Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022987.1 Corchorus olitorius cultivar O-4 contig23020, 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: 41729
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:1248 original size:162 final size:162
Alignment explanation
Indices: 976--1288 Score: 545
Period size: 162 Copynumber: 1.9 Consensus size: 162
966 TAAGGGTTTT
976 TTTTCTTTGTTCAATGAGATTGATTACTTCAAATCTTTGTAAACTAAATGGCCAGATTTTGATGA
1 TTTTCTTTGTTCAATGAGATTGATTACTTCAAATCTTTGTAAACTAAATGGCCAGATTTTGATGA
* * *
1041 TTAATTAATCAAAATTTATGCTAAAATTAATATGATTTACAAGTTATTAACATACGTACAGCGCA
66 TTAATTAATCAAAATTTATACTAAAATTAATATGATTTACAAGTTATTAACATACGTACAACACA
1106 CGTGCTTTAACTAGTATATATATATATATATA
131 CGTGCTTTAACTAGTATATATATATATATATA
* * *
1138 TTTTGTTTGTTCAATGAGATTGATTATTTCAAATCTTTGTAAACTAAATGGCTAGATTTTGATGA
1 TTTTCTTTGTTCAATGAGATTGATTACTTCAAATCTTTGTAAACTAAATGGCCAGATTTTGATGA
* *
1203 TTAATTTATCAAAATTTATACTAAAATTAATATGATTTACAAGTTATTAACATATGTACAACACA
66 TTAATTAATCAAAATTTATACTAAAATTAATATGATTTACAAGTTATTAACATACGTACAACACA
*
1268 TGTGCTTTAACTAGTATATAT
131 CGTGCTTTAACTAGTATATAT
1289 GTATGCTTTA
Statistics
Matches: 142, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
162 142 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.42
Consensus pattern (162 bp):
TTTTCTTTGTTCAATGAGATTGATTACTTCAAATCTTTGTAAACTAAATGGCCAGATTTTGATGA
TTAATTAATCAAAATTTATACTAAAATTAATATGATTTACAAGTTATTAACATACGTACAACACA
CGTGCTTTAACTAGTATATATATATATATATA
Found at i:2824 original size:12 final size:12
Alignment explanation
Indices: 2807--2834 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2797 GCAATATGGA
2807 TATGAAATAGGT
1 TATGAAATAGGT
2819 TATGAAATAGGT
1 TATGAAATAGGT
2831 TATG
1 TATG
2835 GATATGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (12 bp):
TATGAAATAGGT
Found at i:2968 original size:22 final size:23
Alignment explanation
Indices: 2926--2969 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
2916 CATATCAGGG
*
2926 GGTGAAAGCACAGCCATAGAAATA
1 GGTGAAAG-ACAGCCAAAGAAATA
2950 GGTGAAAG-CAGCCAAAGAAA
1 GGTGAAAGACAGCCAAAGAAA
2970 CTGCCAACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
24 8 0.42
ACGTcount: A:0.48, C:0.16, G:0.27, T:0.09
Consensus pattern (23 bp):
GGTGAAAGACAGCCAAAGAAATA
Found at i:5225 original size:14 final size:14
Alignment explanation
Indices: 5206--5253 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
5196 GTCAAGCATG
5206 ACAGGAAAATCAAA
1 ACAGGAAAATCAAA
*
5220 ACAGGAAGAA--AAT
1 ACAGGAA-AATCAAA
*
5233 CCAGGAAAATCAAA
1 ACAGGAAAATCAAA
5247 ACAGGAA
1 ACAGGAA
5254 GAAAAATCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 2 0.07
13 8 0.30
14 15 0.56
15 2 0.07
