGCAAACGT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 6 0.13
25 41 0.87
ACGTcount: A:0.29, C:0.07, G:0.08, T:0.56
Consensus pattern (25 bp):
TTAATTCAAATTCTTAGGTATTTTT
Found at i:4748 original size:204 final size:205
Alignment explanation
Indices: 4495--4910 Score: 712
Period size: 204 Copynumber: 2.0 Consensus size: 205
4485 TTCCTTAATA
*
4495 ATAAATAAATCGGATCTTAATATCTTTAATTTGTAATTTTGAAATTTTGTTTGACATTGATCTAA
1 ATAAATAAATCGGATCTTAATATC-TT-ATTTATAATTTTGAAATTTTGTTTGACATTGATCTAA
* * *
4560 TTTAATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATAT-ATA
64 TTTAATTTAATAAACCAACCACTAATGTTCAACT-ACTTTTTTTGGTATAGTTATATATATAATA
*
4624 ATAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACATAAAAAATTAATA
128 ATAATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACATAAAAAATTAATA
*
4689 ACATTCACCATTG
193 ACATTCACCATTC
4702 ATAAATAAATCGGATCATTAATATC-T-TTTATAATTTTGAAATTTTGTTTGACATTGATCTAAT
1 ATAAATAAATCGGATC-TTAATATCTTATTTATAATTTTGAAATTTTGTTTGACATTGATCTAAT
4765 TTAATTTAATAAACCAACCACTAATGTTCAACTACTTTTTTTGGTATAGTTATATATATAATAAT
65 TTAATTTAATAAACCAACCACTAATGTTCAACTACTTTTTTTGGTATAGTTATATATATAATAAT
*
4830 AATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAAC
130 AATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACATAAAAAATTAATAAC
4895 ATTCACCATTC
195 ATTCACCATTC
4906 ATAAA
1 ATAAA
4911 GTTATTAAGC
Statistics
Matches: 200, Mismatches: 7, Indels: 7
0.93 0.03 0.03
Matches are distributed among these distances:
203 24 0.12
204 151 0.75
206 1 0.00
207 16 0.08
208 8 0.04
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (205 bp):
ATAAATAAATCGGATCTTAATATCTTATTTATAATTTTGAAATTTTGTTTGACATTGATCTAATT
TAATTTAATAAACCAACCACTAATGTTCAACTACTTTTTTTGGTATAGTTATATATATAATAATA
ATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACATAAAAAATTAATAACA
TTCACCATTC
Found at i:5070 original size:144 final size:144
Alignment explanation
Indices: 4884--5177 Score: 579
Period size: 144 Copynumber: 2.0 Consensus size: 144
4874 TAGACTTAAA
4884 AAATTAATAACATTCACCATTCATAAAGTTATTAAGCATGTAAGGTTGCTACATTTCTTGATATA
1 AAATTAATAACATTCACCATTCATAAAGTTATTAAGCATGTAAGGTTGCTACATTTCTTGATATA
4949 ATACTATAGTTTAGCTTTCTAATTAGTAAGCATAAATGAGAAATTTGATAATCAAAATTACTAAG
66 ATACTATAGTTTAGCTTTCTAATTAGTAAGCATAAATGAGAAATTTGATAATCAAAATTACTAAG
5014 AATGTAAGGTTATT
131 AATGTAAGGTTATT
5028 AAATTAATAACATTCACCATTCATAAAGTTATTAAGCATGTAAGGTTGCTACATTTCTTGATATA
1 AAATTAATAACATTCACCATTCATAAAGTTATTAAGCATGTAAGGTTGCTACATTTCTTGATATA
*
5093 ATACTATAGTTTAGCTTTCTAATTAGTAAGCATAAATGAGAAATTTGATAATCAAAATTGCTAAG
66 ATACTATAGTTTAGCTTTCTAATTAGTAAGCATAAATGAGAAATTTGATAATCAAAATTACTAAG
5158 AATGTAAGGTTATT
131 AATGTAAGGTTATT
5172 AAATTA
1 AAATTA
5178 GATGAAAGTT
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 149 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (144 bp):
AAATTAATAACATTCACCATTCATAAAGTTATTAAGCATGTAAGGTTGCTACATTTCTTGATATA
ATACTATAGTTTAGCTTTCTAATTAGTAAGCATAAATGAGAAATTTGATAATCAAAATTACTAAG
AATGTAAGGTTATT
Found at i:7002 original size:58 final size:57
Alignment explanation
Indices: 6912--7020 Score: 173
Period size: 58 Copynumber: 1.9 Consensus size: 57
6902 ATCATGCCTC
6912 GGTCCAAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAACCTT
1 GGTCCAAAAACGTCTTTTTTAGGCATCTAAT-AAAAAACATGTCACTCGATAAACCTT
* * * *
6970 GGTCCGAAAACGTCTTTTTTATGCATCTAATAAAGAACATGTCACTTGATA
1 GGTCCAAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATA
7021 TTTGATTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 18 0.38
58 29 0.62
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (57 bp):
GGTCCAAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAACCTT
Found at i:9822 original size:12 final size:12
Alignment explanation
Indices: 9805--9830 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9795 TTCTTTAACA
9805 ATCTTTCTAGTG
1 ATCTTTCTAGTG
9817 ATCTTTCTAGTG
1 ATCTTTCTAGTG
9829 AT
1 AT
9831 ATACGTAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.50
Consensus pattern (12 bp):
ATCTTTCTAGTG
Found at i:11166 original size:420 final size:431
Alignment explanation
Indices: 10489--11258 Score: 1091
Period size: 422 Copynumber: 1.8 Consensus size: 431
10479 AACCAAATCC
* * *
10489 TTAAATCCAATGTAGTTAAGATTTGGTTCGATGAATTTAGATATTTAAAGGAGGCTTTCTGCCGA
1 TTAAATCCAATGTAGCTAAGATTTGGTTCGATGAATATAGATATTTAAAGGAGGCTTTCTGCCAA
* *
10554 AAATCATGCAAAACGAAGCCAGAGACCCGAAACGCGTTTTTAGCCCCAAAACCGCGATGGTTAGT
66 AAATCATGCAAAACGAAGCCAGAGACCCGAAACGCGTTTTTAGACCCAAAAACGCGATGG-TAGT
** ** *
10619 ACATGATTTCGGCTAAAAATTGACCCGAAAAATTTTTTTCTGAAAATTTTGCCACAATACTCGGA
130 ACACAATTTCGGCTAAAAATTGACCCGAAAAAAATTTTTCTGAAAATTTTGCCACAATACTCGAA
* * * *
10684 AAAAATATAAAATCAAATGCCAAATAGATTAACTGGCTTTTCAGGCTTCTAATATTGTTTTTCCA
195 AAAAATATAAAATCAAACGCCAAATAGATTAACGGGCTTTTCACGCTTCTAATATCGTTTTTCCA
* *
10749 G-TTTTTTCTGAATAAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCC
260 GTTTTTTTCCGAATAAATTTCTAATTAAATCGAAATAAGATTCAGATGCTAGTAAAAACAAATCC
10813 TTATATCCAATGTGGCTGACATTTTGATCGAGGCAAAATTAACCATATTTTTATGGTCATTTTCT
325 TTATATCCAATGTGGCTGACATTTTGATCGAGGCAAAATTAACCATATTTTTATGGTCATTTTCT
10878 TATGCTTTTTGGTGTTTTCCAGATGCTCTTAAAAACAAATAT
390 TATGCTTTTTGGTGTTTTCCAGATGCTCTTAAAAACAAATAT
* * * *
10920 TTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGGTTTTCTGCCAA
1 TTAAATCCAATGTAGCTAAGATTTGGTTCGATGAATATAGATATTTAAAGGAGGCTTTCTGCCAA
* * * *
10985 AAATCATG-GAAAC-AGAGCC-GGGGCCCG-AATGCGTTTTTA-ACCCAAAAAC-CG-T-G-A-T
66 AAATCATGCAAAACGA-AGCCAGAGACCCGAAACGCGTTTTTAGACCCAAAAACGCGATGGTAGT
* ** * *
11040 ACACAATTTCGGCTAAAAATAT-ATCC-AAAAAAATTTTTCTTCAATTTTTTCCACAATACTC-A
130 ACACAATTTCGGCTAAAAAT-TGACCCGAAAAAAATTTTTCTGAAAATTTTGCCACAATACTCGA
* *
11102 AAAAATATATAAAATCCAACGCCAAATAGATTATCGGGCTTTTCACGCTTCTAATATCGTTTTTC
194 AAAAA-ATATAAAATCAAACGCCAAATAGATTAACGGGCTTTTCACGCTTCTAATATCGTTTTTC
* * *
11167 CTGTTTTTTTTCCGAATTAATTTGTAATTAAATCGAAATAAGATTCAGATGCTAGTAAAAACAAA
258 CAG-TTTTTTTCCGAATAAATTTCTAATTAAATCGAAATAAGATTCAGATGCTAGTAAAAACAAA
11232 TCCTTATATCCAATGTGGCTGACATTT
322 TCCTTATATCCAATGTGGCTGACATTT
11259 GGTTCGAAGA
Statistics
Matches: 300, Mismatches: 34, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
419 5 0.02
420 84 0.28
421 22 0.07
422 85 0.28
424 1 0.00
425 1 0.00
426 2 0.01
427 8 0.03
428 11 0.04
429 7 0.02
430 8 0.03
431 66 0.22
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (431 bp):
TTAAATCCAATGTAGCTAAGATTTGGTTCGATGAATATAGATATTTAAAGGAGGCTTTCTGCCAA
AAATCATGCAAAACGAAGCCAGAGACCCGAAACGCGTTTTTAGACCCAAAAACGCGATGGTAGTA
