Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016230.1 Corchorus olitorius cultivar O-4 contig16263, 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: 53907
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:123 original size:18 final size:18
Alignment explanation
Indices: 100--136 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
90 TGACAATATA
100 AATTAAGATAATAATTAT
1 AATTAAGATAATAATTAT
118 AATTAAGATAATAATTAT
1 AATTAAGATAATAATTAT
136 A
1 A
137 TAAACAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
AATTAAGATAATAATTAT
Found at i:172 original size:2 final size:2
Alignment explanation
Indices: 165--189 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
155 TTATTTGACA
165 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
190 GTGGCATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4195 original size:18 final size:18
Alignment explanation
Indices: 4172--4230 Score: 51
Period size: 18 Copynumber: 3.7 Consensus size: 18
4162 GGAGAGCAGA
4172 TGAGGAGGAGATCTATCG
1 TGAGGAGGAGATCTATCG
*
4190 TGAGGA-G-CA-C-AT--
1 TGAGGAGGAGATCTATCG
4202 -GAGGAGGAGATCTATCG
1 TGAGGAGGAGATCTATCG
*
4219 TGAGGAGCAGAT
1 TGAGGAGGAGAT
4231 GAGGAGGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 14
0.65 0.06 0.29
Matches are distributed among these distances:
11 5 0.16
12 1 0.03
13 1 0.03
14 3 0.10
15 3 0.10
16 1 0.03
17 1 0.03
18 16 0.52
ACGTcount: A:0.31, C:0.12, G:0.39, T:0.19
Consensus pattern (18 bp):
TGAGGAGGAGATCTATCG
Found at i:4196 original size:15 final size:15
Alignment explanation
Indices: 4176--4225 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
4166 AGCAGATGAG
4176 GAGGAGATCTATCGT
1 GAGGAGATCTATCGT
*
4191 GAGGAGCA-C-AT-GAG
1 GAGGAG-ATCTATCG-T
4205 GAGGAGATCTATCGT
1 GAGGAGATCTATCGT
4220 GAGGAG
1 GAGGAG
4226 CAGATGAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
13 2 0.07
14 9 0.32
15 15 0.54
16 2 0.07
ACGTcount: A:0.30, C:0.12, G:0.40, T:0.18
Consensus pattern (15 bp):
GAGGAGATCTATCGT
Found at i:4204 original size:29 final size:29
Alignment explanation
Indices: 4165--4271 Score: 196
Period size: 29 Copynumber: 3.7 Consensus size: 29
4155 GCGAGGAGGA
4165 GAGCAGATGAGGAGGAGATCTATCGTGAG
1 GAGCAGATGAGGAGGAGATCTATCGTGAG
*
4194 GAGCACATGAGGAGGAGATCTATCGTGAG
1 GAGCAGATGAGGAGGAGATCTATCGTGAG
4223 GAGCAGATGAGGAGGAGATCTATCGTGAGG
1 GAGCAGATGAGGAGGAGATCTATCGTGA-G
4253 GAGCAGATGAGGAGGAGAT
1 GAGCAGATGAGGAGGAGAT
4272 AGGAGCAGAT
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 55 0.73
30 20 0.27
ACGTcount: A:0.32, C:0.10, G:0.42, T:0.16
Consensus pattern (29 bp):
GAGCAGATGAGGAGGAGATCTATCGTGAG
Found at i:4271 original size:11 final size:11
Alignment explanation
Indices: 4252--4320 Score: 77
Period size: 11 Copynumber: 6.1 Consensus size: 11
4242 CTATCGTGAG
4252 GGAGCAGATGA
1 GGAGCAGATGA
*
4263 GGAGGAGAT-A
1 GGAGCAGATGA
4273 GGAGCAGATGA
1 GGAGCAGATGA
*
4284 GGAGGAGATCGTGA
1 GGAGCAGA---TGA