ACGTcount: A:0.60, C:0.15, G:0.19, T:0.06
Consensus pattern (14 bp):
ACAGGAAAATCAAA
Found at i:5241 original size:27 final size:27
Alignment explanation
Indices: 5207--5258 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
5197 TCAAGCATGA
5207 CAGGAAAATCAAAACAGGAAGAAAATC
1 CAGGAAAATCAAAACAGGAAGAAAATC
5234 CAGGAAAATCAAAACAGGAAGAAAA
1 CAGGAAAATCAAAACAGGAAGAAAA
5259 ATCTGACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.62, C:0.13, G:0.19, T:0.06
Consensus pattern (27 bp):
CAGGAAAATCAAAACAGGAAGAAAATC
Found at i:5275 original size:15 final size:14
Alignment explanation
Indices: 5255--5286 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
5245 AAACAGGAAG
5255 AAAAATCTGACACAA
1 AAAAATCTGACA-AA
5270 AAAAATCTGACAAA
1 AAAAATCTGACAAA
5284 AAA
1 AAA
5287 CAGAAACAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.66, C:0.16, G:0.06, T:0.12
Consensus pattern (14 bp):
AAAAATCTGACAAA
Found at i:8153 original size:14 final size:14
Alignment explanation
Indices: 8134--8187 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
8124 GTCAAGCTAG
8134 ACAGGAAAATCAAA
1 ACAGGAAAATCAAA
*
8148 ACAGGAAGAAAATCAATTG
1 ACA-G--GAAAATCAA--A
8167 ACAGGAAAATCAAA
1 ACAGGAAAATCAAA
8181 ACAGGAA
1 ACAGGAA
8188 GAAAATCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 9 0.27
17 9 0.27
18 1 0.03
19 3 0.09
ACGTcount: A:0.59, C:0.13, G:0.19, T:0.09
Consensus pattern (14 bp):
ACAGGAAAATCAAA
Found at i:8160 original size:17 final size:17
Alignment explanation
Indices: 8138--8196 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
8128 AGCTAGACAG
8138 GAAAATCAAAACAGGAA
1 GAAAATCAAAACAGGAA
*
8155 GAAAATCAATTGACA-G--
1 GAAAATCAA--AACAGGAA
8171 GAAAATCAAAACAGGAA
1 GAAAATCAAAACAGGAA
8188 GAAAATCAA
1 GAAAATCAA
8197 TTGACCAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 3 0.09
15 1 0.03
16 9 0.26
17 18 0.51
18 1 0.03
19 3 0.09
ACGTcount: A:0.61, C:0.12, G:0.17, T:0.10
Consensus pattern (17 bp):
GAAAATCAAAACAGGAA
Found at i:8170 original size:33 final size:33
Alignment explanation
Indices: 8133--8201 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
8123 GGTCAAGCTA
8133 GACAGGAAAATCAAAACAGGAAGAAAATCAATT
1 GACAGGAAAATCAAAACAGGAAGAAAATCAATT
8166 GACAGGAAAATCAAAACAGGAAGAAAATCAATT
1 GACAGGAAAATCAAAACAGGAAGAAAATCAATT
8199 GAC
1 GAC
8202 CAAACAAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.57, C:0.13, G:0.19, T:0.12
Consensus pattern (33 bp):
GACAGGAAAATCAAAACAGGAAGAAAATCAATT
Found at i:13317 original size:22 final size:21
Alignment explanation
Indices: 13265--13318 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
13255 TGCTTCTTGA
13265 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