CACAATTTCGGCTAAAAATTGACCCGAAAAAAATTTTTCTGAAAATTTTGCCACAATACTCGAAA
AAAATATAAAATCAAACGCCAAATAGATTAACGGGCTTTTCACGCTTCTAATATCGTTTTTCCAG
TTTTTTTCCGAATAAATTTCTAATTAAATCGAAATAAGATTCAGATGCTAGTAAAAACAAATCCT
TATATCCAATGTGGCTGACATTTTGATCGAGGCAAAATTAACCATATTTTTATGGTCATTTTCTT
ATGCTTTTTGGTGTTTTCCAGATGCTCTTAAAAACAAATAT
Found at i:11852 original size:321 final size:318
Alignment explanation
Indices: 10897--11963 Score: 933
Period size: 321 Copynumber: 3.3 Consensus size: 318
10887 TGGTGTTTTC
* ** *
10897 CAGATGCTCTTAAAAACAAATATTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGAT
1 CAGATGCTCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATAAATATAGAT
* ** *
10962 ATTTCAAGGAGGT-TTTCTGCCAAAAATCATGGAAACAGAGC--CGGGG-CCCG-AATGCGTTTT
66 ATTTCAAGGA-GTCTTTCTGCCAAAAATCATGCAAA-ACTGCTTCGGGGCCCCGAAACGCGTTTT
* * ** * **
11022 TAACCCAAAAAC-CG-TG-ATACACAATTTCGGCTAAAAATA-T-ATCCAAAAAAATTTTTCTTC
129 T-ACCCAAAAACGTGATGTATACACGATTTCGGC-AAAAA-ACTGA-CCTGAAAATTTTTTCTGA
* * * * * *
11082 AATTTTTTCCACAATAC-T-CAAAAAATATATAAAATCCAACGCCAAATAGATTATCGGGCTTTT
190 AAATTTTGCCACAATACTTGGAAAAAATATAT--AATTCAACGCCAAAAAGATTAACGGGCTTTT
* * * * * *
11145 CACGCTTCTAATATCGTTTTTCCTGTTTTTTTTCCGAATTAATTTGTAATTAAATCGAAATAAGA
253 CACGCTTCTAATATCATTTTTCC-ATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAA
11210 TT
317 TT
* *
11212 CAGATGCT-AGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTCGA-AGAATATAG
1 CAGATGCTCA-TAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATA-AATATAG
* ** * * *** *
11275 TTATTTCAAGGAGTC--TCCACGAAAAACATCATGCAAAATTGAGC-T-GGGGCTGTGGAACGCG
64 ATATTTCAAGGAGTCTTTCTGC-CAAAA-ATCATGCAAAACT--GCTTCGGGGCCCCGAAACGCG
* * *
11336 TTTTTAGCTAAAAAGCGTGATGTGTACACGATTTCGGCTAACATTTTGCAAAAACTGAGCC-GAA
125 TTTTTACCCAAAAA-CGTGATGTATACACGATTTCGG----CA------AAAAACTGA-CCTGAA
* * * ** *
11400 AAGTTTTTCCTCG-AATTTTTGCCACAATAATCAGAATAAATATATAATTCAACGCCAAAGAA-A
178 AA-TTTTTTCT-GAAAATTTTGCCACAATACTTGGAAAAAATATATAATTCAACGCCAAA-AAGA
* *
11463 TTGAA-GGGGTTTTCACGCTTCTAATA-CAGTTTTTCCA-TTTTTCTCTCGAATTTATTTCTAAT
240 TT-AACGGGCTTTTCACGCTTCTAATATCA-TTTTTCCATTTTTTTTC-CGAATTTATTTCTAAT
11525 TAAATCGAAACAAAATT
302 TAAATCGAAACAAAATT
* * * * * * * *
11542 CATATGCTCATAAAACCAAATACTTAAATCCAATCTGACTGAAATTTGGTTTGATAAATACAGAT
1 CAGATGCTCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATAAATATAGAT
11607 ATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGCTTCGGGGCCCCGAAACGCG-TTTTA
66 ATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGCTTCGGGGCCCCGAAACGCGTTTTTA
11671 CCCCAAAAACGTGATGGTAGTACACGATTTCGGCAAAAAACTGACCTGGAAAATTTTTTCTGAAA
131 -CCCAAAAACGTGAT-GTA-TACACGATTTCGGCAAAAAACTGACCT-GAAAATTTTTTCTGAAA
* * * * *
11736 AGTTTGCCACAATACTTGGAAAAAATATATAATTCAACGCTAAAAAGAGTAACGGGCTTTTAATG
192 ATTTTGCCACAATACTTGGAAAAAATATATAATTCAACGCCAAAAAGATTAACGGGCTTTTCACG
* * * * *
11801 CTTCTAATATCATTTTTCCATTTTTTTTCCGCATTAATCTCTAACTAAATCGAAACAAGATT
257 CTTCTAATATCATTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATT
* ** * * * *
11863 CAGATACTCGGAAAAATAAATCCTTATATCCAATGTGGCTGAGATTTGATTCGATGAATATAGAT
1 CAGATGCTCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATAAATATAGAT
***
11928 ATTTCAAGGAGTCTTTGAACCAAAAATCATGCAAAA