4298 GGAGCAGATGA
1 GGAGCAGATGA
*
4309 GGAGGAGATGA
1 GGAGCAGATGA
4320 G
1 G
4321 CGGCGAGGAG
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
10 9 0.18
11 30 0.61
14 10 0.20
ACGTcount: A:0.35, C:0.06, G:0.49, T:0.10
Consensus pattern (11 bp):
GGAGCAGATGA
Found at i:4277 original size:51 final size:46
Alignment explanation
Indices: 4221--4317 Score: 149
Period size: 46 Copynumber: 2.0 Consensus size: 46
4211 ATCTATCGTG
4221 AGGAGCAGATGAGGAGGAGATCTATCGTGAGGGAGCAGATGAGGAGGAGAT
1 AGGAGCAGATGAGGAGGAG----ATCGTGA-GGAGCAGATGAGGAGGAGAT
4272 AGGAGCAGATGAGGAGGAGATCGTGAGGAGCAGATGAGGAGGAGAT
1 AGGAGCAGATGAGGAGGAGATCGTGAGGAGCAGATGAGGAGGAGAT
4318 GAGCGGCGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
46 20 0.43
47 7 0.15
51 19 0.41
ACGTcount: A:0.34, C:0.07, G:0.46, T:0.12
Consensus pattern (46 bp):
AGGAGCAGATGAGGAGGAGATCGTGAGGAGCAGATGAGGAGGAGAT
Found at i:8395 original size:999 final size:997
Alignment explanation
Indices: 4583--9814 Score: 7459
Period size: 999 Copynumber: 5.2 Consensus size: 997
4573 GCAACAGTGT
* * * * * *
4583 CGATATCTAGTACCCTACATCTTCCTTGACCTCGACCACAGTCTACTTGATCACCAACTTTAAAA
1 CGATATCTACTACCCGACATCTTCCTTGACCTTGACCACAGTCTACTTCATCACCAACATTAAAC
* * * * ** ** * *
4648 GATCGGAAATAATATACAAACATTATCCTGTTGAAATAGACTTGACTATACTTGCATAGAAAAAG
66 GACCTGAAATAATATCCATACATTATCCTGTCAAAATAGACTTCCCTACACTTGAATAGAAAAAG
* * * * * *
4713 TTAAGCCCTATCGCTTCCGCCAAAGTATATTTAAAAATTTTCGTAAACAAGACTTTGGAAGTAAG
131 TTAAGTCCTATCACTTCTGCCAAAATATATTTAAGAATTTTCATAAACAAGACTTTGGAAGTAAG
* * * * * * * *
4778 T-GGATTAAGAAGTGCCACT-CCCTTTGTCAAAGATATATTCAGCAAAAAGTCC-AGTTAATCGT
196 TAGG-TAAAAAAGTG-CAATGCCATTTGTTAAAGATATATTCACCAAAAAG-CCTAGCTAATTGT
** * * * * * * * * *
4840 TGGTTGATCCAAACCATGGATTATATGGTCGAAGCCTAACTTTGATTGGAAATAATATGCACCCA
258 TGACTGATCCAAACCTTAGATCATATGGTCGAAGCCCACCATTGATTAGAAATAAAATGCACCTA
* * * * ***
4905 ATAAAAAAGTTAGCTATCGGATCCTTGACCTTCCAAACAATCCAATCCTTAACTGTGACACGTAA
323 ATATAAAAGTCAGCTATCAGATCCGTGACCTTCCAAACAATCCAATCCTTTTTTGTGACACGTAA
* * * **
4970 TTTTTTCAGATCATCT-ATGCTGGAAAAGTATCAAATTGCGTTTATAATTGTGATTATAAAGACA
388 TTTTTTCAGATCAT-TAATGCTGGAAAAGTACCAAATCGCGTTTATAATTATGGCTAT-AAGACA
* * * * * *
5034 GCTATTAAACCATTTCGGTAGCGT-AGCCCAAAATTTTCCGTCTTCGTAATGTTGTTAATACCAT
451 GCTATTAAACCATTTTGGTAGCGTAAG-ACAAACTATT-CGTCGTCGTAATGTTGTTAAAACCAT
* ** * * * *
5098 CCA-AGGAACTGATCTCCTTGGATGATTGTGGCAGTGCGACAA-CTTTATAATGCAAACCAACAA
514 CCACA-GAACTGGTCTCCTTGGATGATTGTGAAAGTGCGAGAACCTTT-TGATGCAGACCAACGA
** * ** * **
5161 GAATA-TAAAACA-ACTATTTAAATCATCATCTAAACTAGATGAGAAACAAAAATTCGACATGGA
577 GAA-AGTAAAACAGA-TGCTTAAATCATCATCTGAACCGGATGAGCAACAAAAATTCGATGTGGA
* *
5224 GATCCAAATATGTGTTTAATAATAAGACTACACACTTTCACATATTTGGTAACGTAATTTATCCC
640 TATCCAAATATGTGTTTAATAATAAGACTACACACTTTCACATATTTTGTAACGTAATTTATCCC
* * * * * * * * *
5289 GTTTCTAAATCTTTATATTCTATTTTGCTTTTTTTTTTCTTGGTATCAAAGTCCTTAACATTCGC
705 CTTTTTATATCTTTATCTTCTATTTTGCTGTTTTTTTACTTGGTATCAGAGTCCTTAACTTTCGT