13286 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
13305 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
13319 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:17939 original size:2 final size:2
Alignment explanation
Indices: 17928--17961 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
17918 ATTAGGCCGT
17928 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17962 TCCATTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18224 original size:12 final size:12
Alignment explanation
Indices: 18207--18235 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18197 CAAAATCAGA
18207 TTATTATTATTC
1 TTATTATTATTC
18219 TTATTATTATTC
1 TTATTATTATTC
18231 -TATTA
1 TTATTA
18236 ATGTGATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATTATTATTC
Found at i:24515 original size:137 final size:137
Alignment explanation
Indices: 24319--24592 Score: 476
Period size: 137 Copynumber: 2.0 Consensus size: 137
24309 GATGGTGCAG
* *
24319 GGTGTGGTTAAATGTGAACAAGTCAAAAAAGAACGGGTCACTTAACTGGTTATCCAAGAAATATC
1 GGTGTGGTTAAATGTGAACAAGTCAAAAAAAAACGGGCCACTTAACTGGTTATCCAAGAAATATC
* *
24384 GGGTTAGCCGCACGAGGGTTCGGTGGTGTGGCTGTGCTAAAAAAAAGATGGTGTGGTATATCTGG
66 GGGTTAGCCGCACGAGAGTTCGGTGGTGCGGCTGTGCTAAAAAAAAGATGGTGTGGTATATCTGG
24449 AGAAAAA
131 AGAAAAA
* * *
24456 GGTGTGGTTAAGTGTGAACAAGTCAAAAAAAAATGGGCCACTTAATTGGTTATCCAAGAAATATC
1 GGTGTGGTTAAATGTGAACAAGTCAAAAAAAAACGGGCCACTTAACTGGTTATCCAAGAAATATC
*
24521 GGGTTAGCCGCACGAGAGTTCGGTGGTGCGGCTGTGCTAAAAAAAAGATGGTGTGGTATTTCTGG
66 GGGTTAGCCGCACGAGAGTTCGGTGGTGCGGCTGTGCTAAAAAAAAGATGGTGTGGTATATCTGG
24586 AGAAAAA
131 AGAAAAA
24593 AAAACAATTG
Statistics
Matches: 129, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
137 129 1.00
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.24
Consensus pattern (137 bp):
GGTGTGGTTAAATGTGAACAAGTCAAAAAAAAACGGGCCACTTAACTGGTTATCCAAGAAATATC
GGGTTAGCCGCACGAGAGTTCGGTGGTGCGGCTGTGCTAAAAAAAAGATGGTGTGGTATATCTGG
AGAAAAA
Found at i:24966 original size:230 final size:230
Alignment explanation
Indices: 24603--25024 Score: 799
Period size: 230 Copynumber: 1.8 Consensus size: 230
24593 AAAACAATTG
* *
24603 GGTGTAGGGTGTGGTTAAGTGTGAACAAGTCCAAAAAAAACGGGCCAGTTAACTGGTTATCCAAG
1 GGTGTAGGGTGTGGTTAAGTGTGAACAAGTCCAAAAAAAACGGGCCACTTAACAGGTTATCCAAG
24668 AAATATCAAGTTAGCCGCACGAGGGAGAGCTGTAACATGTGAACGAGAGAGTTTGTTGGAGTTCA
66 AAATATCAAGTTAGCCGCACGAGGGAGAGCTGTAACATGTGAACGAGAGAGTTTGTTGGAGTTCA
24733 CATGTCAGTGTCGCATCCCACATCACAAAGGGATGAACTGTAAAAAGTGGCATATATACCTGGTA
131 CATGTCAGTGTCGCATCCCACATCACAAAGGGATGAACTGTAAAAAGTGGCATATATACCTGGTA
24798 TTTCTGGAGAAAAAAAAACAATTGGGTGCACAGAT
196 TTTCTGGAGAAAAAAAAACAATTGGGTGCACAGAT
*
24833 GGTGTAGGGTGTGGTTAAGTGTGAACAAGTCCAAAAAGAACGGGCCACTTAACAGGTTATCCAAG