66 ATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAA
11964 TTGAGCACAA
Statistics
Matches: 602, Mismatches: 100, Indels: 94
0.76 0.13 0.12
Matches are distributed among these distances:
313 3 0.00
314 7 0.01
315 75 0.12
316 6 0.01
317 8 0.01
318 11 0.02
319 1 0.00
320 9 0.01
321 206 0.34
322 14 0.02
324 1 0.00
325 1 0.00
327 2 0.00
328 2 0.00
329 20 0.03
330 135 0.22
331 86 0.14
332 5 0.01
333 10 0.02
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (318 bp):
CAGATGCTCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATAAATATAGAT
ATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGCTTCGGGGCCCCGAAACGCGTTTTTA
CCCAAAAACGTGATGTATACACGATTTCGGCAAAAAACTGACCTGAAAATTTTTTCTGAAAATTT
TGCCACAATACTTGGAAAAAATATATAATTCAACGCCAAAAAGATTAACGGGCTTTTCACGCTTC
TAATATCATTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATT
Found at i:13277 original size:21 final size:24
Alignment explanation
Indices: 13248--13298 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
13238 TTTTGAACTC
13248 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
13271 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
13294 ATTAT
1 ATTAT
13299 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:13293 original size:25 final size:25
Alignment explanation
Indices: 13248--13296 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
13238 TTTTGAACTC
*
13248 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
13273 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
13297 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:14253 original size:44 final size:44
Alignment explanation
Indices: 14195--14284 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
14185 TTATTATAGT
14195 TTTAACCATTCTAAATTATCATTTATTCAATAAAATTTGTATTA
1 TTTAACCATTCTAAATTATCATTTATTCAATAAAATTTGTATTA
* * *
14239 TTTAACCATTCTAAATTGTCATTTATTCAATAAATTTTGTGTTA
1 TTTAACCATTCTAAATTATCATTTATTCAATAAAATTTGTATTA
14283 TT
1 TT
14285 GTTATAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.50
Consensus pattern (44 bp):
TTTAACCATTCTAAATTATCATTTATTCAATAAAATTTGTATTA
Found at i:14514 original size:16 final size:16
Alignment explanation
Indices: 14472--14518 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
14462 GATTATAACC
* *
14472 AAATCATGGCTCCACT
1 AAATCATGACTCCAAT
*
14488 -AA-CAAGACTCCAAT
1 AAATCATGACTCCAAT
14502 AAATCATGACTCCAAT
1 AAATCATGACTCCAAT
14518 A
1 A
14519 TCTGATAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 9 0.36
15 4 0.16
16 12 0.48
ACGTcount: A:0.43, C:0.28, G:0.09, T:0.21
Consensus pattern (16 bp):
AAATCATGACTCCAAT
Found at i:17752 original size:26 final size:25
Alignment explanation
Indices: 17710--17781 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 25
17700 AGTCACCTAA
* *
17710 GGGCATTTTGGTTATTTTTTCTCCAG
1 GGGCA-TTTGGTCATTTTTGCTCCAG
17736 GGGCATTTCGGTCATTTTTGCTCCAG
1 GGGCATTT-GGTCATTTTTGCTCCAG
*
17762 GGGCACTTTAGTCATTTTTG
1 GGGCA-TTTGGTCATTTTTG
17782 ATTAATTGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
25 3 0.07
26 35 0.85
27 3 0.07
ACGTcount: A:0.12, C:0.18, G:0.25, T:0.44
Consensus pattern (25 bp):
GGGCATTTGGTCATTTTTGCTCCAG
Found at i:21273 original size:20 final size:19
Alignment explanation