* * * *
5354 AAATTTACTAAAACCAAGAAATTGGGCA-CTCAAGCAAAATAGTTTCATGTAATTAGGGTTTTAA
770 AAATTTACTAAAACCAAGACACTGGACATC-CAAGCAAAATAGTTTCATGTAATTATGGTTTTAA
* * * * * *
5418 TCAAAGTATCGTTTTTCTCATTTTGGGTTTATTTACAGAATTCATTTACGATCTGATATACTCCT
834 TCAAAGTATCGCTTTTCTGATTTTGGGTTTATATACAGAATTGATTTACCATCTGATATTCTCCT
* * * *
5483 CGCATGTATAATTCCTTATATTGCATTC-AAGGGGTTTGAAATTAGGCACATTATTTAATGCACC
899 CGCATGTATAATTCCTTATGTTGCACTCGAA-GAGTTTGAAATTAGGCACATCATTTAATGCACC
* *
5547 CCTA-ACAACAATCTTAAAGCTTGTGGCAGCAATGC
963 CCTATA-AACAGTCTCAAAGCTTGTGGCAGCAATGC
* * *
5582 CGATATCTACTACCCTACATCTTCCTTGACCTTGACCACAGTCTACTTCATTACCAACTTTAAAC
1 CGATATCTACTACCCGACATCTTCCTTGACCTTGACCACAGTCTACTTCATCACCAACATTAAAC
* * **
5647 GACCTGAAATAATA-CACAAACATTATCATGTCGCAATAGACTTCCCTACACTTGAATAGAAAAA
66 GACCTGAAATAATATC-CATACATTATCCTGTCAAAATAGACTTCCCTACACTTGAATAGAAAAA
* * * * *
5711 GTTAAGTCCTATCGCTTCTGACAAAATATATTAAAGAATTTTCATAAACAAGACTTTAGAAATAA
130 GTTAAGTCCTATCACTTCTGCCAAAATATATTTAAGAATTTTCATAAACAAGACTTTGGAAGTAA
* *
5776 GTAGGTAAAAAAGTGCAATGCCATTTGTTAAAGATATATTCACTAAAAAGCCCAGCTAATTGTTG
195 GTAGGTAAAAAAGTGCAATGCCATTTGTTAAAGATATATTCACCAAAAAGCCTAGCTAATTGTTG
** * * *
5841 ACTGATCCAAACCTCGGATTATATGTTCGAAGCCCACCATTGATTAGAATTAAAATGCACCTAAT
260 ACTGATCCAAACCTTAGATCATATGGTCGAAGCCCACCATTGATTAGAAATAAAATGCACCTAAT
* * * *
5906 ATAAAAGTCAGCTATCAGATCCGTGACTTTCCAAATAATCCAACCCTTTTTTGTGACACGCAATT
325 ATAAAAGTCAGCTATCAGATCCGTGACCTTCCAAACAATCCAATCCTTTTTTGTGACACGTAATT
* * * * * *
5971 TCTTCAGATCATTAATGCTGGAAAACTACCAAATCACGATAATAATTGTGGCTATAAAGACAGCT
390 TTTTCAGATCATTAATGCTGGAAAAGTACCAAATCGCGTTTATAATTATGGCTAT-AAGACAGCT
* * * *
6036 ATTAAACCATTTTGGTAGCGTAGGCCAAAATATTCTGTCGTCGTAATGTTGTTAATACCATCCAC
454 ATTAAACCATTTTGGTAGCGTAAGACAAACTATTC-GTCGTCGTAATGTTGTTAAAACCATCCAC
* * * * * *
6101 GGAACTGGTCTCGTTGGATGATTATGAAAGTGCGACAACCTTTTGATGCAGGCCAATGAGAAAGT
518 AGAACTGGTCTCCTTGGATGATTGTGAAAGTGCGAGAACCTTTTGATGCAGACCAACGAGAAAGT
* * * * *
6166 AAAACAGATGCTTAAATCATCATCTTAACCAGTTGAGCAACATAAATTCGATGTGGAGATCCAAA
583 AAAACAGATGCTTAAATCATCATCTGAACCGGATGAGCAACAAAAATTCGATGTGGATATCCAAA
* * * *
6231 TATGTGTTTAATAATAAGACTACAAACTTTCACATATTTTATAACGTAATTTATCCCGTTTGTAT
648 TATGTGTTTAATAATAAGACTACACACTTTCACATATTTTGTAACGTAATTTATCCCCTTTTTAT
* * **
6296 ATCTTTATCTTCTATTTTGATGTTTTTTTTTTACTTGGTACCAGAGTCCTTAACTTTCACAAATT
713 ATCTTTATCTTCTATTTTGCTG---TTTTTTTACTTGGTATCAGAGTCCTTAACTTTCGTAAATT
6361 TACTAAAACCAAGACACTGGACATCCAAGCAAAATAGTTTCATGTAATTATGGTTTTAATCAAAG
775 TACTAAAACCAAGACACTGGACATCCAAGCAAAATAGTTTCATGTAATTATGGTTTTAATCAAAG
* * * *
6426 TATTGCTTTTCTGATTTTGGGTTTATATAGAAAATTGATTTTCCATCTGATATTCTCCTCGCATG
840 TATCGCTTTTCTGATTTTGGGTTTATATACAGAATTGATTTACCATCTGATATTCTCCTCGCATG
6491 TATAATTCCTTATGTTGCACTCGAAGAGTTTGAAATTAGGCACATCATTTAATGCACCCCTATCA
905 TATAATTCCTTATGTTGCACTCGAAGAGTTTGAAATTAGGCACATCATTTAATGCACCCCTAT-A
* *
6556 ATC-GTCTCATAGCTTGTGGCAGCAATGC
969 AACAGTCTCAAAGCTTGTGGCAGCAATGC
*