1 GGTGTAGGGTGTGGTTAAGTGTGAACAAGTCCAAAAAAAACGGGCCACTTAACAGGTTATCCAAG
* *
24898 AAATATCGAGTTAGCCGCACGAGGGAGAGCTGTAACATGTGAACGGGAGAGTTTGTTGGAGTTCA
66 AAATATCAAGTTAGCCGCACGAGGGAGAGCTGTAACATGTGAACGAGAGAGTTTGTTGGAGTTCA
24963 CATGTCAGTGTCGCATCCCACATCACAAAGGGATGAACTGTAAAAAGTGGCATATATACCTG
131 CATGTCAGTGTCGCATCCCACATCACAAAGGGATGAACTGTAAAAAGTGGCATATATACCTG
25025 AAAGATTCAA
Statistics
Matches: 187, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
230 187 1.00
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (230 bp):
GGTGTAGGGTGTGGTTAAGTGTGAACAAGTCCAAAAAAAACGGGCCACTTAACAGGTTATCCAAG
AAATATCAAGTTAGCCGCACGAGGGAGAGCTGTAACATGTGAACGAGAGAGTTTGTTGGAGTTCA
CATGTCAGTGTCGCATCCCACATCACAAAGGGATGAACTGTAAAAAGTGGCATATATACCTGGTA
TTTCTGGAGAAAAAAAAACAATTGGGTGCACAGAT
Found at i:27125 original size:395 final size:395
Alignment explanation
Indices: 26331--27255 Score: 1582
Period size: 395 Copynumber: 2.3 Consensus size: 395
26321 AAAAGTCTGG
* *
26331 TTGGTGTCCGACATGTATATGAGCTACTCGGTGGGCCTTGCTGAAGTAGACAAGGCCCGGGTTCC
1 TTGGTGTCCGACATGTATATGGGCTACTCGGTGGGCCTTGCTGAAGCAGACAAGGCCC-GGTTCC
*
26396 TCTCCCAGCAAGTGGTATCAAAGCTTGGTTAGACTCAATCGGTGTGGCCCATGAGCACGGTGAAC
65 TCTCCCAACAAGTGGTATCAAAGCTTGGTTAGACTCAATCGGTGTGGCCCATGAGCACGGTGAAC
* *
26461 CTGGTGTGACCATCTAAGGTGTGCAATTGTGGAGTGTTGGACCCTTACACTCCACGGGTTAAATC
130 CTGGTGTGACCATCCAAGGTGTGCAATTGTGGAGTATTGGACCCTTACACTCCACGGGTTAAATC
* *
26526 TTGGATGACTAATAATTGGCTTAAGACTTGACGGGTTGGGCCGCATGGGGGAGAGATGAGGACTC
195 TTGGATGACTAATAATTGGCTTAAGACTTGACGGATTGGGCCGCATGAGGGAGAGATGAGGACTC
*
26591 ACAAGTGAATCAGGGGAAATTATTAAGGGGATTCACATGTGAGGGAACATCCCACATCATGAAGA
260 ACAAGCGAATCAGGGGAAATTATTAAGGGGATTCACATGTGAGGGAACATCCCACATCATGAAGA
*
26656 GATGGGTTGTTGGAGTAGCTTATATACATGAAGGACCCCAGAAACCATTAGTCTAGGCTTTTGGG
325 GATGGGTTGTTGGAGTAGCTTATATACATGAAGGACCCAAGAAACCATTAGTCTAGGCTTTTGGG
26721 TTCGGA
390 TTCGGA
*
26727 TTGGTGTCCGACATGTATATGGGCTACTCGGTGGGCCTTGCTGAAGCAGACAGGGCCCGGTTCCT
1 TTGGTGTCCGACATGTATATGGGCTACTCGGTGGGCCTTGCTGAAGCAGACAAGGCCCGGTTCCT
* *
26792 CTCCCAACAAGTGGTATCAAAGCTCGGTTAGACTCAATCGGTGTGGCCCATGAGCACGGTGAACA
66 CTCCCAACAAGTGGTATCAAAGCTTGGTTAGACTCAATCGGTGTGGCCCATGAGCACGGTGAACC
* * *
26857 TGGTGTGACCATCCAGGGTGTGCAATTGTGGAGTATTTGACCCTTACACTCCACGGGTTAAGTCT
131 TGGTGTGACCATCCAAGGTGTGCAATTGTGGAGTATTGGACCCTTACACTCCACGGGTTAAATCT
**
26922 TGGATGACTGGTAATTGGCTTAAGACTTGACGGATTGGGCCGCATGAGGGAGAGATGAGGACTCA
196 TGGATGACTAATAATTGGCTTAAGACTTGACGGATTGGGCCGCATGAGGGAGAGATGAGGACTCA
* *
26987 CAAGCGAATCGGGGGAAATTATTAA-GGGATTCACATGTGAGGGAGCATCCCACATCATGAAGAG
261 CAAGCGAATCAGGGGAAATTATTAAGGGGATTCACATGTGAGGGAACATCCCACATCATGAAGAG
*
27051 ATGGGTTGTTGGAGTAGCTTATATACATGAAGGACCCAAGAAACTATTAGTCTAGGCTTTTGGGT