Indices: 21245--21288 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
21235 TTTAACATTA
**
21245 AATAAAATATTATATATAT
1 AATAAAATAAAATATATAT
*
21264 GAATATAATAAAATATATAT
1 -AATAAAATAAAATATATAT
21284 AATAA
1 AATAA
21289 TGATCACAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AATAAAATAAAATATATAT
Found at i:21387 original size:12 final size:12
Alignment explanation
Indices: 21370--21394 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21360 TTTAAAACTA
21370 AAAAGTACCCTT
1 AAAAGTACCCTT
21382 AAAAGTACCCTT
1 AAAAGTACCCTT
21394 A
1 A
21395 TAACTAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAAGTACCCTT
Found at i:21988 original size:290 final size:293
Alignment explanation
Indices: 21436--22017 Score: 877
Period size: 290 Copynumber: 2.0 Consensus size: 293
21426 TTTTTAATGA
*
21436 CTATAGAAATTACTTAAAGGCCAAATTGAGAATTAATGTGGTGCCTCCTTTTGATCTTTTTTGGT
1 CTATAGAAATTACTTAAAGGCCAAATTGAGAATTAATGTGGTGCCTCCTTTTGAGCTTTTTTGGT
* ***
21501 CATTTCTCACTTTTCGGATGACTAAAAAGGCCCTTGATGAATTTCCTTTTTTACTTTTCCTCTTG
66 CATTTCTCACTTTTCGGATGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTCTTG
* * **
21566 CCCTTTTTTGTAATTTACTATTTTTGTATTTATGGTTAAGTGTGTTTCAATTATGTATTAATTGT
131 CCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTCAATTACATATTAATTGT
* * * * * *
21631 GCGTGGATATTAGGATTTACCGGTTCAATTTCTCTTCTGAAATTCCAAAGGATTGGTGCTATAAA
196 GCGTGGATATTAGGATTTACCGGTTCAACTCCTCTACCGAAATTCCAAAGGATTAGTGATATAAA
21696 TGTATCTACCCGAGTTCATTAATTTAACAATTG
261 TGTATCTACCCGAGTTCATTAATTTAACAATTG
* * *
21729 CTATGGAAATTACTTAAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTG-GCTTTTTT-T
1 CTATAGAAATTACTT-AAAGGCCAAATTGAGAATTAATGTGGTGCCTCCTTTTGAGCTTTTTTGG
* *
21792 TCTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTGC-
65 TCATTTCTCACTTTTCGGATGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCT-CT
* *
21856 TG-CC-TTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTGATT
129 TGCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTCAATTACATATTAATT
* * *
21919 GTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTACCGGAATTCCAAAGGATTAGTGATGTA
194 GTGCGTGGATATTAGGATTTACCGGTTCAACTCCTCTACCGAAATTCCAAAGGATTAGTGATATA
*
21984 AATGTGTCTACCCGAGTTCATTAATTTAACAATT
259 AATGTATCTACCCGAGTTCATTAATTTAACAATT
22018 TCAATCAAGA
Statistics
Matches: 261, Mismatches: 26, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
290 142 0.54
291 2 0.01
292 58 0.22
293 22 0.08
294 37 0.14
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (293 bp):
CTATAGAAATTACTTAAAGGCCAAATTGAGAATTAATGTGGTGCCTCCTTTTGAGCTTTTTTGGT
CATTTCTCACTTTTCGGATGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTCTTG
CCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTCAATTACATATTAATTGT
GCGTGGATATTAGGATTTACCGGTTCAACTCCTCTACCGAAATTCCAAAGGATTAGTGATATAAA
TGTATCTACCCGAGTTCATTAATTTAACAATTG
Found at i:22325 original size:27 final size:26
Alignment explanation
Indices: 22294--22347 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
22284 ACGGCCAATG
*
22294 CAATATCTTCTTTCTAA-CTGACTTAAA
1 CAATATATTCTTT-TAATC-GACTTAAA
22321 CAATATATTCTTTTAATCGACTTAAA
1 CAATATATTCTTTTAATCGACTTAAA
22347 C
1 C
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (26 bp):
CAATATATTCTTTTAATCGACTTAAA
Done.