6584 CGATATCTACTACCCGACATCTTCCTTGACCTTGACCACGGTCTACTTCATCACCAACATTAAAC
1 CGATATCTACTACCCGACATCTTCCTTGACCTTGACCACAGTCTACTTCATCACCAACATTAAAC
*
6649 GACTTGAAATAATA-CACATACATTATCCTGTCAAAATAGACTTCCCTACACTTGAATAGAAAAA
66 GACCTGAAATAATATC-CATACATTATCCTGTCAAAATAGACTTCCCTACACTTGAATAGAAAAA
* *
6713 GTTAAGTCTTATCACTTCTGCCAAAATATATTTACGAATTTTCATAAACAAGACTTTGGAAGTAA
130 GTTAAGTCCTATCACTTCTGCCAAAATATATTTAAGAATTTTCATAAACAAGACTTTGGAAGTAA
* *
6778 GTAGGTAAAAAAGCGCAATGCCATTT-TTCAAAGATATATTCACCAAAAAGCCTAGTTAATTGTT
195 GTAGGTAAAAAAGTGCAATGCCATTTGTT-AAAGATATATTCACCAAAAAGCCTAGCTAATTGTT
* * *
6842 GACTGATCCAAACCTTAAATCATATGGTCGAAGCCCACCGTTGATTAGAAATAAAATGCCCCTAA
259 GACTGATCCAAACCTTAGATCATATGGTCGAAGCCCACCATTGATTAGAAATAAAATGCACCTAA
*
6907 TATAAAAGTCAGCTATCAGATCCGTGACCTTCCAAGCAATCCAATCCTTTTTTGTGACACGTAAT
324 TATAAAAGTCAGCTATCAGATCCGTGACCTTCCAAACAATCCAATCCTTTTTTGTGACACGTAAT
* *
6972 TTTTCCAGATCATTAATGCTGGAAAAGTACCAAATCGCGTTTATAATTATGGCTATAAGACACCT
389 TTTTTCAGATCATTAATGCTGGAAAAGTACCAAATCGCGTTTATAATTATGGCTATAAGACAGCT
* ** *
7037 ATTAAACCATTTTGGTAGCATAACTCAAACTATTCTGTCGTCGTAATGTTGTTAAAACAATCCAC
454 ATTAAACCATTTTGGTAGCGTAAGACAAACTATTC-GTCGTCGTAATGTTGTTAAAACCATCCAC
* * *
7102 AGAACTGGTCTCCTTGCATGATTGTGAAAGTGTGAGAACCTTTTGATGCATACCAACGAGAAAGT
518 AGAACTGGTCTCCTTGGATGATTGTGAAAGTGCGAGAACCTTTTGATGCAGACCAACGAGAAAGT
* ** *
7167 AAGACAGATGCTTAAATCATCATCTGAACCGGATGAGCAACATGAATTCCATGTGGATATCCAAA
583 AAAACAGATGCTTAAATCATCATCTGAACCGGATGAGCAACAAAAATTCGATGTGGATATCCAAA
* *
7232 TATATGTTTAATAATAAGACTACACACTTTCACATATTTTGTAATGTAATTTATCCCCTTTTTAT
648 TATGTGTTTAATAATAAGACTACACACTTTCACATATTTTGTAACGTAATTTATCCCCTTTTTAT
*
7297 ATCTTTATCTTCTATTTTGCTGTTTTTTTTACTTGGTATCAGAGTCCTTAACTTTTGTAAATTTA
713 ATCTTTATCTTCTATTTTGCTG-TTTTTTTACTTGGTATCAGAGTCCTTAACTTTCGTAAATTTA
*
7362 CTAAAACCAAGACACTGGACATCCAAGAAAAATAGTTTCATGTAATTATGGTTTTAATCAAAGTA
777 CTAAAACCAAGACACTGGACATCCAAGCAAAATAGTTTCATGTAATTATGGTTTTAATCAAAGTA
* * *
7427 TCGCTTTTCTGATTTTGGGTTTATAGACAAAATTGATTTTCCATCTGATATTCTCCTCGCATGTA
842 TCGCTTTTCTGATTTTGGGTTTATATACAGAATTGATTTACCATCTGATATTCTCCTCGCATGTA
* *
7492 TATTTCCTTATGTTGCACTCGAAGAGTTTCAAATTAGGCACATCATTTAATGCACCCCTATAAAC
907 TAATTCCTTATGTTGCACTCGAAGAGTTTGAAATTAGGCACATCATTTAATGCACCCCTATAAAC
*
7557 AATCTCAAAGCTTGTGGCAGCAATGC
972 AGTCTCAAAGCTTGTGGCAGCAATGC
* ** * *
7583 CGACATCTACTATGCGGCATCTTCATTGACCTTGACCACAGTCTACTTCATCACCAACATTAAAC
1 CGATATCTACTACCCGACATCTTCCTTGACCTTGACCACAGTCTACTTCATCACCAACATTAAAC
* * * *
7648 AATCTGAAATAATATCCATACATTATCCTGTCAAAACAGACTTCCCTACACTTGAATTGAAAAAG
66 GACCTGAAATAATATCCATACATTATCCTGTCAAAATAGACTTCCCTACACTTGAATAGAAAAAG
* * *
7713 TTAAGTCATATCACTTCTGTCAAAATATATTTACGAATTTTCATAGAA-AAGACTTTGGAAGTAA
131 TTAAGTCCTATCACTTCTGCCAAAATATATTTAAGAATTTTCATA-AACAAGACTTTGGAAGTAA
*
7777 GTAGGTAAAAAAGTGCAATGCCATTTGTTAAAGATATAATCACCAAAAAGCCTAGCTAATTGTTG
195 GTAGGTAAAAAAGTGCAATGCCATTTGTTAAAGATATATTCACCAAAAAGCCTAGCTAATTGTTG
7842 ACTGATCCAAACCTTAGATCATATGGTCGAAGCCCACCATTGATTAGAAATAAAATGCACCTAAT