326 ATGGGTTGTTGGAGTAGCTTATATACATGAAGGACCCAAGAAACCATTAGTCTAGGCTTTTGGGT
27116 TCAGGA
391 TC-GGA
*
27122 TTGGTGTTCGACATGTATATGGGCTACTCGGTGGGCCTTGCTGAAGCAGACAAGGCCCGGTTCCT
1 TTGGTGTCCGACATGTATATGGGCTACTCGGTGGGCCTTGCTGAAGCAGACAAGGCCCGGTTCCT
* * * * * *
27187 TTCCCAACAAGTGGTATCAGAGCTTGATTATACTCGATCGGTGTGGCCCATGAGCACGGTAAACC
66 CTCCCAACAAGTGGTATCAAAGCTTGGTTAGACTCAATCGGTGTGGCCCATGAGCACGGTGAACC
27252 TGGT
131 TGGT
27256 TTCTGTCCCC
Statistics
Matches: 498, Mismatches: 30, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
394 103 0.21
395 340 0.68
396 55 0.11
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.26
Consensus pattern (395 bp):
TTGGTGTCCGACATGTATATGGGCTACTCGGTGGGCCTTGCTGAAGCAGACAAGGCCCGGTTCCT
CTCCCAACAAGTGGTATCAAAGCTTGGTTAGACTCAATCGGTGTGGCCCATGAGCACGGTGAACC
TGGTGTGACCATCCAAGGTGTGCAATTGTGGAGTATTGGACCCTTACACTCCACGGGTTAAATCT
TGGATGACTAATAATTGGCTTAAGACTTGACGGATTGGGCCGCATGAGGGAGAGATGAGGACTCA
CAAGCGAATCAGGGGAAATTATTAAGGGGATTCACATGTGAGGGAACATCCCACATCATGAAGAG
ATGGGTTGTTGGAGTAGCTTATATACATGAAGGACCCAAGAAACCATTAGTCTAGGCTTTTGGGT
TCGGA
Found at i:27818 original size:214 final size:214
Alignment explanation
Indices: 27449--27878 Score: 709
Period size: 214 Copynumber: 2.0 Consensus size: 214
27439 CGGTCATCCA
* *
27449 AGACTTAACCCGTGGAGTGCGAGGGCCCAACACTCCACAATTGCACGCCCCTGGATGATCACATC
1 AGACTTAACCCGTGGAGTGCAAGGGCCCAACACTCCACAATTGCACGCCCCTGGATGATCACACC
* *
27514 AGGCTCACCGTGCTCATGAGCCACACTGATCGAGTCTAACCAAGCTCTGATACCACTTGTTGGGA
66 AGGCTCACCGTGCTCATGAGCCACACTAATCGAGTCTAACCAAGCTCTGATACCACTTGCTGGGA
*
27579 GAGAAACACGGGCCCTGTCTACTCCAGCAAAGTCCACCGAGTAGCTCATATACATGTCGGACACC
131 GAGAAACACGGGCCCTGTCTACTCCAGCAAAGCCCACCGAGTAGCTCATATACATGTCGGACACC
27644 AATCCGAACCCAAAAGTCT
196 AATCCGAACCCAAAAGTCT
* *
27663 AGACTTAATCCGTGGAGTGCAAGGGCCCAACACTCCACAATTGCACGCCCCTGGATGGTCACACC
1 AGACTTAACCCGTGGAGTGCAAGGGCCCAACACTCCACAATTGCACGCCCCTGGATGATCACACC
*
27728 AGGCTCACCGTGCTCATG-GATCACACTAATCGAGTCTAACCAAGCTCTGATACCACTTGCTGGG
66 AGGCTCACCGTGCTCATGAG-CCACACTAATCGAGTCTAACCAAGCTCTGATACCACTTGCTGGG
* ** * *
27792 AGAGGAACACGGGCGTTGTCTACTCCAGCAAGGCCCACCGATTAGCTCATATACATGTCGGACAC
130 AGAGAAACACGGGCCCTGTCTACTCCAGCAAAGCCCACCGAGTAGCTCATATACATGTCGGACAC
* *
27857 TAATCCGAACCCAAAGGTCT
195 CAATCCGAACCCAAAAGTCT
27877 AG
1 AG
27879 GGCCTTTGAG
Statistics
Matches: 200, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
213 1 0.00
214 199 1.00
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (214 bp):
AGACTTAACCCGTGGAGTGCAAGGGCCCAACACTCCACAATTGCACGCCCCTGGATGATCACACC
AGGCTCACCGTGCTCATGAGCCACACTAATCGAGTCTAACCAAGCTCTGATACCACTTGCTGGGA
GAGAAACACGGGCCCTGTCTACTCCAGCAAAGCCCACCGAGTAGCTCATATACATGTCGGACACC
AATCCGAACCCAAAAGTCT
Found at i:29243 original size:14 final size:14
Alignment explanation
Indices: 29221--29282 Score: 76
Period size: 14 Copynumber: 4.5 Consensus size: 14
29211 TAAAGGACGT
29221 TTTTC-AGAAATGA
1 TTTTCAAGAAATGA
29234 TTTTCAAGAAACTG-
1 TTTTCAAGAAA-TGA
*
29248 TTTTCAAGAAATTA
1 TTTTCAAGAAATGA
29262 TTTTCAA-AAATGAA
1 TTTTCAAGAAATG-A
29276 TTTTCAA
1 TTTTCAA
29283 AAAGGTTTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
13 10 0.23
14 31 0.72
15 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (14 bp):
TTTTCAAGAAATGA
Found at i:29555 original size:7 final size:6
Alignment explanation
Indices: 29528--29571 Score: 63
Period size: 6 Copynumber: 7.3 Consensus size: 6
29518 TGATGTGAAT
*
29528 AAAAAG AAAAA- ACAAAG AAAAAG AAAAAAG AAAAAG AAAAAG AA
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG AAAAAG AA
29572 GATTGTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 4 0.12
6 24 0.71
7 6 0.18
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:29559 original size:13 final size:13
Alignment explanation
Indices: 29528--29568 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
29518 TGATGTGAAT
29528 AAAAAG-AAAA-A
1 AAAAAGAAAAAGA
*
29539 ACAAAGAAAAAGA
1 AAAAAGAAAAAGA
29552 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
29565 AAAA
1 AAAA
29569 GAAGATTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 5 0.19
12 4 0.15
13 17 0.65
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:29563 original size:19 final size:18
Alignment explanation
Indices: 29528--29571 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
29518 TGATGTGAAT
*
29528 AAAAAG-AAAAAACAAAG
1 AAAAAGAAAAAAAAAAAG
29545 AAAAAGAAAAAAGAAAAAG
1 AAAAAGAAAAAA-AAAAAG
29564 AAAAAGAA
1 AAAAAGAA
29572 GATTGTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 6 0.25
18 5 0.21
19 13 0.54
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAAAAAAG
Found at i:29953 original size:6 final size:6
Alignment explanation
Indices: 29933--30018 Score: 63
Period size: 6 Copynumber: 14.8 Consensus size: 6
29923 GAAGCAATCT
** * * *
29933 AAAGGA AAAAAA AAAGGA AAAGGA AAAGGC AAAGAA AAAGAGA AAAAGA
1 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAG-GA AAAGGA
* **
29982 AAA-GA AAA-GA AAA-G- AAAGAA AAATCA AAAGGA AAAGG
1 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGG
30019 TTCAAATTGA
Statistics
Matches: 63, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
4 3 0.05
5 11 0.17
6 45 0.71
7 4 0.06
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.01
Consensus pattern (6 bp):
AAAGGA
Found at i:29999 original size:14 final size:15
Alignment explanation
Indices: 29963--30003 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