260 ACTGATCCAAACCTTAGATCATATGGTCGAAGCCCACCATTGATTAGAAATAAAATGCACCTAAT
* * *
7907 ATAAAA-TCCAGCTATCAGATCCGTGACCTTCCAAACAATCCAATCATTTTTTTGTGACATGTTA
325 ATAAAAGT-CAGCTATCAGATCCGTGACCTTCCAAACAATCCAATC-CTTTTTTGTGACACGTAA
* *
7971 TTTTTTCAGATCATTAATGCAGGAAAAGTACCAAATCGCGTTTATAATTATGGCTATATGACAGC
388 TTTTTTCAGATCATTAATGCTGGAAAAGTACCAAATCGCGTTTATAATTATGGCTATAAGACAGC
* *
8036 TATTAAACCATTTTGGTAGCGTAAGACAAACTATTACGTCGTTGTAATGTTGTTAAAACCATCTA
453 TATTAAACCATTTTGGTAGCGTAAGACAAACTATT-CGTCGTCGTAATGTTGTTAAAACCATCCA
* * * * * * *
8101 CAGAATTGGTCTCCTTGGATGACTGTGAAAGTGCAAGAACCTTTTGATGGAGACTAACAACAAAG
517 CAGAACTGGTCTCCTTGGATGATTGTGAAAGTGCGAGAACCTTTTGATGCAGACCAACGAGAAAG
* *
8166 TAAAACAGATGCTTAAATCATCATCTGAACCGGATGAGCAACAGAAATTCGATGTGGATATCGAA
582 TAAAACAGATGCTTAAATCATCATCTGAACCGGATGAGCAACAAAAATTCGATGTGGATATCCAA
*
8231 ATATGTGTTTAATAATAAGACTACACACATTCACATATTTTGTAACGTAATTTATCCCCTTTTTA
647 ATATGTGTTTAATAATAAGACTACACACTTTCACATATTTTGTAACGTAATTTATCCCCTTTTTA
* * *
8296 TACCTTTGTATTCTATTTTGCTAGTTTTTTTACTTGGTATCAGAGTCCTTAACTTTCGTAAATTT
712 TATCTTTATCTTCTATTTTGCT-GTTTTTTTACTTGGTATCAGAGTCCTTAACTTTCGTAAATTT
* * * * * *
8361 ACTGAAACCAAAACACTAGACCT-CAAGCAAAATAGTTTCATGTAATTATAGTTTTAATCAAAGC
776 ACTAAAACCAAGACACTGGACATCCAAGCAAAATAGTTTCATGTAATTATGGTTTTAATCAAAGT
* *
8425 ATCGCTTTTCTGATTTTGGGTTTATATACAGAATTGATTTACCATCTCATATTCTCCTTGCATGT
841 ATCGCTTTTCTGATTTTGGGTTTATATACAGAATTGATTTACCATCTGATATTCTCCTCGCATGT
* * * *
8490 ATAATTCCTTATGTTGCACTTGAAGAGTTCGAAATTAGGCACATCATTTAATGCACCCCTTTTAA
906 ATAATTCCTTATGTTGCACTCGAAGAGTTTGAAATTAGGCACATCATTTAATGCACCCCTATAAA
* *
8555 CTGTCTCAAAGTTTGTGGCAGCAATGC
971 CAGTCTCAAAGCTTGTGGCAGCAATGC
*
8582 CGACATCTACTACCCGACATCTTCCTTGACCTTGACCACAGTCTACTTCATCACCAAC-TCTAAA
1 CGATATCTACTACCCGACATCTTCCTTGACCTTGACCACAGTCTACTTCATCACCAACAT-TAAA
* *
8646 CGACCTGAAATAATATCCATACATTATCCTGTCAAAATAGACTTCCCTACACATGAATTGAAAAA
65 CGACCTGAAATAATATCCATACATTATCCTGTCAAAATAGACTTCCCTACACTTGAATAGAAAAA
* *
8711 GTTAAGTCGTATCACTTCTGCCAAAATATATTTACGAATTTTCATAAACAAGACTTTGGAAGTAA
130 GTTAAGTCCTATCACTTCTGCCAAAATATATTTAAGAATTTTCATAAACAAGACTTTGGAAGTAA
* * *
8776 GTAGGTAAAAAAGTGCAATGCTATCTGTTAAAGATATATTCACCAAAAAGTCTAGCTAATTGTTG
195 GTAGGTAAAAAAGTGCAATGCCATTTGTTAAAGATATATTCACCAAAAAGCCTAGCTAATTGTTG
* *
8841 ACTGAACCAATCCTTAGATCATATGGTCGAAGCCCACCATTGATTAGAAATAAAATGCACCTAAT
260 ACTGATCCAAACCTTAGATCATATGGTCGAAGCCCACCATTGATTAGAAATAAAATGCACCTAAT
*
8906 ATAAAATTCAGCTATCAGATCCGTGACCTTCCAAACAATCCAATCCTTTTTTGTGACACGTAATT
325 ATAAAAGTCAGCTATCAGATCCGTGACCTTCCAAACAATCCAATCCTTTTTTGTGACACGTAATT
* * * *
8971 GTTTCAGATTATTAATGCTGGAAAAGTACCAAATCGCGCTTATAATTATGGCTATAAGACAACTA
390 TTTTCAGATCATTAATGCTGGAAAAGTACCAAATCGCGTTTATAATTATGGCTATAAGACAGCTA
* * *
9036 TTAAACCATTTTGTTAGCGTAGGACAAACTATTATGTCGTCGTAATGTTGTTAAAACCATCCACA
455 TTAAACCATTTTGGTAGCGTAAGACAAACTATT-CGTCGTCGTAATGTTGTTAAAACCATCCACA
* *
9101 GAACTGGTCTCCTTGTATGATTGTGAAAGTGCGAGAACCTTTTGATGGAGACCAACGAGAAAGTA