29953 AGGAAAAGGC
*
29963 AAAGAAA-AAGAGAA
1 AAAGAAAGAAAAGAA
29977 AAAGAAAAGAAAAG-A
1 AAAG-AAAGAAAAGAA
29992 AAAGAAAGAAAA
1 AAAGAAAGAAAA
30004 ATCAAAAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.50
15 8 0.33
16 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAGAA
Found at i:36391 original size:20 final size:20
Alignment explanation
Indices: 36368--36407 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
36358 CCTAATAATT
36368 AAGATAAGAATTTAATTAAA
1 AAGATAAGAATTTAATTAAA
36388 AAGATAAGAATTTAATTAAA
1 AAGATAAGAATTTAATTAAA
36408 GTTTAATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (20 bp):
AAGATAAGAATTTAATTAAA
Found at i:40020 original size:29 final size:30
Alignment explanation
Indices: 39963--40020 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
39953 CCAATACTTA
* *
39963 TTAAAAAGTAAAAAGAAATTAAAAGAAAATC
1 TTAAAAAG-AAAAAGAAAATAAAAAAAAATC
*
39994 TTAAAAA-AAAAATAAAATAAAAAAAAA
1 TTAAAAAGAAAAAGAAAATAAAAAAAAA
40021 AACCAGAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.71
31 7 0.29
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (30 bp):
TTAAAAAGAAAAAGAAAATAAAAAAAAATC
Found at i:40103 original size:38 final size:37
Alignment explanation
Indices: 40056--40176 Score: 101
Period size: 38 Copynumber: 3.3 Consensus size: 37
40046 GCCATGGACC
*
40056 CGGGTCGCGACGCGGGTCGCGCGCGACACGGACCATGG
1 CGGGTCGCGACACGGGTCGCGCGCGAC-CGGACCATGG
* *
40094 CGGGTCGCGA-TC----CGCGCGCTACCTGG-CCATGG
1 CGGGTCGCGACACGGGTCGCGCGCGACC-GGACCATGG
* *
40126 ATCCGAGTCGCGACACGGGTCGCACGCGACCCGGACCATGG
1 ---CGGGTCGCGACACGGGTCGCGCGCGA-CCGGACCATGG
40167 CGGGTCGCGA
1 CGGGTCGCGA
40177 TCCGCGCGTG
Statistics
Matches: 65, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
32 7 0.11
33 11 0.17
35 9 0.14
36 1 0.02
37 1 0.02
38 19 0.29
40 9 0.14
41 8 0.12
ACGTcount: A:0.14, C:0.36, G:0.40, T:0.11
Consensus pattern (37 bp):
CGGGTCGCGACACGGGTCGCGCGCGACCGGACCATGG
Found at i:40191 original size:73 final size:73
Alignment explanation
Indices: 40043--40184 Score: 239
Period size: 73 Copynumber: 1.9 Consensus size: 73
40033 CGGGTCGCGA
* * *
40043 CTGGCCATGGACCCGGGTCGCGACGCGGGTCGCGCGCGACACGGACCATGGCGGGTCGCGATCCG
1 CTGGCCATGGACCCGAGTCGCGACACGGGTCGCACGCGACACGGACCATGGCGGGTCGCGATCCG
40108 CGCGCTAC
66 CGCGCTAC
* *
40116 CTGGCCATGGATCCGAGTCGCGACACGGGTCGCACGCGACCCGGACCATGGCGGGTCGCGATCCG
1 CTGGCCATGGACCCGAGTCGCGACACGGGTCGCACGCGACACGGACCATGGCGGGTCGCGATCCG
40181 CGCG
66 CGCG
40185 TGACCTGCTG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.13, C:0.37, G:0.39, T:0.11
Consensus pattern (73 bp):
CTGGCCATGGACCCGAGTCGCGACACGGGTCGCACGCGACACGGACCATGGCGGGTCGCGATCCG
CGCGCTAC
Done.