519 GAACTGGTCTCCTTGGATGATTGTGAAAGTGCGAGAACCTTTTGATGCAGACCAACGAGAAAGTA
*
9166 AAACAGATGCTTAAATCATCATCTGAACCGGATAAGCAACAAAAATTCGATGTGGATAT-CAAAT
584 AAACAGATGCTTAAATCATCATCTGAACCGGATGAGCAACAAAAATTCGATGTGGATATCCAAAT
* *
9230 ATGTGTTTAATAATAAGACTACACACTTTCACATATTTTGTAATGTAATTTATCCCATTTTTATA
649 ATGTGTTTAATAATAAGACTACACACTTTCACATATTTTGTAACGTAATTTATCCCCTTTTTATA
*
9295 TCTTTATCTTCTATTTTGCT-TTTTTTTACTTCGTATCAGAGTCCTTAACTTTCGTAAATTTACT
714 TCTTTATCTTCTATTTTGCTGTTTTTTTACTTGGTATCAGAGTCCTTAACTTTCGTAAATTTACT
* * *
9359 AAAACCAAGACACTGGACATCCAAGCAAAATAGTTTCATGTAAATATAGTTTAAATCAAAGTATC
779 AAAACCAAGACACTGGACATCCAAGCAAAATAGTTTCATGTAATTATGGTTTTAATCAAAGTATC
* *
9424 GCTTTTCTGATTTAT-GGTTTATATACAGAATTGATTTACCATCTTATATTCTCCTCGCATGTTT
844 GCTTTTCTGATTT-TGGGTTTATATACAGAATTGATTTACCATCTGATATTCTCCTCGCATGTAT
* * * * * *
9488 AATTCCGTATGTTGCACTCGAAGAGTTTGAAATTAGGGACATCATTAAATGCACCTCTATCAACC
908 AATTCCTTATGTTGCACTCGAAGAGTTTGAAATTAGGCACATCATTTAATGCACCCCTATAAACA
* *
9553 GTCTCAAAGCTTGTGGTAACAATGC
973 GTCTCAAAGCTTGTGGCAGCAATGC
*
9578 CGATATTTACTACCCGACATCTTCCTTGACCTTGACCACAGTCTACTTCATCACCAACATTAAAC
1 CGATATCTACTACCCGACATCTTCCTTGACCTTGACCACAGTCTACTTCATCACCAACATTAAAC
* *
9643 GACCTGAAATAATACCCATACATTATCCTGTCGAAATAGACTTCCCTACACTTGAATAGAAAAAG
66 GACCTGAAATAATATCCATACATTATCCTGTCAAAATAGACTTCCCTACACTTGAATAGAAAAAG
* * *
9708 TTAAGTCCTATCGCTTATGCCAAAATATATTTAAGAATTTTCATAGACAAGACTTTGGAAGTAAG
131 TTAAGTCCTATCACTTCTGCCAAAATATATTTAAGAATTTTCATAAACAAGACTTTGGAAGTAAG
*
9773 TAAGTAAAAAAGTGCAATGCCATTTGTTAAAGATATATTCAC
196 TAGGTAAAAAAGTGCAATGCCATTTGTTAAAGATATATTCAC
9815 AAGCTTTGTA
Statistics
Matches: 3833, Mismatches: 367, Indels: 69
0.90 0.09 0.02
Matches are distributed among these distances:
995 59 0.02
996 399 0.10
997 85 0.02
998 266 0.07
999 1725 0.45
1000 402 0.10
1001 264 0.07
1002 627 0.16
1003 5 0.00
1004 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (997 bp):
CGATATCTACTACCCGACATCTTCCTTGACCTTGACCACAGTCTACTTCATCACCAACATTAAAC
GACCTGAAATAATATCCATACATTATCCTGTCAAAATAGACTTCCCTACACTTGAATAGAAAAAG
TTAAGTCCTATCACTTCTGCCAAAATATATTTAAGAATTTTCATAAACAAGACTTTGGAAGTAAG
TAGGTAAAAAAGTGCAATGCCATTTGTTAAAGATATATTCACCAAAAAGCCTAGCTAATTGTTGA
CTGATCCAAACCTTAGATCATATGGTCGAAGCCCACCATTGATTAGAAATAAAATGCACCTAATA
TAAAAGTCAGCTATCAGATCCGTGACCTTCCAAACAATCCAATCCTTTTTTGTGACACGTAATTT
TTTCAGATCATTAATGCTGGAAAAGTACCAAATCGCGTTTATAATTATGGCTATAAGACAGCTAT
TAAACCATTTTGGTAGCGTAAGACAAACTATTCGTCGTCGTAATGTTGTTAAAACCATCCACAGA
ACTGGTCTCCTTGGATGATTGTGAAAGTGCGAGAACCTTTTGATGCAGACCAACGAGAAAGTAAA
ACAGATGCTTAAATCATCATCTGAACCGGATGAGCAACAAAAATTCGATGTGGATATCCAAATAT
GTGTTTAATAATAAGACTACACACTTTCACATATTTTGTAACGTAATTTATCCCCTTTTTATATC
TTTATCTTCTATTTTGCTGTTTTTTTACTTGGTATCAGAGTCCTTAACTTTCGTAAATTTACTAA
AACCAAGACACTGGACATCCAAGCAAAATAGTTTCATGTAATTATGGTTTTAATCAAAGTATCGC
TTTTCTGATTTTGGGTTTATATACAGAATTGATTTACCATCTGATATTCTCCTCGCATGTATAAT
TCCTTATGTTGCACTCGAAGAGTTTGAAATTAGGCACATCATTTAATGCACCCCTATAAACAGTC
TCAAAGCTTGTGGCAGCAATGC
Found at i:19595 original size:13 final size:13
Alignment explanation
Indices: 19577--19604 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19567 ATTACACTTT
19577 ACACATTTATCTA
1 ACACATTTATCTA
19590 ACACATTTATCTA
1 ACACATTTATCTA
19603 AC
1 AC
19605 CACCAACGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (13 bp):
ACACATTTATCTA
Found at i:20798 original size:48 final size:48
Alignment explanation
Indices: 20741--20845 Score: 210
Period size: 48 Copynumber: 2.2 Consensus size: 48
20731 CGAATATCCG
20741 TCGATATATTCGTGTATCCGTCGATATTTATCAATATTTATAGATATC
1 TCGATATATTCGTGTATCCGTCGATATTTATCAATATTTATAGATATC
20789 TCGATATATTCGTGTATCCGTCGATATTTATCAATATTTATAGATATC
1 TCGATATATTCGTGTATCCGTCGATATTTATCAATATTTATAGATATC
20837 TCGATATAT
1 TCGATATAT
20846 CCGTAAATAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (48 bp):
TCGATATATTCGTGTATCCGTCGATATTTATCAATATTTATAGATATC
Found at i:20855 original size:10 final size:10
Alignment explanation
Indices: 20842--20877 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
20832 ATATCTCGAT
20842 ATATCCGTAA
1 ATATCCGTAA
20852 ATATCCGTAA
1 ATATCCGTAA
*
20862 ATATCTGTAA
1 ATATCCGTAA
20872 ATATCC
1 ATATCC
20878 ATATTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:20959 original size:46 final size:45
Alignment explanation
Indices: 20884--20976 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 45
20874 ATCCATATTA
20884 AATTAAATAATTTTTTTTCATTTTCACATCTAGGATTAAAAATAT
1 AATTAAATAATTTTTTTTCATTTTCACATCTAGGATTAAAAATAT
*
20929 AATTAAATATTTTTTTTTTCATTTGT-ACATCTAGGATTAAAAATAT
1 AATTAAATA-ATTTTTTTTCATTT-TCACATCTAGGATTAAAAATAT
20975 AA
1 AA
20977 GCGACATTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
45 9 0.20
46 35 0.78
47 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (45 bp):
AATTAAATAATTTTTTTTCATTTTCACATCTAGGATTAAAAATAT
Found at i:21953 original size:3 final size:3
Alignment explanation
Indices: 21941--21970 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
21931 GCTCATCAAA
21941 GAT G-T GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
21971 GAGAAAATGA
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:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:23074 original size:24 final size:25
Alignment explanation
Indices: 23045--23091 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
23035 CATCGATATC
23045 TCGATATATCCG-TCGATATATCTG
1 TCGATATATCCGTTCGATATATCTG
23069 TCGATATATCCGTTCGATATATC
1 TCGATATATCCGTTCGATATATC
23092 CTTGGATAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (25 bp):
TCGATATATCCGTTCGATATATCTG
Found at i:23077 original size:14 final size:12
Alignment explanation
Indices: 23045--23092 Score: 78
Period size: 12 Copynumber: 3.9 Consensus size: 12
23035 CATCGATATC
23045 TCGATATATCCG
1 TCGATATATCCG
*
23057 TCGATATATCTG
1 TCGATATATCCG
23069 TCGATATATCCG
1 TCGATATATCCG
23081 TTCGATATATCC
1 -TCGATATATCC
23093 TTGGATAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
12 22 0.67
13 11 0.33
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:28413 original size:19 final size:19
Alignment explanation
Indices: 28361--28413 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
28351 CCGACCGACT
* *
28361 ATATATATAATATAATTTTA
1 ATATATATTATAT-ATCTTA
*
28381 A-ATATATTTTATATCTTA
1 ATATATATTATATATCTTA
28399 ATATATATTATATAT
1 ATATATATTATATAT
28414 ATAAATTCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 6 0.21
19 21 0.75
20 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATATATTATATATCTTA
Found at i:29234 original size:18 final size:17
Alignment explanation
Indices: 29213--29263 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 17
29203 TTTATACAAA
29213 TTCTGTATAAGTATATTC
1 TTCT-TATAAGTATATTC
*
29231 TTC-T-TAATTATATTC
1 TTCTTATAAGTATATTC
29246 TTCTATATAAGTACTATT
1 TTCT-TATAAGTA-TATT
29264 TAGTCTAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 13 0.48
16 1 0.04
17 1 0.04
18 8 0.30
19 4 0.15
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (17 bp):
TTCTTATAAGTATATTC
Found at i:32936 original size:11 final size:11
Alignment explanation
Indices: 32920--32955 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
32910 CAGAAATCAG
32920 AAATCAGAATC
1 AAATCAGAATC
*
32931 AAATCAGAAGC
1 AAATCAGAATC
32942 AAATCAGAAATC
1 AAATCAG-AATC
32954 AA
1 AA
32956 CAGAAAGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.58, C:0.17, G:0.11, T:0.14
Consensus pattern (11 bp):
AAATCAGAATC
Found at i:35535 original size:18 final size:18
Alignment explanation
Indices: 35485--35535 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 18
35475 TGTTAGACTA
35485 AATAGTACTTATATAGAAG
1 AATA-TACTTATATAGAAG
*
35504 AATATA-AT-TA-AGAAG
1 AATATACTTATATAGAAG
35519 AATATACTTATATAGAA
1 AATATACTTATATAGAA
35536 TTTGTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 11 0.41
16 3 0.11
17 3 0.11
18 6 0.22
19 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.12, T:0.31
Consensus pattern (18 bp):
AATATACTTATATAGAAG
Found at i:49913 original size:21 final size:21
Alignment explanation
Indices: 49888--49940 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
49878 TGGTGCAAGC
49888 CGCGCGCGGGCAGGCTTGGGA
1 CGCGCGCGGGCAGGCTTGGGA
49909 CGCGCGCGGGCAGGCTTGGGA
1 CGCGCGCGGGCAGGCTTGGGA
*
49930 CTCGCGCGGGC
1 CGCGCGCGGGC
49941 GAGTTGTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.08, C:0.32, G:0.51, T:0.09
Consensus pattern (21 bp):
CGCGCGCGGGCAGGCTTGGGA
Found at i:51149 original size:3 final size:3
Alignment explanation
Indices: 51141--51182 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
51131 ATTTCTACAT
*
51141 ATG ATG ATG ATG ATG ATG ATG ATG ATG AGTG ATG ATC ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A-TG ATG ATG ATG AT
51183 TTCATCATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.33
Consensus pattern (3 bp):
ATG
Done.